Contacts of the helix formed by residues 77 - 100 (chain A) in PDB entry 1GM5
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 PRO 77 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ASN 4.6 0.7 - - - -
76A LEU* 1.3 79.1 - - - +
78A GLU* 1.3 54.7 + - + +
79A ALA 2.9 1.0 + - - -
80A ARG* 2.6 88.0 + - + +
81A LYS* 4.1 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A LEU 3.8 2.0 + - - -
77A PRO* 1.3 67.3 - - + +
79A ALA* 1.3 65.3 + - - +
81A LYS* 2.9 28.4 + - - +
82A ARG* 3.3 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A PRO 2.9 2.0 + - - -
78A GLU* 1.3 77.6 + - - +
80A ARG* 1.3 67.6 + - - +
81A LYS 2.6 1.7 + - - -
82A ARG* 2.8 38.2 + - - +
83A TYR* 3.9 6.1 + - - +
84A ARG 4.8 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ASN 4.9 4.8 + - - -
76A LEU* 2.3 49.9 - - + +
77A PRO* 2.6 56.7 + - + +
79A ALA* 1.3 74.3 - - - +
81A LYS* 1.3 51.9 + - - +
84A ARG* 3.4 12.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A GLN* 5.7 7.9 - - - +
73A ILE* 3.7 20.4 - - + +
74A PRO* 3.7 18.0 + - - +
76A LEU 2.9 27.4 + - - +
77A PRO* 4.5 2.0 - - - +
78A GLU* 2.9 19.5 + - - +
79A ALA 2.6 5.5 + - - -
80A ARG* 1.3 71.8 - - - +
82A ARG* 1.3 62.2 + - + +
84A ARG* 2.7 44.9 + - - +
85A ILE* 3.0 14.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A GLU* 3.7 33.0 + - - +
79A ALA* 2.8 27.0 + - - +
81A LYS* 1.3 67.3 - - + +
83A TYR* 1.3 57.5 + - - +
84A ARG 2.5 8.1 - - - -
85A ILE* 2.2 44.4 + - + +
86A GLN* 3.3 7.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A TYR* 4.3 2.2 - - - -
79A ALA 3.9 5.4 + - - +
82A ARG* 1.3 80.6 - - - +
84A ARG* 1.3 62.0 + - - +
86A GLN* 4.9 7.2 - - + +
87A LYS* 2.8 61.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 5.4 3.4 - - - +
37A VAL* 5.1 0.8 - - - +
69A TYR* 3.4 36.2 + - + +
70A VAL* 4.1 5.9 + - - +
72A GLU* 3.4 31.9 - - - +
73A ILE* 2.8 58.9 - - - +
76A LEU* 3.9 3.6 - - + -
80A ARG 3.4 17.0 + - - +
81A LYS* 2.7 49.4 + - - +
82A ARG 2.3 6.7 + - - -
83A TYR* 1.3 76.7 - - - +
85A ILE* 1.3 87.0 + - - +
87A LYS* 3.3 3.8 - - - +
88A SER* 2.7 29.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 2.4 56.1 - - + +
35A ASN 6.0 0.9 - - - +
73A ILE* 5.0 1.6 - - + -
81A LYS* 3.1 26.9 - - + +
82A ARG* 2.2 25.2 + - + +
84A ARG* 1.3 100.4 - - - +
86A GLN* 1.3 65.2 + - + +
87A LYS 2.8 0.9 - - - -
88A SER* 2.3 42.8 + - - -
89A LEU* 3.1 5.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ARG* 3.3 10.2 + - + +
83A TYR* 4.6 7.6 - - + +
85A ILE* 1.3 84.0 - - + +
87A LYS* 1.3 64.9 + - - +
89A LEU* 4.0 18.7 - - - +
90A GLU* 3.1 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A TYR* 2.8 40.0 + - + +
83A TYR* 2.8 52.5 + - + +
84A ARG 3.3 6.7 - - - +
85A ILE 2.7 3.8 + - - -
86A GLN* 1.3 74.1 - - - +
88A SER* 1.3 65.3 + - - +
90A GLU* 3.5 13.1 - - - +
91A MET* 3.6 6.6 + - - +
94A LYS* 5.3 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 5.3 6.1 - - - +
66A PHE* 3.9 27.6 - - - -
69A TYR* 5.2 6.4 - - - -
70A VAL* 4.0 19.1 - - - +
84A ARG* 2.7 15.1 + - - -
85A ILE* 2.3 30.7 + - - -
87A LYS* 1.3 65.7 - - - +
89A LEU* 1.3 57.8 + - - -
90A GLU 2.4 2.6 + - - -
91A MET* 2.2 41.2 + - - +
92A ILE* 3.3 2.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A GLU* 3.9 33.2 - - + -
33A LEU* 2.9 45.5 - - + -
34A LYS* 4.5 9.6 - - + -
85A ILE* 3.1 4.7 + - + +
86A GLN* 4.0 23.3 - - - +
88A SER* 1.3 78.1 - - - +
90A GLU* 1.3 64.4 + - - +
