Contacts of the helix formed by residues 27 - 46 (chain E) in PDB entry 2GTL
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 PHE 27 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25E SER* 3.1 15.4 + - - +
26E SER* 1.3 85.7 - - - +
28E THR* 1.3 67.8 + - - +
29E ASP* 3.3 8.4 + - - +
30E ARG* 3.8 4.5 + - - +
31E ARG* 4.2 5.3 + - - -
25G ASP* 3.6 24.0 - - - -
27G GLU* 3.9 23.8 - - + -
30G LYS* 3.6 31.4 - - + -
31G ILE* 4.2 13.0 - - + -
15H LEU* 3.9 26.9 - - + -
18H LYS* 3.5 30.3 - - + +
85H ASP* 3.7 25.1 - - + -
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Residues in contact with THR 28 (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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26E SER 4.2 0.4 - - - -
27E PHE* 1.3 69.6 - - - +
29E ASP* 1.3 73.3 + - - -
30E ARG 2.7 3.3 + - - -
31E ARG* 2.9 32.9 + - - +
32E VAL* 3.1 16.2 + - - -
71E VAL* 4.0 18.2 - - + -
82H SER* 3.2 31.5 + - - +
83H MET* 3.9 20.0 - - + -
85H ASP* 4.6 2.8 + - - -
86H THR* 4.2 17.5 + - - +
89H MET* 4.4 10.0 - - + -
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Residues in contact with ASP 29 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E PHE* 4.5 7.9 - - + +
28E THR* 1.3 83.3 + - - +
30E ARG* 1.3 65.3 + - - +
32E VAL* 3.4 6.9 - - - +
33E ALA* 3.2 19.9 + - - +
80F ASP* 4.8 9.8 - - - +
81F GLN* 6.2 0.2 - - - +
27G GLU* 4.1 16.2 - - - +
30G LYS* 3.5 35.1 + - - +
85H ASP* 4.6 8.0 - - - +
86H THR* 5.3 4.0 - - - +
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Residues in contact with ARG 30 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E ASP* 3.4 22.3 + - - -
22E VAL* 3.0 32.0 + - - +
24E SER* 3.8 15.8 + - - +
25E SER* 4.1 12.6 - - - +
27E PHE 3.8 1.4 + - - -
28E THR 2.7 4.8 + - - -
29E ASP* 1.3 74.0 - - - +
31E ARG* 1.3 67.0 + - - +
32E VAL 2.9 1.4 + - - -
33E ALA* 3.0 15.2 + - - +
34E ILE* 3.1 21.6 + - + +
126E VAL* 3.8 20.2 + - - +
127E LEU* 5.2 0.8 - - - +
10F LEU* 3.5 52.1 + - + +
13F LYS* 5.8 3.2 - - - +
14F SER* 4.3 14.0 - - - -
26G THR* 4.5 10.5 + - - -
27G GLU* 3.9 15.9 + - - +
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Residues in contact with ARG 31 (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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22E VAL 5.0 4.0 + - - +
23E TRP* 3.4 57.9 - - + +
25E SER* 3.3 24.0 + - - -
26E SER* 4.0 13.1 - - - +
27E PHE 4.2 3.2 + - - -
28E THR* 2.9 34.3 + - - +
30E ARG* 1.3 77.5 - - - +
32E VAL* 1.3 66.1 + - + +
34E ILE* 3.3 9.2 + - - +
35E VAL* 2.9 29.8 + - - +
71E VAL* 4.5 14.7 - - + +
74E ALA* 4.6 3.8 - - + -
75E ASN* 3.1 23.7 + - - -
78H ASP* 3.8 11.1 + - - -
82H SER* 3.4 24.7 + - - -
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Residues in contact with VAL 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28E THR* 3.5 23.6 - - - +
29E ASP* 3.4 10.3 - - - +
30E ARG 2.9 0.4 + - - -
31E ARG* 1.3 83.8 - - - +
33E ALA* 1.3 68.4 + - - +
34E ILE 3.0 0.7 + - - -
35E VAL* 3.1 3.9 + - - +
36E ARG* 2.8 39.3 + - - +
67E LYS* 4.8 12.8 - - + +
70E LEU* 4.4 22.5 - - + +
71E VAL* 3.8 28.3 - - + +
89H MET* 4.4 8.1 - - + -
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Residues in contact with ALA 33 (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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29E ASP 3.2 8.6 + - - +
