Contacts of the helix formed by residues 15 - 34 (chain E) in PDB entry 4OIR
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 SER 15 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1216D SER* 3.5 13.0 - - - -
1217D ILE* 3.1 29.4 + - - -
1480D PHE* 4.7 5.2 - - - -
1481D VAL* 3.7 20.4 - - - +
13E VAL* 3.2 17.5 - - - +
14E ASP* 1.3 85.8 + - - +
16E LYS* 1.3 65.2 + - - +
17E TYR* 3.4 11.8 + - - -
18E ARG* 3.1 13.8 + - - +
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Residues in contact with LYS 16 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1043C TYR 5.8 0.6 + - - -
710D ARG* 5.4 6.5 - - - +
761D ILE* 5.7 0.2 - - + -
762D GLN* 4.8 24.8 + - + +
768D ASN* 5.3 4.8 + - - -
1208D ASP* 4.8 2.6 + - - -
1210D SER* 5.3 2.0 + - - -
1211D MET* 3.5 35.6 - - + +
1216D SER* 3.2 28.2 + - - +
1219D GLU* 4.6 8.9 + - - +
10E PHE* 3.6 36.5 - - + -
13E VAL* 4.4 3.1 - - - -
15E SER* 1.3 71.8 + - - +
17E TYR* 1.3 91.8 + - + +
19E LEU* 3.0 9.4 + - - +
20E THR* 3.0 22.5 + - - -
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Residues in contact with TYR 17 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1042C ALA 4.6 0.5 + - - -
1043C TYR 3.5 15.4 + - - -
1044C GLY* 4.0 1.8 - - - -
762D GLN* 3.2 37.5 - - - -
1216D SER* 4.3 3.1 - - - -
1217D ILE 3.7 9.0 - - - -
1218D GLY 3.7 1.6 - - - -
1219D GLU* 2.4 57.1 + - + -
1475D GLY* 3.5 42.0 - - - +
1476D THR* 3.9 2.0 - - - +
1481D VAL* 3.8 8.5 - - + -
15E SER* 3.2 13.8 - - - +
16E LYS* 1.3 97.5 + - + +
18E ARG* 1.3 58.5 + - - +
20E THR* 3.1 8.4 + - - -
21E VAL* 2.9 32.1 + - - +
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Residues in contact with ARG 18 (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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1480D PHE* 2.9 28.5 + - - -
1481D VAL* 3.6 26.6 - - + +
1484D THR* 2.8 25.7 + - - +
13E VAL* 3.9 10.1 - - + -
14E ASP* 2.5 44.5 + - - +
15E SER 3.1 12.1 + - - +
17E TYR* 1.3 74.8 - - - +
19E LEU* 1.3 66.8 + - - +
21E VAL* 3.3 4.8 + - - +
22E VAL* 2.9 30.2 + - + +
75E PHE* 4.1 19.7 - - + -
76E GLY* 5.6 2.0 - - - -
77E GLU* 2.7 32.5 + - - +
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Residues in contact with LEU 19 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
761D ILE* 3.7 19.1 - - + -
6E ILE* 4.4 2.9 - - + -
9E LEU* 3.8 33.0 - - + +
10E PHE* 3.5 35.0 - - + -
12E MET* 6.3 0.2 - - - -
13E VAL* 3.6 23.7 - - + +
15E SER 3.5 2.6 + - - -
16E LYS 3.0 7.9 + - - +
18E ARG* 1.3 78.5 - - - +
20E THR* 1.3 64.7 + - - +
22E VAL* 3.3 4.9 + - - +
23E VAL* 2.9 38.4 + - + +
68E LEU* 3.6 27.6 - - + -
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Residues in contact with THR 20 (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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754D PHE* 4.7 2.5 - - + +
757D ALA* 3.9 9.3 - - + +
758D GLU* 3.7 28.5 - - + +
761D ILE* 3.7 15.2 - - - +
762D GLN* 2.9 39.0 + - - +
1476D THR* 3.7 12.3 - - + -
16E LYS 3.0 13.8 + - - -
17E TYR* 3.1 9.2 + - - -
19E LEU* 1.3 77.7 - - - +
21E VAL* 1.3 62.4 + - - +
23E VAL* 3.3 1.9 + - - +
24E ALA* 2.9 22.9 + - - +
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Residues in contact with VAL 21 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
