Contacts of the helix formed by residues 25 - 42 (chain E) in PDB entry 1GEC
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 CYS 25 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E GLN* 3.4 11.6 - - - +
24E SER* 1.3 70.6 - - - +
26E TRP* 1.3 61.9 + - - +
28E PHE* 3.7 5.5 - - - +
29E SER* 2.7 29.3 + - - -
159E HIS* 3.3 34.8 - - + +
160E ALA* 3.4 23.7 - - - +
180E SER* 4.6 0.4 - - - +
3I VAL* 4.1 2.9 - - - -
4I GLY* 2.8 12.6 - - - -
5I 0HQ 1.8 49.8 - - + +
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Residues in contact with TRP 26 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E GLU 3.3 19.2 + - - -
24E SER* 3.6 4.7 - - - +
25E CYS* 1.3 81.4 - - - +
27E ALA* 1.4 73.6 + - + +
29E SER* 3.4 6.1 + - - -
30E THR* 2.8 39.0 + - - +
53E LEU* 3.6 27.1 - - + -
54E VAL* 3.9 6.1 - - + -
57E ASP* 3.7 14.4 - - + -
60E SER* 3.5 26.0 - - - -
62E GLY* 3.2 32.9 + - - -
65E ARG 3.2 12.2 - - - -
66E GLY* 3.2 38.1 - - - +
67E TYR 3.8 9.2 - - - +
68E GLN* 4.7 1.3 - - - +
71E SER* 3.8 20.5 + - - -
160E ALA* 3.9 7.6 - - + -
3I VAL* 3.4 14.4 - - + +
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Residues in contact with ALA 27 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E SER 3.0 9.2 + - - +
26E TRP* 1.4 95.0 - - + +
28E PHE* 1.3 66.7 + - - +
30E THR* 3.2 7.4 + - - -
31E VAL* 3.2 27.4 + - - +
50E GLU* 3.8 27.6 - - + +
53E LEU* 4.1 6.5 - - + -
54E VAL* 4.0 16.2 - - + -
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Residues in contact with PHE 28 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17E LYS* 3.5 29.8 - - + -
18E HIS 3.5 23.6 - - - -
19E GLN* 3.7 8.1 - - + -
24E SER* 3.1 29.2 + - - +
25E CYS 3.3 5.6 + - - +
27E ALA* 1.3 79.6 - - - +
29E SER* 1.3 61.8 + - - +
31E VAL* 3.4 2.9 + - - +
32E ALA* 3.2 20.8 + - - +
50E GLU* 3.6 34.9 - - + +
83E ARG* 4.1 1.8 - - - -
88E TYR* 3.5 35.7 - + - -
160E ALA 5.8 0.2 - - - +
180E SER* 3.7 35.2 - - - +
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Residues in contact with SER 29 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E CYS 2.7 18.3 + - - -
26E TRP* 3.4 7.1 + - - -
28E PHE* 1.3 72.8 - - - +
30E THR* 1.3 58.4 + - - +
32E ALA 3.3 0.5 + - - -
33E THR* 3.0 34.3 + - - +
131E SER* 3.7 10.9 + - - -
160E ALA* 3.1 21.4 + - - +
161E VAL* 3.6 22.7 - - - -
162E THR* 3.3 21.3 + - - -
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Residues in contact with THR 30 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26E TRP 2.8 20.6 + - - +
27E ALA* 3.2 8.3 + - - -
29E SER* 1.3 74.5 - - - +
31E VAL* 1.3 64.9 + - - +
33E THR* 3.1 9.3 + - - -
34E VAL* 3.1 27.8 + - - +
53E LEU* 3.5 16.8 - - - +
68E GLN* 3.7 9.9 - - + +
71E SER* 3.2 25.4 + - - +
72E LEU* 3.5 33.2 - - + -
131E SER* 4.6 6.7 - - - +
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Residues in contact with VAL 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E ALA 3.2 18.6 + - - +
28E PHE 3.8 3.6 - - - +
29E SER 3.3 0.2 - - - -
30E THR* 1.3 77.5 - - - +
32E ALA* 1.3 58.6 + - - +
34E VAL* 3.0 8.0 + - - +
35E GLU* 2.8 52.4 + - - +
48E LEU* 3.7 21.8 - - + +
49E SER 3.8 17.9 - - - +
50E GLU* 3.8 18.6 - - - +
53E LEU* 3.8 19.1 - - + -
80E ILE* 3.9 8.3 - - + -
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Residues in contact with ALA 32 (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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12E ALA 5.0 1.9 - - - +
28E PHE 3.2 10.1 + - - +
29E SER 3.6 1.1 - - - +
31E VAL* 1.3 79.7 - - - +
33E THR* 1.3 61.5 + - - +
35E GLU* 3.6 13.2 + - - +
36E GLY* 3.2 18.4 + - - -
129E PRO* 4.4 4.5 - - - +
162E THR* 3.3 31.9 - - + +
178E LYS* 4.5 22.4 - - + +
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Residues in contact with THR 33 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29E SER 3.0 15.6 + - - +
30E THR* 3.1 16.8 + - - -
31E VAL 3.3 0.2 - - - -
32E ALA* 1.3 74.4 - - - +
34E VAL* 1.3 56.8 + - - +
36E GLY* 3.4 1.6 + - - -
37E ILE* 3.0 23.6 + - - +
72E LEU* 3.9 5.7 - - - +
128E GLN* 5.3 0.3 - - - +
129E PRO* 3.6 17.0 - - - +
130E VAL* 3.5 9.2 - - - -
131E SER* 3.4 34.1 - - - +
162E THR* 3.7 8.5 - - + -
211E TYR 4.6 0.2 - - - +
