Contacts of the strand formed by residues 142 - 146 (chain B) in PDB entry 6OR7
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 ILE 142 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A THR* 3.6 31.0 - - + -
49B LYS* 4.3 17.0 - - + -
130B PHE 3.9 0.5 - - - +
131B THR* 3.4 0.5 - - - -
132B ILE* 2.9 46.9 + - + +
133B PRO 5.9 0.4 - - - +
139B THR* 4.0 12.3 - - + -
140B PRO 3.8 11.9 - - - +
141B GLY* 1.3 70.6 - - - -
143B ARG* 1.3 65.0 + - - +
144B TYR* 3.9 29.9 - - + +
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Residues in contact with ARG 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A TRP* 3.1 30.9 - - - +
90A VAL* 3.7 25.4 - - - -
49B LYS* 3.4 8.8 - - - +
50B ILE* 2.9 43.1 + - + +
51B GLY 3.2 17.7 + - - -
52B PRO* 4.4 0.2 - - - +
54B ASN* 2.9 44.4 + - - +
56B TYR 3.0 24.4 + - - -
57B ASN* 3.3 14.8 + - - -
129B ALA* 3.6 8.2 - - - +
130B PHE 3.3 4.0 + - - +
131B THR* 3.2 24.9 - - + +
141B GLY 3.8 3.9 + - - +
142B ILE* 1.3 75.6 - - - +
144B TYR* 1.3 62.3 + - - +
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Residues in contact with TYR 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B CYS* 4.3 13.0 + - + +
39B THR* 5.3 2.3 + - - -
42B GLU* 3.6 15.3 + - + -
47B ILE* 3.6 25.1 - - + -
48B SER* 3.3 22.4 - - - +
49B LYS* 3.3 39.1 + - + -
50B ILE* 3.4 6.8 - - - +
129B ALA* 3.1 4.9 - - - -
130B PHE* 2.9 63.6 + + + -
132B ILE* 3.6 22.1 - - + +
142B ILE* 3.9 24.1 - - + +
143B ARG* 1.3 75.5 - - - +
145B GLN* 1.3 61.7 + - - +
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Residues in contact with GLN 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ILE* 3.2 7.0 - - - +
48B SER* 2.9 38.2 + - - +
50B ILE* 3.6 31.0 - - + +
54B ASN* 3.9 4.3 + - - -
122B GLU* 5.0 6.5 + - - -
125B ARG* 3.5 44.4 - - - +
126B LYS* 3.5 14.6 - - - +
128B THR* 4.0 6.5 - - - +
129B ALA* 4.5 2.9 - - + -
130B PHE* 4.9 0.4 - - - -
144B TYR* 1.3 75.3 - - - +
146B TYR* 1.3 66.4 + - - +
147B ASN* 4.3 7.4 + - - +
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Residues in contact with TYR 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B MET* 3.6 26.1 - - + +
46B LYS 3.8 8.3 - - - -
47B ILE* 3.7 7.6 - - + -
73B LYS* 2.5 39.2 + - - +
75B VAL* 4.1 7.4 - - + +
77B PHE* 4.4 9.0 - + - -
116B PHE* 4.1 10.0 - + - -
120B LEU* 4.4 3.4 - - + -
125B ARG* 3.2 30.0 - - - +
128B THR* 2.9 30.4 + - - +
130B PHE* 3.6 17.5 - + - -
145B GLN* 1.3 74.0 - - - +
147B ASN* 1.3 59.6 + - - +
148B VAL* 3.8 20.4 - - + +
150B PRO* 3.6 37.2 - - + -
151B GLN* 4.9 5.4 + - - +
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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
------------------------------------------------------------
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