Contacts of the helix formed by residues 38 - 59 (chain E) in PDB entry 6GYS
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 LYS 38 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A ASP* 2.8 29.6 + - - +
202A GLY* 4.5 1.4 - - - -
204A ASP* 2.3 46.1 + - - +
279A ARG* 3.4 41.1 - - - +
316A ARG* 4.2 16.5 - - - +
37E LEU* 1.3 82.2 - - - +
39E PRO* 1.3 72.5 - - + +
40E ARG* 4.0 14.7 - - + +
41E THR* 3.3 21.0 + - - +
42E ALA* 3.0 18.0 + - - +
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Residues in contact with PRO 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ILE* 4.5 12.6 - - + -
134A LYS 3.4 26.5 - - - +
135A ALA* 4.2 16.8 - - - +
136A SER* 4.3 3.4 - - - +
279A ARG* 6.2 0.4 - - - +
316A ARG* 5.6 2.2 - - - +
341A ARG* 6.3 0.2 - - - +
37E LEU 4.2 3.8 - - - +
38E LYS* 1.3 82.8 - - + +
40E ARG* 1.3 60.0 + - - +
42E ALA* 3.0 8.5 + - + +
43E HIS* 2.9 41.6 + - + -
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Residues in contact with ARG 40 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A THR* 4.8 4.4 + - - +
73A TYR* 4.4 10.1 - - - +
76A ILE* 3.7 39.2 - - + +
132A PHE* 3.9 15.0 - - - -
136A SER* 3.7 25.3 + - - +
173A ASP* 3.8 14.4 + - - -
174A ASN* 2.6 50.3 + - - -
38E LYS* 4.5 16.2 - - + +
39E PRO* 1.3 78.6 - - - +
41E THR* 1.3 63.1 + - - +
43E HIS* 3.3 1.1 + - - -
44E GLN* 3.0 42.2 + - - +
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Residues in contact with THR 41 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A ASP* 4.7 5.9 + - - +
37E LEU* 3.8 32.3 - - + +
38E LYS* 3.3 33.2 + - - +
40E ARG* 1.3 78.0 - - - +
42E ALA* 1.3 56.9 - - - +
44E GLN* 3.3 11.6 + - - +
45E TYR* 2.9 48.4 + - + +
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Residues in contact with ALA 42 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ILE* 5.1 12.1 - - + -
40A TYR* 3.9 21.9 + - - +
37E LEU* 4.4 13.7 - - + -
38E LYS 3.0 12.0 + - - +
39E PRO* 3.0 13.1 + - + +
41E THR* 1.3 75.6 - - - +
43E HIS* 1.3 63.4 + - + +
45E TYR* 3.4 5.7 + - - +
46E LYS* 2.8 26.2 + - - +
49E TYR* 4.8 2.8 + - - -
131E PHE* 5.7 0.6 - - - -
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Residues in contact with HIS 43 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A PRO* 4.5 15.1 - - + +
34A TYR 4.5 8.9 + - - -
36A ILE* 3.6 35.8 - - + +
39A LEU* 4.7 6.3 - - + -
76A ILE* 3.1 10.3 - - + +
77A PHE* 3.6 26.2 - + + -
79A TYR* 2.4 34.4 + + - +
135A ALA* 4.1 13.1 + - - +
39E PRO* 2.9 31.4 + - + +
40E ARG* 4.6 0.4 - - - -
42E ALA* 1.3 76.0 - - - +
44E GLN* 1.3 62.8 + - - +
46E LYS* 3.9 8.8 - - + +
47E THR* 2.8 31.9 + - - -
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Residues in contact with GLN 44 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ILE* 3.7 35.0 - - + +
40E ARG* 3.0 34.2 + - - +
41E THR* 3.7 9.8 - - - +
43E HIS* 1.3 76.6 - - - +
45E TYR* 1.3 65.0 + - + +
47E THR* 3.3 9.7 + - - -
48E TYR* 3.0 27.6 + - + -
124E LYS* 2.8 40.0 + - - +
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Residues in contact with TYR 45 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E LEU* 4.1 14.8 - - + +
41E THR* 2.9 37.9 + - + +
42E ALA* 3.7 6.1 - - - +
44E GLN* 1.3 81.6 - - + +
46E LYS* 1.3 56.9 + - - +
