Contacts of the helix formed by residues 54 - 81 (chain A) in PDB entry 4GCK
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 54 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A TYR* 4.0 4.9 - - - -
52A PHE* 3.2 6.3 - - - +
53A PRO* 1.3 82.6 - - - +
55A LYS* 1.3 64.1 + - - +
56A THR* 3.4 11.8 + - - -
57A ARG* 3.0 38.5 + - - +
58A MET* 3.5 10.9 + - - +
30Z C 3.4 24.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU* 5.9 0.9 - - + -
31A ARG* 4.1 3.6 - - - +
32A ILE* 2.8 31.4 + - + +
33A THR 5.4 0.2 - - - -
34A THR* 4.4 17.9 - - + -
37A LEU* 5.1 5.2 - - + -
49A TYR* 4.6 1.2 + - - -
54A SER* 1.3 70.2 - - - +
56A THR* 1.3 68.2 + - - +
58A MET* 2.9 35.7 + - - +
59A PHE* 3.2 29.6 + - + -
117A GLU* 2.7 35.6 + - - +
29Z A 2.6 41.9 + - - -
30Z C 2.9 18.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A SER* 3.4 12.2 + - - -
55A LYS* 1.3 78.6 - - - +
57A ARG* 1.3 58.9 + - - +
59A PHE* 3.2 6.6 + - - +
60A ASP* 3.0 24.9 + - - +
117A GLU* 4.4 9.4 + - - -
118A GLN* 3.6 24.3 + - + +
120A ARG* 3.1 40.6 - - - +
121A LEU* 4.0 14.7 - - + +
30Z C 4.8 3.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A PHE* 4.2 7.4 - - + -
53A PRO* 3.4 36.3 - - + +
54A SER* 3.0 20.9 + - - +
55A LYS 3.0 0.2 - - - -
56A THR* 1.3 75.6 - - - +
58A MET* 1.3 60.6 + - - +
60A ASP* 3.1 34.3 + - - +
61A SER* 2.9 33.6 + - - -
120A ARG* 3.8 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ILE* 3.8 16.6 - - + -
16A LEU* 3.7 16.3 - - + +
19A LEU* 3.9 18.2 - - + -
34A THR* 6.2 1.3 - - + -
37A LEU* 3.6 22.2 - - + -
48A LEU* 3.8 27.4 - - + -
49A TYR* 6.2 4.0 - - + -
52A PHE* 3.4 42.6 - - + -
54A SER 3.6 11.0 - - - +
55A LYS* 2.9 23.0 + - + +
57A ARG* 1.3 77.4 - - - +
59A PHE* 1.3 56.6 + - + +
61A SER* 3.2 5.0 + - - -
62A LEU* 2.9 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU* 4.2 25.4 - - + -
23A LEU* 4.2 12.8 - - + -
32A ILE* 4.8 10.3 - - + -
55A LYS* 3.2 29.5 + - + -
56A THR 3.2 7.9 + - - +
58A MET* 1.3 74.5 - - - +
60A ASP* 1.3 55.1 + - - +
62A LEU* 3.1 7.7 + - + +
63A ILE* 2.7 40.9 + - + +
108A ILE* 3.9 29.4 - - + -
113A ALA* 4.4 16.6 - - + -
114A LEU* 3.9 14.6 - - + -
117A GLU* 3.8 32.8 - - + -
121A LEU* 3.8 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A THR 3.0 14.3 + - - +
57A ARG* 3.1 32.0 + - - +
59A PHE* 1.3 75.9 - - - +
61A SER* 1.3 52.0 + - - +
63A ILE* 3.1 3.6 + - - -
64A GLU* 2.7 33.2 + - - +
120A ARG* 2.4 37.9 + - - -
121A LEU* 3.5 11.8 - - - +
124A ARG* 3.1 38.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ARG* 2.7 33.0 + - - -
16A LEU* 3.7 18.9 - - - +
52A PHE* 3.9 4.2 - - - -
57A ARG* 2.9 16.2 + - - -
58A MET 3.2 7.8 + - - -
60A ASP* 1.3 73.3 - - - +
62A LEU* 1.3 68.9 + - - +
64A GLU* 3.3 12.5 + - - +