30E ARG* 3.0 8.6 + - - +
32E VAL* 1.3 83.4 - - - +
34E ILE* 1.3 58.3 + - - +
36E ARG* 3.6 9.9 - - - +
37E ALA* 2.8 31.1 + - - +
6F VAL* 4.5 21.1 - - + +
7F LEU* 5.0 2.3 - - + +
10F LEU* 4.5 13.2 - - + -
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Residues in contact with ILE 34 (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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19E TRP* 6.5 0.4 - - + -
22E VAL* 4.1 27.8 - - + +
30E ARG* 3.1 32.3 + - + +
31E ARG* 3.6 8.7 - - - +
32E VAL 3.0 0.8 - - - -
33E ALA* 1.3 73.1 - - - +
35E VAL* 1.3 69.8 + - + +
37E ALA* 3.0 8.1 + - - +
38E VAL* 2.9 34.4 + - + +
119E PHE* 5.7 2.7 - - + -
122E VAL* 4.6 7.2 - - + -
123E LEU* 4.4 18.4 - - + -
126E VAL* 3.9 29.6 - - + -
7F LEU* 5.0 2.2 - - - -
10F LEU* 4.0 8.1 - - + -
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Residues in contact with VAL 35 (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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19E TRP* 6.3 2.5 - - + -
23E TRP* 5.2 1.6 - - + -
31E ARG* 2.9 22.7 + - + +
32E VAL 3.8 1.8 - - - +
34E ILE* 1.3 75.1 - - + +
36E ARG* 1.3 64.6 + - - +
38E VAL* 3.1 13.2 + - + +
39E PHE* 3.0 41.8 + - + -
70E LEU* 3.7 25.8 - - + +
73E VAL* 4.3 7.4 - - + -
74E ALA* 3.3 35.0 - - + -
77E LEU* 6.3 1.1 - - + -
119E PHE* 5.6 10.8 - - + -
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Residues in contact with ARG 36 (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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32E VAL* 2.8 26.1 + - - +
33E ALA* 3.6 8.0 - - - +
35E VAL* 1.3 73.2 - - - +
37E ALA* 1.3 54.8 + - - +
38E VAL 2.7 5.0 + - - -
39E PHE* 2.6 28.1 + - + +
40E ASP* 2.9 30.8 + - - +
61E PRO* 3.4 32.5 + - - +
62E GLU* 3.5 24.9 + - - -
66E PHE* 3.7 23.4 - - + -
67E LYS* 4.0 14.8 - - - +
70E LEU* 4.0 25.3 - - + +
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Residues in contact with ALA 37 (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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33E ALA 2.8 21.8 + - - +
34E ILE 3.4 4.7 - - - +
36E ARG* 1.3 73.4 - - - +
38E VAL* 1.3 61.6 + - - +
40E ASP* 3.8 13.2 + - - +
41E ASP* 3.5 13.9 + - - +
122E VAL* 3.8 16.1 - - + +
6F VAL* 6.4 1.1 - - + -
7F LEU* 4.0 27.1 - - + -
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Residues in contact with VAL 38 (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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34E ILE* 2.9 24.7 + - + +
35E VAL* 3.2 10.8 - - + +
36E ARG 2.7 4.9 + - - -
37E ALA* 1.3 71.8 - - - +
39E PHE* 1.3 68.1 + - + +
41E ASP* 3.0 15.2 + - - +
42E LEU 3.2 7.6 + - - -
115E ILE* 4.0 10.1 - - + -
118E ALA* 3.5 24.3 - - + +
119E PHE* 3.7 48.5 - - + -
122E VAL* 3.7 23.3 - - + -
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Residues in contact with PHE 39 (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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35E VAL* 3.0 34.6 + - + -
36E ARG* 2.6 13.4 + - + +
38E VAL* 1.3 76.9 - - + +
40E ASP* 1.3 54.7 + - - +
42E LEU* 2.6 44.6 + - + +
43E PHE* 2.8 40.6 + + + -
53E PHE* 4.1 18.2 - + - -
66E PHE* 5.8 3.4 - + + -
69E HIS* 4.8 2.0 - + - -
70E LEU* 3.5 21.5 - - + -
73E VAL* 4.0 15.3 - - + -
115E ILE* 3.8 26.7 - - + -
