Contacts of the helix formed by residues 10 - 19 (chain A) in PDB entry 2OJW
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 10 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A HIS 3.8 1.2 + - - -
9A LEU* 1.3 70.2 - - - +
11A LYS* 1.3 61.8 + - - +
12A GLY* 3.1 17.5 + - - -
13A ILE* 3.3 38.1 + - + +
14A LYS 3.8 0.2 + - - -
7B SER 5.2 5.6 + - - +
9B LEU 5.1 1.8 + - - -
11B LYS* 3.6 27.2 - - + +
232B PHE* 3.5 23.1 + - - +
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Residues in contact with LYS 11 (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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6A SER* 3.1 23.2 + - - -
7A SER* 4.1 10.5 - - - +
9A LEU 3.2 11.8 + - - +
10A ASN* 1.3 71.1 + - - +
12A GLY* 1.3 65.9 + - - +
14A LYS* 3.3 12.1 + - + +
15A GLN* 3.1 21.8 + - - +
230A GLU 5.1 1.4 + - - -
231A ASP* 3.5 29.2 + - + +
174B ASP* 2.6 37.3 + - - +
10E ASN* 3.7 26.9 + - + +
13E ILE* 3.9 27.1 - - + +
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Residues in contact with GLY 12 (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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10A ASN* 3.1 9.6 + - - -
11A LYS* 1.3 77.7 - - - +
13A ILE* 1.3 59.2 + - - +
15A GLN* 3.3 8.7 + - - +
16A VAL* 3.2 26.6 + - - +
11B LYS* 6.1 0.9 - - - -
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Residues in contact with ILE 13 (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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10A ASN* 3.3 35.3 + - + +
11A LYS 3.2 0.8 - - - -
12A GLY* 1.3 71.8 - - - +
14A LYS* 1.3 67.7 + - - +
16A VAL* 3.1 17.8 + - - +
17A TYR* 3.2 41.1 + - + -
11B LYS* 3.8 27.4 - - + -
231B ASP* 3.3 40.8 - - + +
232B PHE* 3.8 20.2 - - + +
1502B GOL 4.8 6.3 - - - +
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Residues in contact with LYS 14 (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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10A ASN 3.8 2.6 + - - -
11A LYS* 3.3 18.5 + - + +
13A ILE* 1.3 78.8 - - - +
15A GLN* 1.3 57.1 + - - +
17A TYR* 3.2 8.5 + - - +
18A MET* 3.0 54.0 + - + +
89A PHE 5.1 1.0 + - - -
227A ARG* 3.9 18.8 - - - +
231A ASP* 4.4 5.8 + - - +
1501A GOL 3.5 35.0 + - - +
174B ASP* 3.5 37.8 + - - +
177B GLU* 3.9 23.0 - - + +
178B ALA* 4.9 2.5 - - + -
232B PHE* 3.8 15.8 - - + -
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Residues in contact with GLN 15 (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 LYS 3.1 10.6 + - - +
12A GLY* 3.6 11.2 - - - +
13A ILE 3.2 0.4 - - - -
14A LYS* 1.3 79.2 - - - +
16A VAL* 1.3 60.4 + - + +
18A MET* 3.4 13.9 + - - +
19A SER* 2.9 43.9 + - - +
91A LYS* 4.4 12.5 + - - +
1501A GOL 5.2 4.2 + - - -
16E VAL* 3.6 44.5 - - + +
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Residues in contact with VAL 16 (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 GLY 3.2 15.0 + - - +
13A ILE* 3.1 9.9 + - - +
15A GLN* 1.3 77.5 - - - +
17A TYR* 1.3 62.4 + - - +
19A SER* 3.3 17.5 + - - -
20A LEU* 3.8 8.5 + - - +
15B GLN* 3.5 47.3 - - + +
1502B GOL 3.7 33.5 + - - +
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Residues in contact with TYR 17 (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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13A ILE* 3.2 41.7 + - + -
14A LYS 3.6 6.1 - - - +
16A VAL* 1.3 77.9 - - - +
18A MET* 1.3 57.0 + - - +
20A LEU* 3.1 29.3 + - + +
88B PRO 4.6 1.3 - - - -
89B PHE* 3.3 34.1 - + - -
178B ALA* 3.6 45.5 - - + +
181B ARG* 3.3 17.9 - - - +
182B ALA* 4.3 9.9 - - + -
228B VAL* 3.7 19.5 - - + -
231B ASP* 2.7 23.6 + - - -
232B PHE* 4.6 4.9 - + - -
1502B GOL 3.6 25.7 - - - -
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Residues in contact with MET 18 (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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14A LYS* 3.0 39.2 + - + +
15A GLN* 3.4 18.6 + - - +
16A VAL 3.3 0.2 - - - -
17A TYR* 1.3 73.9 - - - +
19A SER* 1.3 58.3 + - - +
20A LEU 3.3 0.9 - - - -
89A PHE 3.9 22.0 - - - +
90A ARG* 4.1 15.5 - - + -
91A LYS* 5.6 6.8 + - - +
1501A GOL 5.7 2.7 - - - +
177B GLU* 4.0 37.5 - - - +
178B ALA* 4.7 1.3 - - - -
181B ARG* 2.9 50.7 + - - +
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Residues in contact with SER 19 (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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15A GLN* 2.9 34.1 + - - +
16A VAL* 3.7 9.4 - - - -
17A TYR 3.1 1.0 - - - -
18A MET* 1.3 78.2 - - - +
20A LEU* 1.3 61.8 + - - +
21A PRO* 3.5 8.1 - - - +
91B LYS* 5.1 3.0 + - - -
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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