Contacts of the strand formed by residues 163 - 169 (chain B) in PDB entry 2JI8
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 GLY 163 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91B LEU* 3.6 15.7 - - - -
95B THR* 3.0 23.1 + - - +
99B PHE 3.8 2.5 + - - -
101B MET* 3.4 10.8 - - - -
133B CYS* 3.2 5.9 - - - +
134B LYS* 2.7 36.7 + - - +
162B GLY* 1.3 73.2 - - - -
164B VAL* 1.3 58.1 + - - -
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Residues in contact with VAL 164 (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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91B LEU* 3.5 6.1 - - - +
101B MET 2.9 10.0 + - - +
102B ILE* 3.4 6.4 - - + -
103B LEU 3.0 24.6 + - - -
133B CYS* 4.2 0.2 - - - -
135B ALA 3.4 13.2 - - - +
137B PHE* 3.8 20.6 - - + -
152B ALA* 3.3 39.5 - - + +
155B THR* 3.6 19.5 - - + -
156B ALA* 3.5 19.1 - - + +
163B GLY* 1.3 76.8 - - - +
165B TYR* 1.3 74.0 + - - +
166B VAL* 4.0 0.8 + - + -
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Residues in contact with TYR 165 (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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84B PHE* 3.4 20.9 - + - -
91B LEU* 3.9 10.2 - - + +
103B LEU* 3.2 20.2 - - + -
105B SER* 3.4 22.3 + - - -
125B GLN* 2.7 42.2 + - - +
126B MET* 3.6 5.8 - - - -
129B ALA* 3.5 24.2 - - + -
133B CYS* 4.1 3.3 - - - -
135B ALA 3.0 7.8 + - - +
136B SER* 3.4 21.7 - - - +
137B PHE 2.8 31.5 + - - -
164B VAL* 1.3 76.1 - - - +
166B VAL* 1.3 64.7 + - - +
167B ASP* 2.6 36.7 + - + -
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Residues in contact with VAL 166 (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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102B ILE* 3.9 14.1 - - + -
103B LEU 2.9 8.3 + - - +
104B LEU* 3.5 17.9 - - + -
105B SER 3.3 22.0 + - - -
137B PHE* 3.6 12.6 - - + +
139B ILE* 3.2 38.1 - - + +
148B GLY 5.0 1.3 - - - +
149B ILE* 4.7 3.1 - - + -
152B ALA* 3.6 30.7 - - + -
164B VAL* 4.0 3.4 - - + -
165B TYR* 1.3 81.6 - - - +
167B ASP* 1.3 62.9 + - - +
168B LEU* 3.7 9.6 + - + +
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Residues in contact with ASP 167 (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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105B SER 3.8 0.4 - - - +
107B SER* 2.6 36.3 + - - -
110B ARG* 5.1 0.2 + - - -
125B GLN* 3.3 9.6 + - - +
126B MET* 4.5 3.6 - - + -
137B PHE 2.9 17.8 + - - +
138B ARG* 3.0 37.0 + - + +
139B ILE 3.2 24.4 + - - -
165B TYR* 2.6 35.1 + - + -
166B VAL* 1.3 71.3 - - - +
168B LEU* 1.3 62.5 + - - +
169B PRO* 3.4 3.1 - - - +
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Residues in contact with LEU 168 (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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16B LEU* 3.9 31.6 - - + -
36B ILE* 5.5 0.2 - - + -
39B LEU* 4.7 4.7 - - + -
77B LEU* 4.9 2.2 - - + -
104B LEU* 3.9 30.7 - - + -
105B SER 3.0 15.8 + - - +
106B GLY* 3.2 5.2 - - - +
107B SER 3.1 17.1 + - - -
139B ILE* 4.0 20.6 - - + -
166B VAL* 4.0 11.4 - - + +
167B ASP* 1.3 81.8 - - - +
169B PRO* 1.3 71.4 - - - +
170B ALA 3.4 0.3 + - - -
172B LEU* 3.6 21.3 - - + -
173B PHE* 3.8 22.5 - - + -
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Residues in contact with PRO 169 (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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107B SER* 3.2 17.0 - - - +
108B SER 4.5 7.6 - - - +
110B ARG* 5.1 5.8 - - + +
138B ARG* 3.8 22.0 - - + -
139B ILE 3.2 24.2 - - - +
140B ASN* 4.5 12.1 - - - +
167B ASP* 3.4 9.9 - - - +
168B LEU* 1.3 85.5 - - - +
170B ALA* 1.3 66.4 + - - +
171B LYS* 4.2 8.3 - - + +
172B LEU* 2.9 23.5 + - + +
173B PHE* 4.0 3.3 - - - -
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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