65A PHE* 3.1 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU* 3.8 40.6 - - + +
19A LEU* 3.4 39.0 - - + -
20A ALA* 4.6 4.9 - - + +
23A LEU* 4.2 6.3 - - + -
58A MET 2.9 7.8 + - - +
59A PHE* 3.1 10.1 + - + +
61A SER* 1.3 76.4 - - - +
63A ILE* 1.3 63.4 + - - +
65A PHE* 3.2 12.7 + - + +
66A ILE* 3.0 26.8 + - - +
105A LEU* 3.7 21.0 - - + +
108A ILE* 3.8 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A PHE* 2.7 24.3 + - - +
60A ASP* 3.5 5.4 - - - +
62A LEU* 1.3 73.7 - - - +
64A GLU* 1.3 62.8 + - - +
66A ILE* 3.1 7.7 + - - +
67A GLU* 2.9 25.4 + - + +
108A ILE* 3.9 23.3 - - + -
114A LEU* 4.6 3.8 - - + -
121A LEU* 3.7 46.4 - - + +
124A ARG* 3.9 31.4 - - + +
125A ILE* 4.0 24.2 - - + -
128A LEU* 5.5 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ASP* 2.7 18.2 + - - +
61A SER* 3.6 12.2 - - - +
63A ILE* 1.3 72.1 - - - +
65A PHE* 1.3 58.6 + - - +
67A GLU* 3.4 5.4 + - - +
68A ASP* 2.8 45.2 + - - +
124A ARG* 3.1 37.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU* 6.5 0.2 - - + -
61A SER 3.1 13.3 + - - +
62A LEU* 3.2 13.7 + - + +
64A GLU* 1.3 77.8 - - - +
66A ILE* 1.3 53.4 + - - +
68A ASP* 3.9 7.0 - - + +
69A SER* 2.6 56.2 + - - -
73A ARG* 6.0 1.6 - - - -
98A PHE* 4.0 10.5 - + - -
102A ASN* 4.4 7.0 - - - -
105A LEU* 3.6 33.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LEU 3.0 20.9 + - - +
63A ILE* 3.1 11.4 + - - +
65A PHE* 1.3 73.2 - - - +
67A GLU* 1.3 66.8 + - - +
69A SER* 3.8 0.7 - - - -
70A LEU* 3.0 33.7 + - + +
98A PHE* 4.0 21.8 - - + -
105A LEU* 3.8 48.7 - - + +
108A ILE* 4.0 20.6 - - + -
109A LEU* 4.3 13.0 - - + -
125A ILE* 4.8 2.9 - - + -
128A LEU* 3.6 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ILE* 2.9 18.5 + - + +
64A GLU* 3.8 5.0 - - - +
66A ILE* 1.3 72.6 - - - +
68A ASP* 1.3 67.4 - - - +
71A ILE* 2.7 44.2 + - + +
124A ARG* 4.0 19.6 + - - -
127A GLN* 5.7 1.0 - - - +
128A LEU* 3.7 37.3 - - + +
131A ARG* 3.6 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A GLU* 2.8 36.2 + - - +
65A PHE* 3.9 7.1 + - + +
67A GLU* 1.3 79.6 - - - +
69A SER* 1.3 64.3 + - - +
71A ILE* 4.9 2.2 - - - -
72A THR* 2.9 35.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A PHE* 2.6 51.1 + - - -
66A ILE 3.8 0.7 - - - -
68A ASP* 1.3 75.6 - - - +
70A LEU* 1.3 63.8 + - - +
72A THR* 4.1 2.0 - - - -
73A ARG* 3.1 38.8 + - - +
98A PHE* 3.5 26.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ILE* 3.0 34.7 + - + +
67A GLU* 4.1 1.6 - - - +
69A SER* 1.3 78.7 - - - +
71A ILE* 1.3 66.9 + - + +
73A ARG 3.4 0.9 + - - -
74A ILE* 2.9 37.3 + - + +
94A LEU* 3.9 24.9 - - + +
95A ILE* 4.3 16.4 - - + -
98A PHE* 3.7 39.3 - - + -
109A LEU* 4.9 9.2 - - + -
128A LEU* 4.5 4.9 - - + -
132A ILE* 3.9 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A GLU* 2.7 27.6 + - + +