91A MET 3.2 0.3 + - - -
92A ILE* 3.2 21.5 + - + +
93A GLU* 3.4 17.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A GLN* 3.1 18.0 + - - +
87A LYS* 3.5 8.0 - - - +
88A SER 2.4 4.6 + - - -
89A LEU* 1.3 80.0 - - - +
91A MET* 1.3 56.4 + - - +
93A GLU* 3.7 4.9 + - - +
94A LYS* 2.2 65.2 + - - +
297A LYS* 5.6 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LYS* 4.2 33.2 - - + +
65A ALA* 6.3 0.4 - - + -
66A PHE* 3.3 31.2 - - + +
87A LYS 3.6 5.4 + - - +
88A SER* 2.2 25.2 + - - +
90A GLU* 1.3 66.6 - - - +
92A ILE* 1.3 53.8 + - - +
94A LYS* 2.6 27.2 - - + +
95A LEU* 2.3 56.5 + - + +
98A TRP* 5.4 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU* 4.2 19.1 - - + +
29A VAL* 4.6 8.5 - - + -
30A GLU* 3.6 39.3 - - + +
66A PHE* 3.6 25.6 - - + -
88A SER* 5.6 1.1 - - - -
89A LEU* 3.2 22.2 + - + +
91A MET* 1.3 73.2 - - - +
93A GLU* 1.3 60.9 + - + +
95A LEU* 2.2 35.0 + - - +
96A ARG* 2.6 49.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A GLU* 4.6 3.6 - - - +
89A LEU* 3.4 11.6 + - + +
90A GLU* 3.9 7.6 - - - +
92A ILE* 1.3 80.0 - - + +
94A LYS* 1.3 63.1 + - - +
96A ARG* 2.3 56.8 + - - +
97A SER* 3.0 26.5 + - - -
297A LYS* 3.8 28.7 + - - +
315A TYR* 3.7 18.3 + - - +
319A LYS* 4.2 10.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LYS 5.3 1.2 + - - -
90A GLU* 2.2 62.1 + - - +
91A MET* 2.6 39.0 - - + +
92A ILE 2.7 0.2 + - - -
93A GLU* 1.3 80.3 - - - +
95A LEU* 1.3 58.9 + - - +
97A SER* 3.6 5.0 + - - -
98A TRP* 3.4 37.1 + - + +
297A LYS* 5.4 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 6.3 0.2 - - + -
26A LEU* 3.7 32.3 - - + -
62A LYS* 4.9 6.1 - - + +
63A LEU* 3.6 31.0 - - + -
66A PHE* 4.7 13.9 - - + -
91A MET* 2.3 45.9 + - + +
92A ILE* 2.2 24.0 + - - +
94A LYS* 1.3 63.3 - - - +
96A ARG* 1.3 59.3 + - - +
98A TRP* 2.7 40.1 + - + +
99A PHE* 3.1 31.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU* 4.2 11.5 - - + +
27A ASN* 4.0 31.0 + - - +
30A GLU* 2.4 36.7 + - - -
92A ILE* 2.6 44.6 + - + +
93A GLU* 2.3 40.6 + - - +
95A LEU* 1.3 71.2 - - - +
97A SER* 1.3 60.0 + - - +
100A LEU* 2.9 54.0 + - + +
101A ILE* 4.0 1.7 + - - +
315A TYR* 3.6 38.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A GLU 3.0 17.9 + - - -
94A LYS* 3.7 6.3 - - - -
96A ARG* 1.3 78.3 - - - +
98A TRP* 1.3 70.2 - - - +
101A ILE* 4.4 11.9 - - - +
103A TYR* 3.2 34.8 + - - -
297A LYS* 5.4 14.0 - - - +
315A TYR* 4.6 5.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LYS* 4.0 23.3 - - + +
91A MET* 5.4 4.4 - - + +
94A LYS* 3.4 25.8 + - + +
95A LEU* 2.7 23.6 + - + +
97A SER* 1.3 86.2 - - - +
99A PHE* 1.3 92.1 + + + +
101A ILE 4.8 1.1 - - - +
103A TYR* 4.7 9.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 4.9 4.9 - - + -
53A LEU* 5.4 8.4 - - + +
56A ASN* 3.6 22.7 - - - -
58A ASP* 5.0 2.7 - - + -
59A LEU* 3.2 56.8 - - + -
62A LYS* 4.5 11.4 - - + -
63A LEU* 6.4 0.4 - - + -
95A LEU* 3.1 29.1 + - + +
98A TRP* 1.3 114.2 - + + +
100A LEU* 1.3 66.6 + - + +
101A ILE 2.8 19.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 4.2 22.0 - - + -
23A GLU* 4.0 25.4 - - + -
26A LEU* 4.8 6.5 - - + -
53A LEU* 3.8 23.3 - - + -
96A ARG* 2.9 44.7 + - + +
99A PHE* 1.3 74.9 - - + +
101A ILE* 1.3 59.3 + - - +
312A LYS* 4.4 6.0 + - - +
313A THR* 2.9 47.9 + - + +
315A TYR* 4.2 15.0 - - + -
316A HIS* 4.1 2.6 + - - +
----------------------------------------------------------
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