Contacts of the helix formed by residues 13 - 32 (chain A) in PDB entry 2OCT
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 THR 13 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A PRO 4.1 8.1 - - - +
12A ALA* 1.3 78.4 - - - +
14A ALA* 1.3 66.1 + - - +
15A GLU* 3.2 17.9 + - - +
16A THR* 3.0 24.8 + - - +
17A GLN* 3.0 13.0 + - - +
43A PHE* 4.9 8.1 - - + -
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Residues in contact with ALA 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A THR* 1.3 74.2 - - - +
15A GLU* 1.3 56.1 + - - +
17A GLN* 3.2 7.2 + - - +
18A HIS* 2.8 54.4 + - + +
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Residues in contact with GLU 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A THR* 3.1 11.0 + - - +
14A ALA* 1.3 77.5 - - - +
16A THR* 1.3 64.8 + - - +
18A HIS* 3.1 31.7 + - - +
19A ILE* 3.0 38.9 + - + +
71B GLN* 4.9 9.0 + - - +
78B LYS* 6.1 0.7 - - - +
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Residues in contact with THR 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ALA* 3.9 7.9 - - + -
13A THR* 3.0 30.4 + - - -
15A GLU* 1.3 80.3 - - - +
17A GLN* 1.3 62.2 + - - +
19A ILE* 3.2 12.0 + - + +
20A ALA* 3.0 21.5 + - - +
40A ALA* 3.9 8.0 - - + +
42A SER 4.7 0.2 - - - +
43A PHE* 3.4 34.8 - - + -
53B TYR* 6.1 1.1 - - + -
55B ILE* 3.7 32.7 - - + +
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Residues in contact with GLN 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ALA* 6.1 0.4 - - + -
13A THR 3.0 11.4 + - - +
14A ALA* 3.2 11.4 + - - +
16A THR* 1.3 74.7 - - - +
18A HIS* 1.3 63.9 + - + +
20A ALA* 3.2 4.9 + - - +
21A ASP* 2.8 58.4 + - - +
38A PHE 2.9 23.4 + - - -
39A LYS* 3.6 9.3 - - - +
40A ALA* 2.8 32.5 + - + +
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Residues in contact with HIS 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ALA* 2.8 44.0 + - + +
15A GLU* 3.1 31.6 - - + +
17A GLN* 1.3 76.1 - - + +
19A ILE* 1.3 63.1 + - - +
21A ASP* 3.3 15.3 + - - +
22A GLN* 3.0 27.0 + - - +
80B LEU* 5.3 0.2 - - - -
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Residues in contact with ILE 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A GLU* 3.0 30.5 + - + +
16A THR* 3.5 10.8 - - + +
17A GLN 3.2 0.2 - - - -
18A HIS* 1.3 75.6 - - - +
20A ALA* 1.3 65.4 + - - +
22A GLN* 3.0 12.0 + - - +
23A VAL* 3.1 14.3 + - + +
53B TYR* 3.7 39.3 - - + -
55B ILE* 3.5 22.7 - - + -
67B LEU* 5.8 0.2 - - + -
69B VAL* 3.9 27.8 - - + -
71B GLN* 4.3 8.1 - - - +
80B LEU* 3.9 22.7 - - + -
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Residues in contact with ALA 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A THR 3.0 13.3 + - - +
17A GLN* 3.6 17.9 - - - +
19A ILE* 1.3 79.9 - - - +
21A ASP* 1.3 63.2 + - - +
23A VAL* 3.2 6.4 + - - +
24A ARG* 3.1 19.6 + - - +
38A PHE* 3.3 33.6 - - + +
40A ALA* 4.4 5.6 - - + -
55B ILE* 5.0 1.9 - - + +
57B VAL* 4.3 16.2 - - + -
67B LEU* 4.6 3.4 - - + -
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Residues in contact with ASP 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A GLN* 2.8 55.2 + - - +
18A HIS* 3.7 14.2 + - - +
19A ILE 3.3 0.2 - - - -
20A ALA* 1.3 74.4 - - - +
22A GLN* 1.3 63.3 + - - +
23A VAL 3.3 0.5 + - - -
24A ARG* 3.6 22.3 + - - +
25A SER 4.8 1.0 + - - -
38A PHE* 4.6 2.4 - - - +
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Residues in contact with GLN 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A HIS* 3.0 17.2 + - - +
19A ILE 3.0 6.0 + - - +
21A ASP* 1.3 78.4 - - - +
23A VAL* 1.3 64.3 + - + +
25A SER* 5.0 2.3 + - - -
26A GLN* 5.6 0.5 + - - +
78B LYS* 3.1 38.1 + - - +
79B SER* 4.0 4.0 - - - +
80B LEU* 3.5 29.7 + - + +
