Contacts of the helix formed by residues 10 - 19 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A SER 5.6 4.3 - - - +
9A LEU 5.3 0.3 - - - +
11A LYS* 3.7 22.7 + - + +
232A PHE* 3.4 25.0 + - - +
8E HIS 3.8 1.2 + - - -
9E LEU* 1.3 69.2 - - - +
11E LYS* 1.3 63.0 + - - +
12E GLY* 3.1 20.8 - - - +
13E ILE* 3.1 42.3 + - + +
14E LYS 3.6 0.3 + - - -
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Residues in contact with LYS 11 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A ASP* 2.7 37.5 + - - +
10D ASN* 3.6 30.0 - - + +
12D GLY 6.1 0.2 - - - -
13D ILE* 3.7 26.0 - - + +
6E SER* 3.5 19.0 + - - -
7E SER* 3.9 11.6 - - - +
9E LEU 3.1 14.1 + - - +
10E ASN* 1.3 70.4 - - - +
12E GLY* 1.3 60.4 + - - +
14E LYS* 3.4 11.3 + - + +
15E GLN* 3.1 26.0 + - - +
230E GLU 5.2 1.0 + - - -
231E ASP* 3.5 29.5 + - + +
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Residues in contact with GLY 12 (chain E).
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* 6.1 0.4 - - - -
10E ASN* 3.1 10.9 - - - +
11E LYS* 1.3 76.0 - - - +
13E ILE* 1.3 64.6 + - - +
15E GLN* 3.2 7.9 + - - +
16E VAL* 3.2 27.9 + - - +
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Residues in contact with ILE 13 (chain E).
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* 3.9 26.4 - - + +
231A ASP* 3.2 40.8 - - + +
232A PHE* 3.7 21.3 - - + +
1501A GOL 4.7 7.6 - - - +
10E ASN* 3.1 36.6 + - + +
12E GLY* 1.3 71.1 - - - +
14E LYS* 1.3 67.0 + - - +
16E VAL* 3.3 16.4 + - - +
17E TYR* 3.3 37.3 + - + -
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Residues in contact with LYS 14 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A ARG* 6.0 0.2 - - - +
174A ASP* 3.6 39.8 + - + +
177A GLU* 4.0 22.7 - - + +
178A ALA* 4.9 2.2 - - + -
232A PHE* 3.8 16.3 - - + -
10E ASN 3.6 3.4 + - - +
11E LYS* 3.4 14.5 + - + +
12E GLY 3.3 0.4 - - - -
13E ILE* 1.3 79.7 - - - +
15E GLN* 1.3 58.5 + - - +
17E TYR* 3.3 8.1 + - - +
18E MET* 3.1 55.0 + - + +
89E PHE 4.8 2.2 + - - -
227E ARG* 4.1 18.0 - - - +
231E ASP* 4.4 5.8 + - - +
1505E GOL 3.4 35.1 + - - +
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Residues in contact with GLN 15 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D VAL* 3.5 44.1 - - + +
11E LYS 3.1 14.6 + - - +
12E GLY* 3.2 11.3 + - - +
14E LYS* 1.3 74.2 - - - +
16E VAL* 1.3 59.2 + - + +
18E MET* 3.4 15.6 + - - +
19E SER* 2.7 49.0 + - - +
1505E GOL 5.0 7.3 + - - -
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Residues in contact with VAL 16 (chain E).
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* 3.6 48.7 - - + +
91A LYS* 4.5 9.9 + - - +
1501A GOL 3.7 36.1 - - - +
12E GLY 3.2 16.6 + - - +
13E ILE* 3.3 9.2 + - - +
15E GLN* 1.3 74.3 - - + +
17E TYR* 1.3 65.0 + - - +
19E SER* 3.3 18.1 + - - -
20E LEU* 3.7 9.4 + - - +
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Residues in contact with TYR 17 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A PRO 4.5 1.8 - - - -
89A PHE* 3.3 28.0 - + - -
178A ALA* 3.6 48.2 - - + +
181A ARG* 3.0 22.8 - - - +
182A ALA* 4.2 9.6 - - + -
228A VAL* 3.8 23.9 - - + +
231A ASP* 2.5 25.3 + - - -
232A PHE* 4.6 4.0 - + - -
1501A GOL 3.7 26.2 - - - -
13E ILE* 3.3 41.1 + - + -
14E LYS 3.3 6.6 + - - +
16E VAL* 1.3 77.7 - - - +
18E MET* 1.3 59.5 + - + +
19E SER 3.4 1.0 + - - -
20E LEU* 3.4 19.8 + - + +
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Residues in contact with MET 18 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A GLU* 4.1 28.9 - - - +
178A ALA 4.7 1.3 - - - -
181A ARG* 2.8 58.5 + - - +
14E LYS* 3.1 46.8 + - + +
15E GLN* 3.9 20.4 - - - +
16E VAL 3.2 0.6 - - - -
17E TYR* 1.3 77.3 - - - +
19E SER* 1.3 58.0 + - - +
20E LEU 3.3 0.4 - - - -
27E GLN* 5.7 0.4 - - - +
89E PHE 3.8 21.8 - - - +
90E ARG* 4.1 14.1 - - + -
1505E GOL 5.8 2.5 - - - +
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Residues in contact with SER 19 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A LYS* 5.7 5.2 - - - -
15E GLN* 2.7 35.8 + - - +
16E VAL* 3.6 9.8 - - - -
17E TYR 3.2 0.4 - - - -
18E MET* 1.3 76.2 - - - +
20E LEU* 1.3 63.3 + - - +
21E PRO* 3.3 8.3 - - - +
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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