754D PHE* 4.1 21.5 - - + -
1476D THR* 4.1 25.6 - - + +
1481D VAL* 3.7 27.1 - - + +
1482D ARG* 4.1 7.9 - - - +
1484D THR* 4.2 7.9 - - - +
17E TYR 2.9 19.6 + - - +
18E ARG 3.7 6.5 - - - +
20E THR* 1.3 74.1 - - - +
22E VAL* 1.3 63.1 + - - +
24E ALA* 3.3 1.0 + - - +
25E LYS* 2.9 53.6 + - + +
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Residues in contact with VAL 22 (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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1484D THR* 3.8 14.8 - - + -
1486D VAL* 3.5 34.6 - - + +
13E VAL* 5.4 0.9 - - + -
18E ARG* 2.9 23.4 + - + +
19E LEU* 3.5 7.0 - - - +
20E THR 3.3 0.2 - - - -
21E VAL* 1.3 77.5 - - - +
23E VAL* 1.3 58.4 + - - +
25E LYS* 3.9 0.2 - - - +
26E ARG* 2.9 30.9 + - + +
68E LEU* 3.6 36.1 - - + -
75E PHE* 3.6 26.5 - - + -
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Residues in contact with VAL 23 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
757D ALA* 4.8 2.0 - - + -
761D ILE* 4.1 11.0 - - + -
19E LEU* 2.9 37.6 + - + +
20E THR 3.8 3.1 - - - +
22E VAL* 1.3 76.2 - - - +
24E ALA* 1.3 58.4 + - - +
26E ARG* 4.5 0.4 - - - -
27E ALA* 2.9 28.4 + - - +
61E VAL* 3.7 20.9 - - + -
64E ALA* 3.5 16.7 - - + +
65E MET* 3.6 34.5 - - + +
68E LEU* 3.9 11.7 - - + -
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Residues in contact with ALA 24 (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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753D SER* 4.1 3.7 - - - +
754D PHE* 3.7 47.6 - - + +
757D ALA* 4.0 11.4 - - + +
20E THR 2.9 17.6 + - - +
21E VAL 3.8 2.9 - - - +
23E VAL* 1.3 77.2 - - - +
25E LYS* 1.3 57.3 + - - +
27E ALA* 3.2 8.0 + - - +
28E GLN* 2.9 34.2 + - - +
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Residues in contact with LYS 25 (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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754D PHE* 4.5 15.7 - - + -
1482D ARG 3.5 15.6 + - - -
1483D PHE* 4.0 4.9 + - - +
1484D THR 2.6 32.1 + - - +
1485D GLN* 4.7 10.9 - - + +
1486D VAL* 4.9 9.2 - - + +
21E VAL* 2.9 33.8 + - + +
22E VAL* 3.9 3.6 - - - +
24E ALA* 1.3 75.3 - - - +
26E ARG* 1.3 63.9 + - - +
28E GLN* 3.1 14.7 + - - +
29E GLN* 2.9 30.6 + - - +
32E ARG* 5.0 0.2 + - - -
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Residues in contact with ARG 26 (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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1486D VAL* 4.3 12.3 - - + +
1487D VAL 5.4 0.2 - - - -
1488D ASP* 4.0 16.2 + - - +
22E VAL* 2.9 19.9 + - + +
23E VAL* 3.7 4.5 - - - +
25E LYS* 1.3 75.7 - - - +
27E ALA* 1.3 57.2 + - - +
29E GLN* 2.8 40.9 + - - +
30E LEU* 2.9 38.1 + - + +
37E ASN* 3.0 41.6 + - - +
38E THR* 3.7 0.6 - - - +
39E VAL* 3.8 8.7 - - - +
64E ALA* 3.7 16.6 - - + +
67E GLU* 2.4 43.9 + - - +
73E LEU* 3.9 28.5 - - + +
89E MET* 4.6 0.2 - - - +
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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
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753D SER* 4.5 6.7 - - - -
23E VAL 2.9 18.1 + - - +
24E ALA* 3.4 6.1 - - - +
26E ARG* 1.3 75.9 - - - +
28E GLN* 1.3 57.1 + - - +
30E LEU* 3.2 5.4 + - - +
31E LEU* 2.9 32.8 + - - +
60E ALA* 3.7 34.7 - - + +