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Residues in contact with VAL 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ILE 3.1 16.3 + - - +
20A ALA 3.7 4.7 - - - +
22A GLN* 1.3 83.0 - - + +
24A ARG* 1.3 67.6 + - - +
25A SER 3.3 2.7 - - - -
26A GLN* 3.2 22.9 + - - +
27A LEU* 3.3 11.6 + - + +
38A PHE* 4.8 1.1 - - + -
67B LEU* 3.8 28.3 - - + -
69B VAL* 4.4 21.1 - - + -
80B LEU* 4.5 22.2 - - + +
82B LEU* 4.4 27.3 - - + +
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Residues in contact with ARG 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ALA 3.1 16.3 + - - +
21A ASP* 3.7 16.4 + - - +
22A GLN 3.5 1.0 - - - -
23A VAL* 1.3 76.8 - - - +
25A SER* 1.3 59.9 + - - +
27A LEU* 3.1 5.2 + - - +
28A GLU* 2.6 56.1 + - + +
34A LYS* 5.4 6.2 - - - +
35A PHE* 2.6 32.3 + - - +
36A PRO 4.2 7.9 + - - -
37A VAL* 4.3 1.4 - - - +
38A PHE* 3.5 50.3 + - + +
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Residues in contact with SER 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ASP 4.8 1.8 + - - -
22A GLN 5.0 2.1 + - - -
23A VAL 3.3 0.6 - - - -
24A ARG* 1.3 76.6 - - - +
26A GLN* 1.3 66.7 + - - +
28A GLU* 3.4 16.5 + - - +
29A GLU* 3.1 21.1 + - - +
34A LYS* 5.9 1.0 + - - -
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Residues in contact with GLN 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A GLN 5.6 0.8 + - - +
23A VAL* 3.2 16.2 + - - +
25A SER* 1.3 80.6 - - - +
27A LEU* 1.3 61.2 + - - +
29A GLU* 3.2 8.7 + - - +
30A LYS* 2.6 41.9 + - - +
82B LEU* 3.8 41.9 - - + +
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Residues in contact with LEU 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A VAL* 3.3 7.9 + - + +
24A ARG* 3.1 11.0 + - - +
26A GLN* 1.3 79.5 - - - +
28A GLU* 1.3 55.2 + - - +
29A GLU 3.0 0.2 - - - -
30A LYS* 2.8 35.1 + - + +
31A TYR* 3.4 17.5 + - + -
35A PHE* 4.3 7.2 - - + -
38A PHE* 4.0 14.4 - - + -
65B VAL* 4.0 18.2 - - + -
67B LEU* 3.8 27.1 - - + -
82B LEU* 4.5 9.1 - - + +
85B TYR* 3.4 52.3 - - + -
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Residues in contact with GLU 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ARG* 2.6 52.2 + - + +
25A SER* 3.7 18.1 + - - +
27A LEU* 1.3 71.7 - - - +
29A GLU* 1.3 65.4 + - - +
31A TYR 3.6 2.2 + - - +
32A ASN* 3.2 17.2 + - - -
33A LYS 3.5 22.3 + - - +
34A LYS* 3.7 24.1 + - + +
35A PHE* 2.9 45.0 + - + +
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Residues in contact with GLU 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A SER 3.1 11.5 + - - +
26A GLN* 3.4 12.6 - - - +
27A LEU 3.0 0.8 - - - -
28A GLU* 1.3 76.3 - - - +
30A LYS* 1.3 87.6 + - + +
32A ASN* 3.1 13.7 + - - +
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Residues in contact with LYS 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A GLN* 2.6 40.4 + - - +
27A LEU* 2.8 20.2 + - + +
29A GLU* 1.3 109.1 + - + +
31A TYR* 1.3 62.4 + - + +
32A ASN* 3.3 2.1 + - - +
82B LEU* 6.1 1.8 - - - -
85B TYR* 2.9 44.0 - - + +
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Residues in contact with TYR 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LEU* 3.4 29.9 + - + -
28A GLU 3.6 2.6 + - - +
29A GLU 3.3 0.2 - - - -
30A LYS* 1.3 80.9 - - + +
32A ASN* 1.3 71.7 + - - +
33A LYS* 3.0 38.7 + - + +
35A PHE* 3.6 37.7 - + + -
59B VAL* 6.0 0.9 - - + -
65B VAL* 3.0 26.4 - - + +
85B TYR* 4.4 2.8 - + - -
87B THR* 3.4 34.2 - - + +
88B ASN 4.3 2.5 + - - -
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Residues in contact with ASN 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A GLU 3.2 4.5 + - - -
29A GLU* 3.1 17.9 + - - +
30A LYS 3.2 2.0 - - - +
31A TYR* 1.3 80.0 - - - +
33A LYS* 1.3 57.6 + - - +
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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