Contacts of the helix formed by residues 68 - 85 (chain A) in PDB entry 2KG4
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 ASP 68 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ASP* 3.3 13.9 + - - +
65A ASP* 3.1 14.5 + - - +
66A ASP 3.8 0.2 - - - -
67A ARG* 1.3 75.7 - - - +
69A VAL* 1.3 62.0 + - - +
70A ALA* 3.3 12.0 + - - +
71A LEU* 3.0 30.2 + - + +
72A GLN* 3.1 26.1 + - - +
120A PRO* 3.8 23.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ARG* 3.8 7.5 + - - +
68A ASP* 1.3 71.6 + - - +
70A ALA* 1.3 65.0 + - + +
72A GLN* 3.7 9.7 - - + +
73A ILE* 3.2 27.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ASP* 3.2 9.3 + - - +
69A VAL* 1.3 82.6 - - + +
71A LEU* 1.3 57.7 + - - +
73A ILE* 3.2 8.9 + - - +
74A HIS* 2.9 46.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A VAL* 4.0 22.4 - - + -
60A ALA 5.6 2.5 - - - +
62A ASP* 5.2 4.0 - - - +
65A ASP* 3.4 26.2 - - + +
68A ASP* 3.0 21.1 + - + +
70A ALA* 1.3 71.9 - - - +
72A GLN* 1.3 59.6 + - - +
74A HIS* 3.1 17.0 + - + +
75A PHE* 3.0 57.7 + - + -
120A PRO* 3.2 48.0 - - + +
123A HIS* 5.6 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ASP* 3.4 34.3 + - - +
66A ASP* 4.2 18.2 + - - +
68A ASP 3.1 18.9 + - - +
69A VAL* 3.7 11.0 - - - +
71A LEU* 1.3 74.0 - - - +
73A ILE* 1.3 61.7 + - + +
75A PHE* 3.4 13.3 + - - +
76A THR* 3.3 20.3 + - - +
91A ARG* 5.1 9.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A VAL* 3.2 13.8 + - + +
70A ALA* 3.2 11.9 + - - +
72A GLN* 1.3 76.4 - - + +
74A HIS* 1.3 61.2 + - + +
76A THR* 3.1 17.3 + - + +
77A LEU* 2.8 41.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A VAL* 3.9 24.9 - - + +
41A TYR* 3.5 46.8 - + + +
43A ALA* 5.0 0.5 - - - +
70A ALA* 2.9 38.2 + - + +
71A LEU* 3.1 23.0 + - + +
73A ILE* 1.3 79.2 - - + +
75A PHE* 1.3 57.2 + - - +
77A LEU* 3.6 15.1 - - + +
78A ILE* 3.1 33.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A VAL* 3.9 13.7 - - + -
59A LEU* 3.6 40.7 - - + +
60A ALA 4.0 22.0 - - - -
61A ALA* 3.8 24.0 - - + -
65A ASP* 4.9 4.7 - - - -
71A LEU* 3.0 39.6 + - + +
72A GLN* 3.5 15.9 - - - +
73A ILE 3.3 0.2 - - - -
74A HIS* 1.3 74.9 - - - +
76A THR* 1.3 60.4 + - - +
78A ILE* 3.4 9.0 - - - +
79A GLN* 3.2 22.5 + - - +
89A ILE* 5.6 0.5 - - - +
91A ARG* 3.6 46.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A GLN 3.3 10.4 + - - +
73A ILE* 3.3 29.6 - - + +
75A PHE* 1.3 75.9 - - - +
77A LEU* 1.3 58.6 + - - +
79A GLN* 3.3 18.0 + - - +
80A ALA* 3.0 28.2 + - - +
91A ARG* 5.4 3.1 - - - +
156A TRP* 5.6 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A TYR* 5.8 6.5 - - + -
43A ALA* 4.3 11.4 - - + -