48E TYR* 3.2 3.3 + + - +
49E TYR* 2.9 42.5 + - + -
124E LYS* 3.6 22.4 - - + -
127E GLY* 3.5 27.9 - - - -
128E SER* 3.5 28.2 - - - -
131E PHE* 3.7 31.4 - + + -
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Residues in contact with LYS 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU* 5.1 25.3 + - + +
45A VAL* 4.2 13.9 - - - +
46A GLU* 3.7 24.4 - - - +
79A TYR* 3.5 43.1 - - + +
42E ALA 2.8 17.4 + - - +
43E HIS* 3.5 14.6 - - + +
44E GLN 3.2 0.4 - - - -
45E TYR* 1.3 74.9 - - - +
47E THR* 1.3 56.8 + - - +
49E TYR* 3.4 36.2 + - + +
50E THR* 2.3 42.8 + - - +
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Residues in contact with THR 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A ASN 4.6 4.0 - - - +
76A ILE* 2.6 29.9 + - - -
78A GLU* 3.7 30.0 + - + -
79A TYR* 3.2 14.2 - - - +
43E HIS 2.8 3.7 + - - -
44E GLN* 3.4 10.8 - - - -
46E LYS* 1.3 76.7 - - - +
48E TYR* 1.3 69.9 + - + +
50E THR* 3.3 4.8 + - - -
51E LYS* 3.0 43.0 + - - +
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Residues in contact with TYR 48 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44E GLN* 3.0 19.4 + - - -
45E TYR* 3.2 2.6 + + - +
47E THR* 1.3 89.5 - - + +
49E TYR* 1.3 58.9 + - - +
51E LYS* 3.2 15.5 + - + +
52E TYR* 3.0 23.0 + - - +
88E PHE* 4.2 4.8 - - + -
121E THR* 3.7 23.8 - - - +
124E LYS* 3.6 57.0 + - + -
125E ILE* 3.5 35.4 - - + -
128E SER* 3.5 22.0 - - - +
129E LEU* 4.9 1.6 - - - -
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Residues in contact with TYR 49 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU* 5.5 2.3 + - - +
40A TYR* 4.1 19.7 + + - -
45A VAL* 4.3 11.0 - - + -
42E ALA 4.8 2.1 + - - -
45E TYR* 2.9 32.8 + - + -
46E LYS* 3.4 49.1 + - + +
48E TYR* 1.3 74.0 - - - +
50E THR* 1.3 64.0 + - - +
52E TYR* 3.4 8.0 - - - +
53E ILE* 2.9 42.6 + - + +
128E SER 4.6 6.7 - - - -
129E LEU* 4.1 8.4 - - + +
131E PHE* 4.5 18.4 - + - -
132E LEU* 3.7 49.4 - - + -
135E LEU* 5.2 4.7 - - + +
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Residues in contact with THR 50 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A VAL* 5.6 2.0 - - + +
46A GLU* 4.9 19.3 + - + +
47A LEU* 6.2 0.2 - - + -
48A PRO* 5.6 2.9 - - + -
79A TYR* 3.5 29.9 - - + +
80A SER 5.3 0.7 - - - +
46E LYS* 2.3 37.4 + - - +
47E THR 3.5 4.9 - - - -
49E TYR* 1.3 79.6 - - - +
51E LYS* 1.3 64.0 + - - +
53E ILE* 3.3 8.3 + - + +
54E GLN* 3.0 44.5 + - + +
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Residues in contact with LYS 51 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A GLU* 4.2 15.4 + - - +
79A TYR 5.4 0.2 - - - +
47E THR* 3.0 36.9 + - - +
48E TYR* 3.3 17.0 - - + +
50E THR* 1.3 77.1 - - + +
52E TYR* 1.3 55.9 + - - +
54E GLN* 3.4 15.7 + - - +
55E TRP* 2.9 29.8 + - - +
88E PHE* 3.5 15.9 - - + -
92E THR* 5.8 1.8 - - + -
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Residues in contact with TYR 52 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48E TYR 3.0 12.6 + - - +
49E TYR* 3.2 12.7 + - - +
51E LYS* 1.3 77.8 - - - +
53E ILE* 1.3 58.6 + - - +
55E TRP* 3.3 21.8 + + - +
56E CYS* 2.9 46.9 + - - -
78E LEU* 4.2 22.2 - - + -
79E PRO* 3.1 25.9 + - - +
80E ILE* 4.4 10.2 - - + -
84E LEU* 3.6 25.8 - - - +
