Contacts of the strand formed by residues 4 - 14 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B LEU* 4.4 9.9 - - + -
2B ASN 3.5 13.0 - - - -
3B ASN* 1.3 75.8 - - - +
5B ASN* 1.3 63.1 + - - +
6B LEU* 3.9 17.3 - - + -
213B HIS* 4.8 1.3 - + - -
258B ALA* 3.6 40.8 - - + -
259B GLY* 3.7 13.2 - - - +
12C ILE* 4.5 3.4 - - + -
13C LEU* 3.6 2.4 - - - +
14C PHE* 2.8 71.7 + + + +
246C TRP* 3.7 37.9 - + - -
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Residues in contact with ASN 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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4B PHE* 1.3 76.8 - - - +
6B LEU* 1.3 60.8 + - - +
7B HIS 4.2 0.7 - - - -
11C ARG* 2.9 48.3 + - - +
12C ILE 3.3 3.8 - - - +
13C LEU* 4.2 9.6 - - + +
25C GLN* 3.6 20.0 - - - +
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Residues in contact with LEU 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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4B PHE* 3.9 17.0 - - + -
5B ASN* 1.3 75.4 + - - +
7B HIS* 1.3 64.2 + - - +
8B THR* 4.2 18.4 - - + -
253B ASN 4.6 0.7 - - - +
254B GLY* 3.6 35.7 - - - +
255B LEU* 4.0 24.2 - - + +
258B ALA* 4.5 5.4 - - + -
10C THR 4.3 1.2 - - - +
11C ARG* 3.6 1.2 - - - -
12C ILE* 2.9 46.1 + - + +
246C TRP* 4.0 25.6 - - + -
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Residues in contact with HIS 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ASN 4.2 1.6 - - - +
6B LEU* 1.3 77.0 - - - +
8B THR* 1.3 68.0 + - - +
9B PRO* 3.4 31.6 - - + +
166B ALA* 6.0 3.8 - - - +
169B GLN* 3.3 21.8 + - - +
253B ASN 5.0 1.2 - - - +
9C PRO* 3.0 32.1 + - - +
10C THR 4.5 0.7 - - - -
11C ARG* 3.2 53.0 + - + +
171C VAL 5.6 0.2 + - - -
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Residues in contact with THR 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B LEU* 4.2 22.4 - - + -
7B HIS* 1.3 79.0 - - - +
9B PRO* 1.3 63.8 - - - +
10B THR 3.4 7.2 + - - +
146B SER 5.9 2.0 - - - -
169B GLN* 4.8 3.4 - - - +
253B ASN* 3.7 37.7 - - - +
255B LEU* 5.3 2.2 - - + +
8C THR* 3.1 38.1 + - - +
10C THR 5.5 0.8 + - - -
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Residues in contact with PRO 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B HIS* 3.4 39.9 - - + +
8B THR* 1.3 87.1 - - - +
10B THR* 1.3 65.7 + - - +
11B ARG 3.2 3.1 + - - -
169B GLN* 3.7 28.9 - - + +
170B PRO 4.7 2.5 - - - +
171B VAL* 4.0 4.4 - - - +
7C HIS* 3.3 19.4 + - - +
9C PRO* 4.4 13.7 - - + -
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Residues in contact with THR 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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8B THR 3.4 6.7 - - - +
9B PRO* 1.3 75.5 - - - +
11B ARG* 1.3 66.4 + - - +
12B ILE* 3.5 10.4 + - + +
145B GLU 3.4 21.8 - - - +
146B SER* 3.7 22.9 - - - -
169B GLN* 3.5 18.5 + - - +
170B PRO 2.6 29.4 + - - +
171B VAL 3.7 0.9 - - - -
172B PHE 3.7 19.7 - - - -
173B ALA* 3.9 3.4 - - + +
6C LEU 3.9 4.5 - - - +
7C HIS* 4.5 2.0 - - - -
8C THR 5.4 0.2 + - - -
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Residues in contact with ARG 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 PRO 3.2 3.0 + - - -
10B THR* 1.3 70.8 - - - +
12B ILE* 1.3 61.9 + - - +
13B LEU* 3.8 18.2 + - + +
25B GLN* 3.5 26.6 + - - +
171B VAL 3.0 15.9 + - - +
172B PHE* 3.1 6.6 - - + +
173B ALA 2.9 27.0 + - - +
5C ASN* 2.9 50.7 + - - +
6C LEU 3.4 8.3 - - - +
7C HIS* 3.3 45.3 + - + +
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Residues in contact with ILE 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 THR* 3.9 9.0 - - + +
11B ARG* 1.3 77.2 - - - +
13B LEU* 1.3 62.7 + - - +
14B PHE* 4.1 8.3 - - + +
145B GLU* 5.3 0.4 - - + -
146B SER* 4.1 28.7 - - - +
173B ALA* 3.6 17.0 - - + +
175B LEU* 3.8 28.9 - - + -
246B TRP* 3.9 22.4 - - + -
249B THR* 4.7 4.7 - - + -
4C PHE* 3.5 12.5 - - + +
5C ASN* 3.3 6.4 - - - -
6C LEU* 2.9 48.4 + - + +
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Residues in contact with LEU 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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11B ARG* 4.0 15.0 - - + +
12B ILE* 1.3 72.1 - - - +
14B PHE* 1.3 59.3 + - - +
18B ALA* 3.5 18.5 - - + +
21B GLY* 3.7 37.2 - - - +
22B LEU 4.3 0.2 - - - +
25B GLN* 3.9 16.4 - - + +
172B PHE* 5.1 3.4 - - + -
173B ALA 2.9 13.3 + - - +
174B VAL* 3.4 19.6 - - + -
175B LEU 2.8 25.7 + - - -
4C PHE 3.6 2.9 - - - +
5C ASN* 3.3 40.2 - - + +
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Residues in contact with PHE 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ILE* 4.1 2.2 - - + -
13B LEU* 1.3 73.6 - - - +
15B GLY* 1.3 77.3 + - - +
18B ALA* 3.8 4.1 - - - +
175B LEU* 3.3 27.4 - - + -
177B PRO* 3.8 23.6 - - + -
238B TYR* 4.1 7.9 - - - -
242B ALA* 3.9 21.1 - - + -
245B MET* 4.5 8.7 - - + -
246B TRP* 4.1 27.8 - + + -
1C LEU* 3.9 24.0 - - + -
2C ASN 4.9 3.8 - - - -
3C ASN* 3.2 9.9 + - - +
4C PHE* 2.8 73.9 + + + +
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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