68A ASP* 4.3 1.6 - - - +
70A LEU* 1.3 77.4 - - + +
72A THR* 1.3 65.0 + - - +
74A ILE* 3.2 8.5 + - + +
75A ASN* 3.1 38.8 + - - +
128A LEU* 3.6 26.0 - - + -
131A ARG* 3.5 53.4 - - + +
132A ILE* 4.5 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ASP* 2.9 28.4 + - - +
69A SER* 4.1 2.9 - - - -
71A ILE* 1.3 79.6 - - - +
73A ARG* 1.3 65.1 + - + +
75A ASN* 3.5 10.4 + - + +
76A LEU* 3.2 35.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A PHE* 6.0 1.4 - - - -
69A SER* 3.1 29.5 + - - +
72A THR* 1.3 77.2 - - + +
74A ILE* 1.3 67.4 + - - +
76A LEU* 3.2 14.7 + - + +
77A ILE* 3.0 26.8 + - + +
94A LEU* 3.6 35.1 - - + +
98A PHE* 3.9 25.4 - - - -
101A ARG* 2.7 37.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LEU* 2.9 31.1 + - + +
71A ILE* 3.2 10.9 + - + +
73A ARG* 1.3 77.2 - - - +
75A ASN* 1.3 64.9 + - - +
77A ILE* 3.0 8.1 + - + +
78A LEU* 3.0 28.9 + - + +
91A ILE* 3.3 50.5 - - + -
94A LEU* 3.2 24.2 - - + -
95A ILE* 5.3 3.4 - - + -
132A ILE* 5.5 8.1 - - + -
135A GLN* 4.2 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ILE* 3.1 32.6 + - - +
72A THR* 3.8 8.5 - - - +
74A ILE* 1.3 77.0 - - - +
76A LEU* 1.3 64.0 + - + +
78A LEU* 3.1 12.2 + - - +
79A LYS* 3.0 25.2 + - - +
135A GLN* 4.3 16.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A THR* 3.2 40.7 + - + +
73A ARG* 3.4 16.6 - - + +
74A ILE 3.2 0.2 - - - -
75A ASN* 1.3 76.8 - - + +
77A ILE* 1.3 65.2 + - + +
79A LYS* 3.3 35.5 - - + +
80A ASP* 3.0 33.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ARG* 3.0 19.7 + - + +
74A ILE* 3.3 7.4 - - + +
76A LEU* 1.3 78.3 - - + +
78A LEU* 1.3 59.1 + - + +
80A ASP* 4.9 2.5 - - - -
81A GLU* 2.9 32.0 + - + +
87A ARG* 4.0 22.7 - - + +
90A LEU* 3.6 60.3 - - + +
91A ILE* 3.8 15.3 - - + +
94A LEU* 4.2 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ILE* 3.0 24.1 + - + +
75A ASN* 3.1 13.9 + - - +
77A ILE* 1.3 76.8 - - + +
79A LYS* 1.3 60.4 + - - +
81A GLU 3.4 2.3 - - - +
82A LYS* 3.0 12.3 + - - -
87A ARG* 2.8 53.0 + - + +
91A ILE* 4.5 8.1 - - + -
135A GLN* 3.3 35.7 - - - +
138A GLN* 5.4 5.2 - - - +
139A VAL* 3.7 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ASN 3.0 13.8 + - - +
76A LEU* 3.3 35.0 - - + +
78A LEU* 1.3 77.0 - - - +
80A ASP* 1.3 89.0 + - - +
82A LYS* 3.1 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A LEU* 3.0 23.4 + - - +
77A ILE* 4.3 2.2 - - - +
79A LYS* 1.3 124.9 + - - +
81A GLU* 1.3 60.4 + - + +
82A LYS* 4.1 4.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ILE* 2.9 17.0 + - + +
78A LEU 3.4 1.4 - - - +
80A ASP* 1.3 79.2 - - + +
82A LYS* 1.3 63.8 + - - +
83A ASP* 2.5 39.5 + - - +
86A ALA* 3.4 30.1 - - + +
87A ARG* 2.7 34.4 + - + +
90A LEU* 3.9 24.5 - - + +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il