Contacts of the helix formed by residues 61 - 70 (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 61 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A GLU* 4.8 10.3 + - - +
59A LYS* 3.2 7.6 - - + +
60A MET* 1.3 81.9 - - - +
62A LYS* 1.3 85.2 + - - +
63A LYS* 3.1 29.5 - - + +
64A MET* 3.8 6.4 - - - +
65A GLU* 2.7 32.9 + - - +
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Residues in contact with LYS 62 (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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61A ASN* 1.3 98.3 + - - +
63A LYS* 1.3 85.8 + - + +
65A GLU* 3.1 10.6 - - - +
66A GLU* 3.1 28.4 + - + +
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Residues in contact with LYS 63 (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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17A LEU* 5.4 0.5 - - - +
19A LEU* 3.3 39.0 - - + +
44A ALA* 4.6 0.9 - - - +
56A GLU* 4.6 1.1 - - - +
61A ASN* 3.1 24.7 - - + +
62A LYS* 1.3 97.4 - - + +
64A MET* 1.3 63.3 + - - +
66A GLU* 3.0 24.8 + - - +
67A VAL* 3.6 7.6 + - - +
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Residues in contact with MET 64 (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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19A LEU* 3.2 11.5 - - + +
50A CYS* 4.7 0.4 - - - -
52A SER* 3.4 24.7 - - - +
56A GLU* 3.2 29.1 + - - +
57A VAL* 3.4 36.1 - - + +
60A MET* 3.2 36.1 - - + +
61A ASN* 3.3 10.6 + - - +
63A LYS* 1.3 79.2 - - - +
65A GLU* 1.3 61.5 + - - +
67A VAL* 3.1 10.8 + - - +
68A LYS* 3.0 19.9 + - - +
74A VAL* 4.0 23.8 - - - -
102A TRP* 4.1 2.6 - - - -
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Residues in contact with GLU 65 (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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60A MET* 3.8 20.2 - - - +
61A ASN 2.7 22.7 + - - +
62A LYS* 3.1 12.3 - - - +
63A LYS 3.0 0.2 - - - -
64A MET* 1.3 74.4 - - - +
66A GLU* 1.3 55.6 + - + +
68A LYS* 2.8 15.0 + - - +
69A GLU* 2.6 58.1 + - + +
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Residues in contact with GLU 66 (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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43A THR* 5.2 7.1 - - - +
44A ALA* 3.3 22.5 + - + +
45A ASN* 3.6 23.1 + - - +
62A LYS 3.1 17.4 + - - +
63A LYS* 3.0 7.8 + - - +
65A GLU* 1.3 75.5 - - + +
67A VAL* 1.3 57.2 + - - +
69A GLU* 3.3 18.7 + - - +
70A ALA* 2.9 30.5 + - - +
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Residues in contact with VAL 67 (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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17A LEU* 3.6 18.6 - - + -
19A LEU* 4.5 1.6 - - + -
44A ALA* 3.5 21.1 - - + -
50A CYS* 3.6 14.8 - - + -
63A LYS 3.7 11.0 - - - +
64A MET* 3.4 14.8 - - - +
65A GLU 3.1 0.2 - - - -
66A GLU* 1.3 74.0 - - - +
68A LYS* 1.3 59.5 + - - +
70A ALA 3.4 1.0 + - - -
71A ASN 2.9 8.0 + - - -
72A ILE* 2.8 71.9 + - + +
74A VAL* 3.6 16.6 - - + -
102A TRP* 3.7 0.9 - - - +
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Residues in contact with LYS 68 (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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60A MET* 3.6 31.2 - - + -
64A MET 3.0 12.2 + - - +
65A GLU* 2.8 16.9 + - - +
67A VAL* 1.3 76.7 - - - +
69A GLU* 1.3 62.7 + - - +
71A ASN* 3.2 17.7 + - - +
102A TRP* 3.5 40.8 - - + +
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Residues in contact with GLU 69 (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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45A ASN* 5.1 8.1 - - - +
65A GLU* 2.6 52.1 + - - +
66A GLU* 3.5 20.2 - - - +
68A LYS* 1.3 72.7 - - - +
70A ALA* 1.3 57.1 + - - +
71A ASN* 3.0 9.6 + - - +
106A VAL* 5.2 4.5 - - - +
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Residues in contact with ALA 70 (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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45A ASN* 3.8 24.5 - - - +
66A GLU 2.9 13.6 + - - +
69A GLU* 1.3 75.9 - - - +
71A ASN* 1.3 72.3 + - - +
72A ILE* 3.2 31.5 - - + +
106A VAL* 5.1 3.8 - - - +
107A LYS 5.3 4.7 - - - +
108A SER* 5.0 7.8 + - - -
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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