Contacts of the helix formed by residues 25 - 36 (chain A) in PDB entry 2COK
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 ASN 25 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A LYS* 5.4 9.1 - - - +
22A LEU* 6.5 0.2 - - - -
24A ARG* 1.3 77.3 - - - +
26A LYS* 1.3 66.3 + - - +
27A ASP* 3.1 29.8 - - - +
28A GLU* 3.2 19.5 + - + +
29A VAL* 2.8 36.5 + - - +
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Residues in contact with LYS 26 (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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18A THR* 3.9 20.2 - - - +
22A LEU* 6.5 0.9 - - - -
25A ASN* 1.3 82.2 + - - +
27A ASP* 1.3 52.6 + - - +
29A VAL* 3.5 5.8 - - - +
30A LYS* 2.5 41.0 + - + +
40A LEU* 3.7 27.6 - - + +
41A THR 5.5 1.8 - - - -
42A GLY* 6.3 1.8 - - - -
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Residues in contact with ASP 27 (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 ASN* 3.1 17.0 - - - +
26A LYS* 1.3 75.2 - - - +
28A GLU* 1.3 61.9 + - + +
29A VAL 2.8 1.9 + - - -
30A LYS* 2.8 14.4 + - - +
31A ALA* 2.6 42.1 + - - +
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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
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24A ARG* 3.5 46.2 + - - +
25A ASN* 3.2 26.7 + - + +
27A ASP* 1.3 81.4 + - + +
29A VAL* 1.3 60.6 + - - +
31A ALA* 3.7 7.6 - - - +
32A MET* 3.3 23.0 + - - +
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Residues in contact with VAL 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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18A THR* 3.9 16.8 - - + -
22A LEU* 4.6 9.9 - - + -
24A ARG* 3.5 24.9 - - + +
25A ASN 2.8 23.1 + - - +
26A LYS* 3.6 5.4 - - - +
27A ASP 2.8 0.4 + - - -
28A GLU* 1.3 74.5 - - - +
30A LYS* 1.3 68.0 + - - +
31A ALA 2.9 1.6 - - - -
32A MET* 2.7 18.3 + - - +
33A ILE* 2.8 38.0 + - + +
40A LEU* 4.0 0.2 - - + -
51A ILE* 4.8 0.4 - - + -
77A GLU* 4.2 16.6 - - + +
80A LEU* 3.5 16.4 - - + -
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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 LYS* 2.5 26.4 + - + +
27A ASP* 2.8 13.6 + - - +
29A VAL* 1.3 72.7 - - - +
31A ALA* 1.3 61.4 + - - +
33A ILE* 3.9 2.1 + - - +
34A GLU* 3.1 38.2 + - - +
40A LEU* 3.8 46.2 - - + +
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Residues in contact with ALA 31 (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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27A ASP* 2.6 26.9 + - - +
28A GLU* 3.7 9.0 - - - +
30A LYS* 1.3 72.4 - - - +
32A MET* 1.3 52.5 + - - +
34A GLU* 2.9 9.4 + - - +
35A LYS* 2.5 37.5 + - - +
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Residues in contact with MET 32 (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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24A ARG* 4.9 17.5 - - - +
28A GLU 3.3 13.0 + - - +
29A VAL* 2.7 16.3 + - - +
31A ALA* 1.3 69.1 - - - +
33A ILE* 1.3 53.3 + - - +
34A GLU 2.7 5.1 + - - -
35A LYS* 2.5 41.5 + - + +
36A LEU* 2.6 45.1 + - + +
77A GLU* 5.6 2.5 - - - +
80A LEU* 3.0 50.5 - - + +
81A GLN* 4.2 6.1 - - - +
84A SER* 3.8 10.5 - - - +
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Residues in contact with ILE 33 (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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11A LEU* 4.2 1.9 - - - +
16A ILE* 3.3 47.8 - - + -
18A THR* 4.0 1.6 - - + -
29A VAL* 2.8 27.8 + - + +
30A LYS 4.2 3.1 - - - +
32A MET* 1.3 74.3 - - - +
34A GLU* 1.3 49.3 + - - +
36A LEU* 3.9 3.3 + - - -
37A GLY 3.6 0.9 + - - -
38A GLY* 2.5 41.2 + - - -
39A LYS 3.2 27.8 - - - +
40A LEU* 3.1 35.9 - - + +
80A LEU* 3.6 26.2 - - + +
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Residues in contact with GLU 34 (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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9A LYS* 5.8 0.2 - - - +
30A LYS* 3.1 31.7 + - + +
31A ALA* 2.9 12.9 + - - +
32A MET 2.7 1.2 + - - -
33A ILE* 1.3 76.7 - - - +
35A LYS* 1.3 58.1 + - - +
36A LEU 3.2 2.0 - - - -
37A GLY* 3.1 17.7 + - - -
38A GLY 3.3 11.5 - - - +
39A LYS* 3.7 29.6 - - + +
40A LEU 4.6 2.1 + - - +
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Residues in contact with LYS 35 (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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8A ASP 4.6 4.7 - - - +
9A LYS* 4.5 9.2 - - - +
31A ALA 2.5 12.9 + - - +
32A MET* 2.5 33.3 + - - +
34A GLU* 1.3 68.4 - - - +
36A LEU* 1.3 80.7 + - + +
37A GLY* 3.0 6.1 + - - -
84A SER* 4.0 12.3 - - - +
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Residues in contact with LEU 36 (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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8A ASP* 4.4 7.9 - - + +
9A LYS* 2.8 31.8 - - - +
10A PRO* 3.1 28.3 - - + +
11A LEU* 3.3 22.4 - - + -
12A SER 3.3 2.3 + - - -
32A MET* 2.6 65.7 + - + +
33A ILE 4.2 1.3 - - - +
35A LYS* 1.3 79.8 - - + +
37A GLY* 1.3 56.2 + - - +
38A GLY 3.4 2.5 - - - -
80A LEU* 4.5 3.4 - - + -
83A VAL* 3.4 23.6 - - + +
84A SER* 3.3 23.8 - - - +
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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