Contacts of the helix formed by residues 66 - 76 (chain A) in PDB entry 2OQS
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 66 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A GLY 3.0 7.6 - - - +
19A GLY* 3.7 9.4 - - - -
20A VAL* 5.4 7.6 - - + +
22A ASN* 5.0 2.9 - - - +
65A VAL* 1.3 80.2 - - - +
67A HIS* 1.3 64.7 + - - +
68A GLU* 3.4 30.2 + - - +
69A GLU* 3.6 9.6 + - - +
70A ALA* 3.3 16.3 + - - +
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Residues in contact with HIS 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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16A ILE* 3.0 30.5 - - + -
17A ALA* 3.4 5.4 - - - -
18A GLY 2.7 26.9 + - - +
22A ASN* 3.4 12.6 + - - +
66A THR* 1.3 73.7 - - - +
68A GLU* 1.3 70.5 + - - +
70A ALA* 2.8 15.6 + - - +
71A VAL* 2.9 28.9 + - + +
302B ARG* 3.2 59.8 + - - +
304B THR* 3.3 24.1 + - - -
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Residues in contact with GLU 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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22A ASN* 4.1 4.0 + - - -
66A THR* 3.4 26.9 + - - +
67A HIS* 1.3 80.6 + - - +
69A GLU* 1.3 50.3 + - - +
71A VAL* 3.3 4.2 + - - +
72A THR* 2.7 44.7 + - - +
302B ARG* 3.5 19.4 + - - +
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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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60A VAL* 4.4 20.5 - - - +
61A CYS 4.5 2.1 - - - +
62A LEU* 4.5 1.5 - - - +
65A VAL* 3.3 46.2 - - + +
66A THR* 3.6 9.4 + - - +
67A HIS 3.2 0.2 - - - -
68A GLU* 1.3 75.9 - - - +
70A ALA* 1.3 60.2 + - - +
72A THR* 4.0 18.7 - - + +
73A ALA* 2.9 42.7 + - - +
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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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16A ILE* 4.0 9.2 - - + -
17A ALA 4.3 3.1 - - - +
18A GLY* 4.5 0.2 - - - -
31A ILE* 3.3 48.9 - - + -
62A LEU* 4.2 2.9 - - - -
65A VAL* 4.3 0.6 - - - +
66A THR 3.3 6.2 + - - +
67A HIS* 2.8 17.1 + - + +
69A GLU* 1.3 78.7 - - - +
71A VAL* 1.3 57.0 + - - +
74A LEU* 2.9 35.2 + - - +
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Residues in contact with VAL 71 (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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16A ILE* 3.4 11.7 - - + -
67A HIS* 2.9 38.7 + - + +
68A GLU* 3.9 6.7 - - - +
70A ALA* 1.3 74.4 - - - +
72A THR* 1.3 61.4 + - - +
73A ALA 3.3 0.2 - - - -
74A LEU* 3.7 0.7 - - - +
75A LYS* 2.8 45.5 + - + +
304B THR* 3.4 21.1 - - + -
305B GLN 4.9 0.7 - - - +
306B VAL* 3.4 18.3 - - + +
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Residues in contact with THR 72 (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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68A GLU* 2.7 30.6 + - - +
69A GLU* 3.8 17.9 - - + +
71A VAL* 1.3 74.0 - - - +
73A ALA* 1.3 59.1 + - - +
75A LYS* 3.1 19.1 - - + +
76A ASN* 2.9 31.5 + - + +
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Residues in contact with ALA 73 (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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57A VAL* 3.1 33.2 - - + +
58A ASN* 3.4 19.0 - - - +
60A VAL* 4.1 9.4 - - + -
62A LEU* 3.3 10.5 - - + -
69A GLU* 2.9 22.1 + - - +
70A ALA 4.3 0.9 - - - +
72A THR* 1.3 75.1 - - - +
74A LEU* 1.3 65.8 + - - +
75A LYS 3.2 0.2 - - - -
76A ASN* 3.3 14.7 + - - +
77A THR* 4.6 1.0 - - - +
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Residues in contact with LEU 74 (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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12A LEU* 3.3 47.2 - - + +
14A PHE* 3.4 22.9 - - + -
16A ILE* 4.1 12.6 - - + -
31A ILE* 4.7 1.3 - - + -
54A LEU* 3.5 17.9 - - + -
57A VAL* 4.4 6.7 - - + -
62A LEU* 3.3 26.9 - - + -
70A ALA 2.9 26.6 + - - +
71A VAL 3.3 4.2 + - - +
73A ALA* 1.3 78.8 - - + +
75A LYS* 1.3 59.8 + - - +
77A THR* 3.5 13.3 - - - +
81A VAL* 5.4 0.2 - - - +
83A LEU* 4.6 7.4 - - + -
306B VAL* 3.9 10.1 - - + -
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Residues in contact with LYS 75 (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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7A LYS* 5.5 1.3 + - - +
12A LEU* 4.7 7.2 - - + -
71A VAL* 2.8 32.6 + - + +
72A THR* 3.1 30.3 - - + +
74A LEU* 1.3 75.6 - - - +
76A ASN* 1.3 55.0 + - - +
77A THR* 2.8 19.6 + - - +
306B VAL* 5.7 4.9 - - + +
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Residues in contact with ASN 76 (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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58A ASN* 3.3 31.3 + - - +
72A THR* 2.9 21.4 + - + +
73A ALA* 3.3 12.8 + - - +
75A LYS* 1.3 73.6 - - + +
77A THR* 1.3 60.7 + - - +
78A SER* 4.2 1.2 + - - -
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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