Contacts of the strand formed by residues 2 - 12 (chain B) in PDB entry 2OFJ
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 ARG 2 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1B MET* 1.3 89.4 - - - +
3B SER* 1.3 63.8 + - - +
35B ARG 3.3 4.9 - - - -
36B GLU* 3.6 31.1 + - + -
70B TRP* 2.7 83.5 + - + +
71B LEU* 4.0 24.4 - - + +
73B GLY* 3.7 20.5 + - - -
74B ASP 5.0 0.4 + - - -
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Residues in contact with SER 3 (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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1B MET 5.1 0.9 + - - -
2B ARG* 1.3 74.9 - - - +
4B ALA* 1.3 65.0 + - - +
5B GLN* 4.3 3.0 + - - -
35B ARG* 2.9 54.7 + - - +
70B TRP* 3.5 4.3 - - - -
71B LEU* 3.9 9.0 - - - -
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Residues in contact with ALA 4 (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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3B SER* 1.3 80.7 - - - +
5B GLN* 1.3 70.7 + - - +
32B VAL* 5.1 0.2 - - + -
33B CYS 3.1 13.7 - - - +
34B LEU* 4.0 11.4 - - + -
67B VAL* 3.3 34.5 - - + -
70B TRP* 4.7 0.9 - - + -
71B LEU* 4.3 9.4 - - + +
318B ARG* 4.4 2.1 + - - -
320B LEU* 2.9 22.0 - - + +
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Residues in contact with GLN 5 (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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3B SER* 4.3 2.3 + - - -
4B ALA* 1.3 88.1 + - - +
6B VAL* 1.3 66.3 + - - +
7B TYR* 3.9 23.8 + - + +
31B TYR 4.1 0.2 - - - +
32B VAL* 3.4 4.2 - - - +
33B CYS* 2.8 62.7 + - + +
35B ARG* 2.9 36.8 + - - +
42B TRP* 5.0 1.2 - - - -
318B ARG* 3.5 27.6 - - - +
320B LEU* 3.2 11.4 - - - +
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Residues in contact with VAL 6 (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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5B GLN* 1.3 79.9 - - - +
7B TYR* 1.3 68.5 + - - +
30B LEU* 4.6 1.8 - - + -
31B TYR 3.4 11.9 - - - +
32B VAL* 4.4 2.5 - - + -
60B GLN* 5.8 0.4 - - + -
63B LEU* 3.6 26.0 - - + -
64B LEU* 4.1 23.6 - - + -
67B VAL* 4.3 19.3 - - + -
318B ARG* 3.5 4.5 - - - +
319B LEU* 2.7 49.6 + - + -
320B LEU* 3.2 25.2 + - + +
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Residues in contact with TYR 7 (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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5B GLN* 3.9 31.5 + - + +
6B VAL* 1.3 78.2 - - - +
8B ARG* 1.3 62.2 + - - +
9B TRP* 4.4 1.6 - - + -
30B LEU* 3.2 12.8 - - - +
31B TYR* 3.0 40.7 + - + +
33B CYS* 4.6 1.3 - - + -
42B TRP* 3.7 33.9 - + - -
313B VAL* 3.6 28.6 - - + +
316B LEU* 3.6 35.2 - - + -
317B GLU 3.2 11.7 - - - +
318B ARG* 3.5 36.4 + - + -
319B LEU* 4.6 0.2 - - - -
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Residues in contact with ARG 8 (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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6B VAL 4.3 0.2 + - - -
7B TYR* 1.3 74.9 - - - +
9B TRP* 1.3 67.2 + - - +
29B GLY 3.8 3.1 - - - -
30B LEU* 3.8 6.5 - - + -
56B TRP* 3.4 30.1 - - + -
60B GLN* 3.5 29.3 + - - +
316B LEU* 4.9 0.3 - - - +
317B GLU* 2.8 73.4 + - - +
319B LEU* 3.1 40.0 - - + +
296D GLN* 2.8 44.4 + - - +
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Residues in contact with TRP 9 (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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7B TYR* 4.2 5.4 - - + -
8B ARG* 1.3 82.0 - - - +
10B GLN* 1.3 73.7 + - - +
11B ILE* 3.5 23.1 - - + -
27B ARG* 3.3 28.0 - - + -
28B ASP* 3.4 2.5 - - - -
29B GLY* 3.0 40.8 + - - +
30B LEU* 3.4 25.3 - - - -
31B TYR* 3.4 39.3 - + - -
44B GLU* 3.4 26.0 - - - -
46B SER* 3.4 16.8 - - - -
56B TRP* 3.6 3.5 - - - -
267B SER* 3.9 9.6 - - - -
299B GLN* 3.4 23.3 - - - +
316B LEU* 4.4 8.5 - - + -
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Residues in contact with GLN 10 (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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9B TRP* 1.3 80.8 - - - +
11B ILE* 1.3 63.8 + - - +
12B PRO* 4.0 6.0 - - - +
26B THR* 3.9 18.6 + - + +
27B ARG 3.2 6.1 - - - -
28B ASP* 2.8 29.4 - - - +
56B TRP* 3.8 20.9 - - + -
299B GLN* 5.0 1.7 - - - +
12D PRO* 4.2 24.9 - - - +
296D GLN* 5.7 0.8 + - - -
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Residues in contact with ILE 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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9B TRP* 3.5 24.9 - - + -
10B GLN* 1.3 72.4 - - - +
12B PRO* 1.3 81.8 - - + +
13B MET* 4.2 0.3 - - - +
26B THR* 3.3 3.4 - - - -
27B ARG* 2.7 43.8 + - + +
267B SER* 3.5 23.8 - - - -
295B MET* 4.1 17.7 - - + -
297B ALA* 3.7 32.1 - - + +
299B GLN* 3.6 34.3 - - + +
311B VAL* 6.2 0.4 - - + -
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Residues in contact with PRO 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 GLN 4.0 6.3 - - - +
11B ILE* 1.3 92.3 - - + +
13B MET* 1.3 61.3 + - - +
25B LYS 3.6 9.6 - - - +
26B THR* 4.5 6.0 - - + -
295B MET* 3.7 1.4 - - - -
296B GLN* 2.8 55.6 + - + +
297B ALA* 5.6 4.0 - - + -
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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