Contacts of the strand formed by residues 4 - 14 (chain A) in PDB entry 1OJ7
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 PHE 4 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A LEU* 4.5 9.0 - - + -
2A ASN 3.5 13.5 - - - -
3A ASN* 1.3 75.2 - - - +
5A ASN* 1.3 63.3 + - - +
6A LEU* 3.9 17.9 - - + -
213A HIS* 4.8 1.6 - - - -
258A ALA* 3.7 40.2 - - + -
259A GLY* 3.8 12.6 - - - +
12D ILE* 4.2 3.8 - - + -
13D LEU* 3.7 2.3 - - - -
14D PHE* 2.9 73.1 + + + +
246D TRP* 3.9 36.1 - + - -
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Residues in contact with ASN 5 (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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4A PHE* 1.3 75.5 - - - +
6A LEU* 1.3 57.9 + - - +
7A HIS 4.1 1.4 + - - -
11D ARG* 3.1 43.8 + - - +
12D ILE 3.3 4.0 - - - -
13D LEU* 3.2 22.4 - - + +
25D GLN* 4.8 5.1 - - - +
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Residues in contact with LEU 6 (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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4A PHE* 3.9 18.5 - - + -
5A ASN* 1.3 73.9 - - - +
7A HIS* 1.3 60.6 + - - +
8A THR* 4.0 24.2 + - + +
253A ASN 4.7 0.2 - - - +
254A GLY* 3.6 34.1 - - - +
255A LEU* 4.2 15.0 - - + -
258A ALA* 4.4 4.9 - - + -
10D THR 4.0 2.8 - - - +
11D ARG* 3.5 2.1 - - - -
12D ILE* 2.8 47.1 + - + +
246D TRP* 3.8 31.6 - - + -
250D GLN* 5.4 0.2 - - - +
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Residues in contact with HIS 7 (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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5A ASN 4.1 2.0 + - - -
6A LEU* 1.3 75.6 - - - +
8A THR* 1.3 67.5 + - - +
9A PRO* 3.3 38.0 - - + +
166A ALA* 6.4 0.6 - - - +
169A GLN* 4.5 7.1 - - - +
253A ASN 5.2 0.7 - - - +
9D PRO* 3.2 30.3 + - - +
10D THR 4.5 0.9 - - - -
11D ARG* 3.3 52.2 + - + +
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Residues in contact with THR 8 (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 LEU* 4.0 25.1 - - + +
7A HIS* 1.3 79.3 - - - +
9A PRO* 1.3 63.0 - - - +
10A THR 3.4 7.2 + - - +
146A SER 5.9 0.4 - - - -
169A GLN* 4.7 4.9 - - - +
253A ASN* 3.4 39.3 - - - +
255A LEU* 5.0 2.7 - - + +
8D THR* 3.0 38.8 + - - +
10D THR 5.2 1.9 + - - -
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Residues in contact with PRO 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A HIS* 3.3 41.7 - - + +
8A THR* 1.3 88.0 - - - +
10A THR* 1.3 64.2 + - - +
11A ARG 3.2 2.9 + - - -
169A GLN* 3.8 28.9 - - + +
170A PRO 4.8 1.3 - - - +
171A VAL* 4.0 5.1 - - - +
7D HIS* 3.3 20.7 + - - +
8D THR 4.5 3.8 - - - +
9D PRO* 4.6 7.2 - - + -
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Residues in contact with THR 10 (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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8A THR 3.4 7.4 - - - +
9A PRO* 1.3 76.3 - - - +
11A ARG* 1.3 67.4 + - - +
12A ILE* 3.5 10.8 + - + +
145A GLU 3.4 20.6 + - - +
146A SER* 3.6 21.9 - - - -
169A GLN* 3.2 20.9 + - - +
170A PRO* 2.8 24.3 + - - +
171A VAL 3.6 4.9 - - - -
172A PHE 3.8 19.5 - - - -
173A ALA* 3.9 3.8 - - + +
6D LEU 3.9 3.5 - - - +
7D HIS* 4.5 3.2 - - - -
8D THR* 5.2 1.2 + - - -
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Residues in contact with ARG 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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9A PRO 3.2 2.8 + - - -
10A THR* 1.3 71.4 - - - +
12A ILE* 1.3 61.1 + - - +
13A LEU* 3.9 7.1 + - + -
25A GLN* 3.5 31.5 + - - +
171A VAL* 3.0 16.0 + - + +
172A PHE* 3.1 7.3 - - + +
173A ALA 2.8 27.5 + - - -
5D ASN* 2.9 47.8 + - - +
6D LEU 3.5 6.7 - - - +
7D HIS* 3.4 46.2 + - + +
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Residues in contact with ILE 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 THR* 3.9 11.9 - - + +
11A ARG* 1.3 78.1 - - - +
13A LEU* 1.3 65.7 + - - +
14A PHE* 4.2 7.2 - - + +
145A GLU* 5.2 0.4 - - + -
146A SER* 4.3 24.5 - - - +
173A ALA* 3.6 16.2 - - + +
175A LEU* 4.1 20.0 - - + -
246A TRP* 3.8 30.7 - - + -
249A THR* 4.6 5.2 - - + -
4D PHE* 3.6 12.7 - - + +
5D ASN* 3.3 6.4 - - - +
6D LEU* 2.8 49.3 + - + +
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Residues in contact with LEU 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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11A ARG* 4.1 13.7 - - + +
12A ILE* 1.3 73.7 - - - +
14A PHE* 1.3 55.4 + - - +
18A ALA* 3.5 20.0 - - + +
21A GLY* 3.6 38.4 - - - +
22A LEU 4.2 2.0 - - - +
25A GLN* 3.9 17.0 - - + +
172A PHE* 5.2 2.9 - - + -
173A ALA 2.8 15.4 + - - +
174A VAL* 3.4 17.8 - - + -
175A LEU 2.7 30.6 + - - -
4D PHE 3.6 3.6 - - - +
5D ASN* 3.5 39.3 - - + +
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Residues in contact with PHE 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ILE* 3.8 2.2 - - + -
13A LEU* 1.3 73.2 - - - +
15A GLY* 1.3 77.0 + - - +
18A ALA* 3.7 4.8 - - - +
175A LEU* 3.3 26.7 - - + -
177A PRO* 3.7 26.9 - - + -
238A TYR* 4.2 4.3 - - - -
242A ALA* 3.9 21.5 - - + -
245A MET* 4.3 10.8 - - + -
246A TRP* 3.9 27.8 - + + -
1D LEU* 3.9 22.7 - - + -
2D ASN 5.0 3.6 - - - -
3D ASN* 3.2 9.0 - - - +
4D PHE* 2.9 72.3 + + + +
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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