160E HEM 5.3 1.3 - + - -
161E CMO 3.4 23.8 - - - -
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Residues in contact with ASP 40 (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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36E ARG* 2.9 42.7 + - - +
37E ALA* 3.9 10.4 - - - +
39E PHE* 1.3 75.1 - - - +
41E ASP* 1.3 58.2 + - - +
43E PHE* 3.7 13.5 + - - +
44E LYS* 3.1 28.4 + - - +
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Residues in contact with ASP 41 (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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37E ALA 3.5 9.9 + - - +
38E VAL 3.0 11.1 + - - +
39E PHE 3.0 0.8 - - - -
40E ASP* 1.3 77.4 - - - +
42E LEU* 1.3 62.7 + - - +
44E LYS* 3.9 6.0 - - - +
45E HIS* 3.0 29.1 + - - +
114E GLY 5.0 1.0 - - - +
118E ALA* 3.5 20.6 - - + +
121E ARG* 2.7 46.6 + - - +
122E VAL* 4.6 5.2 - - + +
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Residues in contact with LEU 42 (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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38E VAL 3.2 5.8 + - - +
39E PHE* 2.6 47.7 + - + +
41E ASP* 1.3 74.4 + - - +
43E PHE* 1.3 55.3 + - + +
45E HIS 3.4 0.3 + - - -
46E TYR* 2.7 57.2 + - + +
49E SER* 3.9 10.8 - - - +
111E TYR* 3.9 20.4 - - - +
114E GLY 3.9 2.2 - - - -
115E ILE* 3.9 29.8 - - + +
118E ALA* 4.6 2.9 - - + +
160E HEM 4.1 21.8 - - + -
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Residues in contact with PHE 43 (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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39E PHE* 2.8 43.4 + + + +
40E ASP* 4.1 13.7 - - - +
42E LEU* 1.3 85.7 - - + +
44E LYS* 1.3 63.7 + - - +
45E HIS 3.0 2.0 - - - -
46E TYR 4.2 4.0 - - - -
47E PRO* 3.1 27.1 - - - +
49E SER* 3.4 22.4 - - - -
50E LYS* 3.8 46.9 - - + -
53E PHE* 3.9 28.0 - + - -
58E ILE* 5.1 11.0 - - + -
66E PHE* 5.3 7.9 - + - -
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Residues in contact with LYS 44 (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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40E ASP 3.1 19.0 + - - +
41E ASP* 4.2 2.7 - - - +
42E LEU 3.4 0.6 - - - -
43E PHE* 1.3 76.9 - - - +
45E HIS* 1.3 80.5 + - + +
47E PRO* 4.5 3.6 - - - +
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Residues in contact with HIS 45 (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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41E ASP* 3.0 30.4 + - - +
42E LEU 3.4 1.2 + - - -
43E PHE 3.0 0.2 - - - -
44E LYS* 1.3 100.7 - - + +
46E TYR* 1.3 82.6 + + + +
47E PRO* 3.3 11.4 - - - +
117E GLU* 5.1 4.7 - - - -
121E ARG* 3.3 34.7 + - - +
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Residues in contact with TYR 46 (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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42E LEU* 2.7 33.7 + - + +
43E PHE* 4.2 0.3 - - - -
45E HIS* 1.3 95.3 - + + +
47E PRO* 1.3 55.5 - - - +
48E THR* 2.9 13.6 + - - +
49E SER* 2.7 30.0 + - - -
110E GLU* 3.6 42.4 - - + -
111E TYR* 4.1 22.9 - + + -
113E ARG* 3.6 16.2 + - - -
114E GLY* 3.7 18.3 - - - -
117E GLU* 3.0 33.3 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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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