44A ALA* 5.3 5.2 - - + +
73A ILE* 2.8 25.7 + - + +
74A HIS* 3.6 18.4 - - + +
76A THR* 1.3 76.2 - - - +
78A ILE* 1.3 62.0 + - - +
80A ALA* 3.1 18.3 + - + +
81A PHE* 3.2 52.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A VAL 4.4 7.4 - - - +
43A ALA* 3.8 29.4 - - + +
46A LEU* 4.0 20.6 - - + -
57A CYS* 3.6 29.2 - - + -
59A LEU* 4.0 24.0 - - + -
74A HIS 3.1 16.9 + - - +
75A PHE* 3.4 15.7 - - - +
77A LEU* 1.3 75.8 - - - +
79A GLN* 1.3 59.6 + - - +
81A PHE* 3.4 6.5 + - + +
82A CYS* 3.1 31.3 + - + +
89A ILE* 5.7 1.6 - - + -
124A CYS* 4.3 12.8 - - - -
126A LEU* 4.6 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A PHE 3.2 19.4 + - - +
76A THR* 3.4 16.8 + - - +
77A LEU 3.1 0.4 - - - -
78A ILE* 1.3 74.9 - - - +
80A ALA* 1.3 68.5 + - - +
82A CYS* 3.2 9.3 - - - -
83A CYS* 3.2 39.0 + - - +
89A ILE* 3.7 24.5 - - + -
91A ARG* 6.3 0.4 - - - +
156A TRP* 3.6 36.7 - - - +
157A VAL* 4.2 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A THR 3.0 13.7 + - - +
77A LEU* 3.3 12.3 - - + +
79A GLN* 1.3 83.1 - - - +
81A PHE* 1.3 71.7 + - + +
83A CYS* 3.6 3.5 + - - +
84A GLU* 3.2 23.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ALA* 3.5 40.4 - - + +
44A ALA* 3.8 12.6 - - + -
46A LEU* 5.9 4.5 - - + -
47A LEU* 3.8 32.8 - - + -
77A LEU* 3.2 47.9 + - + -
78A ILE* 3.7 7.9 - - + +
79A GLN 3.3 0.2 - - - -
80A ALA* 1.3 79.1 - - + +
82A CYS* 1.3 65.3 + - - +
84A GLU* 3.2 14.1 + - - +
85A ASN* 3.0 25.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A VAL* 5.2 5.4 - - + -
57A CYS* 5.4 3.1 - - + -
78A ILE* 3.1 19.2 + - + +
79A GLN* 3.2 19.3 - - - -
81A PHE* 1.3 74.5 - - - +
83A CYS* 1.3 77.0 + - - +
85A ASN* 3.2 10.7 + - - +
87A ILE* 3.1 55.7 + - + +
89A ILE* 3.4 32.3 - - + -
126A LEU* 5.8 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A GLN* 3.2 39.0 + - - +
80A ALA* 3.7 4.9 - - - +
82A CYS* 1.3 86.5 - - - +
84A GLU* 1.3 62.2 + - - +
86A ASP* 3.3 13.8 + - - +
87A ILE 4.6 6.3 - - - +
89A ILE* 6.0 1.1 - - - -
151A ARG* 5.1 15.9 - - - -
156A TRP 5.6 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LEU* 5.0 10.3 - - - +
80A ALA 3.2 11.2 + - - +
81A PHE* 3.2 16.7 + - - +
83A CYS* 1.3 77.6 - - - +
85A ASN* 1.3 68.1 + - - +
86A ASP 3.5 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LEU* 3.9 21.6 - - - +
51A PRO* 3.8 27.9 - - - +
52A ASP* 5.5 0.2 - - - -
54A VAL* 6.0 0.8 - - - +
81A PHE 3.0 22.6 + - - +
82A CYS* 3.2 3.6 + - - +
84A GLU* 1.3 85.5 + - - +
86A ASP* 1.3 68.7 + - - +
87A ILE* 3.5 23.3 - - + +
----------------------------------------------------------
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