61E VAL* 3.9 14.6 - - + +
64E ALA* 3.9 4.9 - - + +
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Residues in contact with GLN 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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1075C ASP* 3.7 28.5 + - + +
752D SER* 5.2 2.0 - - - -
753D SER* 3.9 19.7 - - - +
754D PHE* 4.2 27.1 - - - +
24E ALA 2.9 16.7 + - - +
25E LYS* 3.5 12.7 - - - +
27E ALA* 1.3 72.7 - - - +
29E GLN* 1.3 61.0 + - - +
31E LEU* 3.3 7.0 + - - +
32E ARG* 2.9 50.2 + - - +
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Residues in contact with GLN 29 (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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1486D VAL* 2.9 30.2 + - - +
1487D VAL* 4.9 1.6 - - - +
25E LYS* 2.9 21.6 + - + +
26E ARG* 2.8 40.5 + - - +
28E GLN* 1.3 75.7 - - - +
30E LEU* 1.3 57.6 + - - +
32E ARG* 3.3 19.2 + - - +
33E HIS* 2.9 38.9 + - + -
37E ASN* 3.5 11.3 + - - +
85E LEU* 4.4 12.3 - - - +
89E MET* 4.1 22.0 - - - +
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Residues in contact with LEU 30 (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 ARG* 2.9 39.9 + - - +
27E ALA* 3.6 8.1 - - - +
29E GLN* 1.3 76.4 - - - +
31E LEU* 1.3 63.1 + - - +
34E GLY* 3.0 3.8 + - - -
35E PHE* 2.8 55.1 + - + -
37E ASN* 3.3 20.6 - - - +
38E THR* 3.9 8.1 - - - +
60E ALA* 4.4 4.0 - - + +
63E TRP* 3.6 31.4 - - + -
64E ALA* 4.3 6.7 - - - +
67E GLU* 3.6 21.3 - - - +
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Residues in contact with LEU 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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1073C GLY 6.1 0.9 - - - +
1075C ASP* 4.1 21.1 - - + +
753D SER* 3.7 23.3 - - - +
27E ALA 2.9 17.7 + - - +
28E GLN* 3.7 7.0 - - - +
29E GLN 3.3 0.2 - - - -
30E LEU* 1.3 77.7 - - - +
32E ARG* 1.3 62.6 + - - +
34E GLY* 3.4 8.7 + - - -
35E PHE* 4.5 13.7 - - + -
58E PRO 5.0 5.4 - - - +
60E ALA* 3.8 19.3 - - + +
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Residues in contact with ARG 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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28E GLN* 2.9 28.3 + - - +
29E GLN* 3.7 33.1 - - - +
31E LEU* 1.3 78.0 - - - +
33E HIS* 1.3 83.4 + - + +
34E GLY 3.4 0.6 + - - -
90E GLU* 6.5 0.4 - - - -
95E VAL* 4.9 10.4 - - - -
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Residues in contact with HIS 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 GLN* 2.9 19.0 + - - +
32E ARG* 1.3 101.0 + - + +
34E GLY* 1.3 63.1 + - - +
35E PHE 3.3 1.5 + - - -
36E LYS* 3.5 24.1 + - - +
37E ASN* 3.3 37.5 - - - +
86E GLN* 5.1 0.6 - - - -
89E MET* 3.2 50.7 - - + +
90E GLU* 4.1 13.9 - - + -
93E TYR* 3.5 25.4 + - + +
94E PRO 4.6 8.0 + - - +
95E VAL* 5.7 1.4 + - - -
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Residues in contact with GLY 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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30E LEU 3.0 6.1 + - - -
31E LEU 3.4 6.3 + - - -
32E ARG 3.4 4.2 + - - -
33E HIS* 1.3 74.3 - - - +
35E PHE* 1.3 69.1 + - - +
36E LYS* 3.0 20.6 + - - +
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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