Contacts of the helix formed by residues 10 - 19 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8B HIS 3.8 1.2 + - - -
9B LEU* 1.3 70.8 - - - +
11B LYS* 1.3 62.7 + - - +
12B GLY* 3.1 17.2 + - - -
13B ILE* 3.3 36.3 + - + +
14B LYS 3.6 0.7 + - - -
7C SER 5.2 6.0 + - - +
9C LEU 5.2 1.8 + - - -
11C LYS* 3.4 26.6 - - - +
232C PHE* 3.2 26.8 + - + -
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Residues in contact with LYS 11 (chain B).
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* 3.6 31.0 - - - +
12A GLY 6.1 0.4 - - - -
13A ILE* 3.8 22.4 - - + +
6B SER* 3.2 25.5 + - - -
7B SER* 4.0 9.4 - - - +
9B LEU 3.2 9.8 + - - +
10B ASN* 1.3 70.9 + - - +
12B GLY* 1.3 63.9 + - - +
13B ILE 3.3 0.2 - - - -
14B LYS* 3.5 11.1 + - + +
15B GLN* 3.2 20.4 + - - +
230B GLU 5.0 1.8 + - - -
231B ASP* 3.4 34.4 + - + +
174C ASP* 2.8 36.3 + - - +
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Residues in contact with GLY 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ASN* 3.1 10.2 + - - -
11B LYS* 1.3 76.4 - - - +
13B ILE* 1.3 62.4 + - - +
15B GLN* 3.2 7.3 + - - +
16B VAL* 3.1 28.8 + - - +
11C LYS* 6.1 1.1 - - - -
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Residues in contact with ILE 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ASN* 3.3 35.9 + - + +
12B GLY* 1.3 71.1 - - - +
14B LYS* 1.3 70.0 + - - +
15B GLN 3.2 0.3 + - - -
16B VAL* 3.2 16.7 + - - +
17B TYR* 3.3 41.9 + - + -
7C SER 5.9 0.4 - - - +
11C LYS* 3.7 29.4 - - + -
231C ASP* 3.2 43.3 - - + +
232C PHE* 3.8 18.6 - - + +
1503C GOL 4.8 6.1 - - - +
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Residues in contact with LYS 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ASN 3.6 3.6 + - - +
11B LYS* 3.5 12.9 + - + +
12B GLY 3.4 0.8 - - - -
13B ILE* 1.3 77.8 - - - +
15B GLN* 1.3 58.5 + - - +
17B TYR* 3.2 9.1 + - - +
18B MET* 2.9 49.8 + - + +
89B PHE 4.9 1.2 + - - -
227B ARG* 4.1 17.6 - - - +
231B ASP* 4.6 6.3 + - - -
1502B GOL 3.2 33.9 + - - +
174C ASP* 3.3 40.6 + - + +
177C GLU* 4.1 21.3 + - + +
178C ALA* 4.9 2.5 - - + -
232C PHE* 3.7 15.9 - - + -
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Residues in contact with GLN 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A VAL* 3.5 43.4 - - + +
11B LYS 3.2 10.2 + - - +
12B GLY* 3.2 10.9 + - - +
13B ILE 3.2 1.4 - - - -
14B LYS* 1.3 75.7 - - - +
16B VAL* 1.3 58.6 + - + +
18B MET* 3.3 14.3 + - - +
19B SER* 2.5 47.8 + - - +
1502B GOL 5.0 5.9 + - - -
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Residues in contact with VAL 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B GLY 3.1 16.0 + - - +
13B ILE* 3.6 8.7 - - - +
15B GLN* 1.3 75.2 - - + +
17B TYR* 1.3 62.6 + - - +
19B SER* 3.1 21.0 + - - -
20B LEU* 3.7 8.0 + - - +
15C GLN* 3.4 47.1 - - + +
1503C GOL 3.8 33.7 - - - +
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Residues in contact with TYR 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ILE* 3.3 42.9 + - + -
14B LYS 3.2 7.6 + - - +
16B VAL* 1.3 76.2 - - - +
18B MET* 1.4 61.7 + - - +
19B SER 3.1 1.1 + - - -
20B LEU* 3.4 19.2 + - + +
88C PRO 4.6 1.1 - - - -
89C PHE* 3.2 33.9 - + - -
178C ALA* 3.6 45.3 - - + +
181C ARG* 3.2 21.6 - - - +
182C ALA* 4.1 10.3 - - + -
228C VAL* 3.8 22.0 - - + -
231C ASP* 2.5 24.4 + - - -
1503C GOL 3.7 26.6 - - - -
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Residues in contact with MET 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B LYS* 2.9 45.8 + - + +
15B GLN* 3.3 18.4 + - - +
16B VAL 3.3 0.6 - - - -
17B TYR* 1.4 75.1 - - - +
19B SER* 1.3 56.4 + - - +
20B LEU 3.4 0.7 - - - -
27B GLN* 6.0 0.2 - - - +
89B PHE 3.8 22.4 - - - +
90B ARG* 4.2 7.6 - - + -
1502B GOL 5.9 1.8 - - - +
177C GLU* 4.0 39.5 - - - +
178C ALA* 4.6 2.0 - - - -
181C ARG* 2.9 49.8 + - - +
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Residues in contact with SER 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B GLN* 2.5 32.9 + - - +
16B VAL* 3.4 12.6 - - - -
17B TYR 3.1 0.6 - - - -
18B MET* 1.3 77.6 - - - +
20B LEU* 1.3 62.0 + - - +
21B PRO* 3.5 7.3 - - - +
91C LYS* 6.0 0.2 + - - -
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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