85E ILE* 4.4 7.5 + - + -
88E PHE* 3.5 38.3 - + + -
129E LEU* 4.2 12.8 - - + -
132E LEU* 4.4 11.2 - - + -
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Residues in contact with ILE 53 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A VAL* 3.7 38.4 - - + -
46A GLU 4.7 3.1 - - - +
47A LEU* 4.2 22.0 - - + -
49E TYR* 2.9 28.0 + - + +
50E THR* 3.8 7.2 - - + +
52E TYR* 1.3 78.3 - - + +
54E GLN* 1.3 59.6 + - - +
56E CYS* 3.2 6.5 + - - +
57E GLN* 3.0 34.8 + - - +
62E ILE* 3.9 12.2 - - + +
73E VAL* 4.5 9.9 - - + -
78E LEU* 4.1 26.9 - - + -
132E LEU* 5.6 2.5 - - + -
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Residues in contact with GLN 54 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LEU* 4.5 14.6 - - + -
48A PRO* 3.4 35.7 - - + +
79A TYR* 6.2 0.6 - - - +
50E THR* 3.0 34.0 + - + +
51E LYS* 3.8 16.8 - - - +
53E ILE* 1.3 74.7 - - - +
55E TRP* 1.3 57.4 + - - +
57E GLN* 3.2 12.7 + - - +
58E LEU* 2.9 36.0 + - + +
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Residues in contact with TRP 55 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E LYS 2.9 18.3 + - - +
52E TYR* 3.6 11.7 - + - +
53E ILE 3.2 0.2 - - - -
54E GLN* 1.3 74.0 - - - +
56E CYS* 1.3 86.4 + - - +
58E LEU* 2.9 34.5 + - + +
59E ASN* 3.1 13.3 + - + +
61E ILE* 4.5 7.9 - - + -
84E LEU* 3.7 11.7 - - + -
87E TRP* 3.5 36.1 - + - -
88E PHE* 3.4 53.8 - + + -
91E ASP* 2.9 42.3 + - + +
92E THR* 5.1 4.3 - - + -
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Residues in contact with CYS 56 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52E TYR* 2.9 55.0 + - - +
53E ILE 3.2 1.3 + - - +
55E TRP* 1.3 88.9 - - - +
57E GLN* 1.3 54.3 + - - +
59E ASN 3.3 1.4 - - - -
60E GLN 2.8 4.9 + - - -
61E ILE* 2.4 57.7 + - + -
62E ILE* 3.6 20.0 - - + -
78E LEU* 4.4 8.3 - - + -
79E PRO* 5.4 1.1 - - - -
84E LEU* 6.4 0.4 - - - -
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Residues in contact with GLN 57 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LEU* 3.4 36.5 - - - +
53E ILE* 3.0 16.9 + - - +
54E GLN* 3.5 10.4 - - - +
56E CYS* 1.3 77.3 - - - +
58E LEU* 1.3 59.6 + - - +
59E ASN 3.2 0.4 - - - -
60E GLN* 2.9 17.8 + - - +
62E ILE* 3.3 31.0 - - + +
63E PRO 4.0 12.7 + - - +
64E THR* 4.5 15.0 + - - +
72E SER 3.3 25.3 + - - -
387E LEU* 5.2 2.3 - - - +
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Residues in contact with LEU 58 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54E GLN* 2.9 23.1 + - + +
55E TRP* 2.9 28.2 + - + +
57E GLN* 1.3 78.0 - - + +
59E ASN* 1.3 58.4 + - - +
60E GLN 3.4 0.2 - - - -
387E LEU* 3.6 19.4 - - - +
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Residues in contact with ASN 59 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55E TRP* 3.1 13.0 + - + +
56E CYS 3.3 0.2 - - - -
58E LEU* 1.3 75.9 - - - +
60E GLN* 1.3 59.7 + - - +
61E ILE* 2.9 28.4 + - + +
87E TRP* 3.2 29.3 - - + -
386E TRP* 3.3 20.3 - - - +
387E LEU* 2.7 34.8 + - - +
388E GLU* 2.7 37.6 + - - +
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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) + - + + + + + -
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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