213E PRO* 3.3 32.5 - - - +
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Residues in contact with VAL 34 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30E THR 3.1 18.5 + - - +
31E VAL* 3.0 7.3 + - - +
33E THR* 1.3 73.3 - - - +
35E GLU* 1.3 64.9 + - - +
36E GLY 3.0 1.6 - - - -
37E ILE* 3.4 1.0 + - - +
38E ASN* 3.0 23.0 + - - +
48E LEU* 3.9 18.6 - - + -
72E LEU* 4.3 8.7 - - + -
75E VAL* 4.1 27.4 - - + -
80E ILE* 4.7 1.1 - - + -
105E VAL* 4.0 11.7 - - + -
107E THR* 3.8 21.5 - - + -
213E PRO* 4.0 23.6 - - + -
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Residues in contact with GLU 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E ALA 5.1 1.6 - - - +
14E THR* 2.7 30.6 + - + +
17E LYS* 5.1 1.9 + - - -
31E VAL* 2.8 34.2 + - + +
32E ALA* 3.9 14.1 - - - +
34E VAL* 1.3 72.8 - - - +
36E GLY* 1.3 59.9 + - - +
38E ASN* 4.0 5.4 + - - +
39E LYS* 3.2 17.3 + - - +
44E ASN 4.5 0.3 - - - +
45E LEU* 3.4 22.9 - - + +
46E VAL* 3.2 24.4 + - - +
47E GLU* 3.1 10.5 - - - +
48E LEU* 2.9 36.8 + - + +
50E GLU* 4.9 1.9 - - - +
83E ARG* 5.7 0.2 - - - -
178E LYS* 4.7 0.3 + - - -
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Residues in contact with GLY 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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12E ALA* 3.5 20.9 + - - +
32E ALA 3.2 10.7 + - - -
33E THR 3.6 4.3 - - - -
34E VAL 3.0 1.0 - - - -
35E GLU* 1.3 81.1 - - - +
37E ILE* 1.3 57.1 + - - +
39E LYS* 3.5 4.0 + - - +
40E ILE* 3.1 35.7 + - - +
129E PRO* 4.1 12.8 - - - -
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Residues in contact with ILE 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 THR 3.0 11.0 + - - +
34E VAL* 3.7 10.1 - - + +
36E GLY* 1.3 72.2 - - - +
38E ASN* 1.3 62.1 + - - +
40E ILE* 3.5 9.6 - - + +
41E LYS* 2.9 63.6 + - - +
105E VAL* 6.4 0.2 - - + -
107E THR* 4.3 13.5 - - + -
127E HIS 4.6 2.0 - - - +
128E GLN* 3.5 42.0 - - + +
129E PRO* 4.8 1.0 - - - +
213E PRO* 3.7 28.5 - - + +
215E LYS* 4.1 18.6 - - + +
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Residues in contact with ASN 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 VAL 3.0 18.1 + - - +
35E GLU* 4.0 7.3 + - - +
36E GLY 3.3 0.2 - - - -
37E ILE* 1.3 75.8 - - + +
39E LYS* 1.3 56.9 + - - +
42E THR* 2.7 47.2 + - - +
44E ASN* 3.0 34.4 + - - +
46E VAL* 4.4 10.9 - - - +
48E LEU* 5.7 0.7 - - + -
105E VAL* 3.6 35.9 - - + +
215E LYS* 3.2 26.3 + - - +
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Residues in contact with LYS 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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10E LYS 4.3 8.5 - - - +
11E GLY* 2.9 33.0 + - - +
12E ALA* 4.1 8.7 - - + -
35E GLU 3.2 15.3 + - - +
36E GLY 3.9 4.0 - - - +
37E ILE 3.4 0.2 - - - -
38E ASN* 1.3 78.0 - - - +
40E ILE* 1.3 60.3 + - + +
43E GLY* 2.5 50.7 + - - -
44E ASN 3.1 27.5 + - - +
45E LEU* 3.4 22.1 - - + +
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Residues in contact with ILE 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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7E TRP* 3.5 37.5 - - + -
12E ALA* 4.6 4.9 - - + -
36E GLY 3.1 18.6 + - - +
37E ILE* 3.5 10.1 - - + +
39E LYS* 1.3 80.6 - - + +
41E LYS* 1.3 83.0 + - + +
43E GLY 4.5 0.9 + - - -
127E HIS 3.6 20.0 - - - +
128E GLN* 3.8 16.6 - - + -
129E PRO* 4.1 2.5 - - + -
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Residues in contact with LYS 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 ILE* 2.9 44.6 + - - +
38E ASN 4.0 0.7 - - - +
40E ILE* 1.3 91.8 - - + +
42E THR* 1.3 62.5 + - - +
43E GLY 3.7 0.2 - - - -
215E LYS* 3.6 54.1 - - + +
216E ASN* 5.0 8.7 - - - +
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Residues in contact with THR 42 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38E ASN* 2.7 29.8 + - - +
41E LYS* 1.3 74.1 - - - +
43E GLY* 1.3 57.5 + - - -
44E ASN* 3.3 40.4 + - + +
215E LYS* 3.7 15.6 + - - -
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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
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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