Contacts of the strand formed by residues 125 - 134 (chain B) in PDB entry 3IIV
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 VAL 125 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100B VAL* 3.9 3.1 - - + +
102B ILE* 4.5 9.4 - - + -
113B ILE* 3.9 20.9 - - + +
116B ILE* 3.5 37.5 - - + -
117B ALA* 3.7 20.9 - - + +
121B GLY 4.4 0.7 - - - +
122B SER 2.9 9.4 + - - +
123B GLN 3.3 1.7 - - - +
124B ALA* 1.3 78.5 - - - +
126B VAL* 1.3 66.0 + - - +
127B VAL* 4.2 13.0 - - + -
164B GLY 4.6 0.2 - - - +
165B ALA* 3.9 17.0 - - - -
166B GLY* 2.9 29.5 + - - +
167B GLU* 3.3 7.1 + - - +
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Residues in contact with VAL 126 (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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78B THR* 4.2 9.2 - - + +
99B LYS* 3.7 26.7 - - + -
100B VAL 2.8 14.9 + - - +
101B GLU* 3.3 17.3 - - + -
102B ILE* 3.0 28.6 + - - +
125B VAL* 1.3 77.2 - - - +
127B VAL* 1.3 63.7 + - - +
167B GLU* 3.5 37.9 - - + +
169B VAL* 3.6 30.5 - - + -
222B LYS* 6.1 0.4 - - - +
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Residues in contact with VAL 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B ILE* 3.4 13.7 - - + +
103B ASN* 5.3 0.7 - - - +
106B ALA* 4.3 10.5 - - + -
113B ILE* 3.8 24.5 - - + -
125B VAL* 4.2 4.5 - - + -
126B VAL* 1.3 75.5 - - - +
128B TYR* 1.3 69.8 + - - +
129B ILE* 3.7 11.0 + - + -
156B TRP* 4.3 3.6 - - - +
160B VAL* 3.7 44.2 - - + -
165B ALA* 3.8 9.6 - - + -
167B GLU 3.1 8.2 + - - +
168B ILE* 3.3 7.2 - - + +
169B VAL 2.9 22.5 + - - +
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Residues in contact with TYR 128 (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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101B GLU* 3.2 32.8 - - + +
102B ILE 2.9 13.0 + - - +
103B ASN* 3.2 49.7 - - + +
126B VAL 3.9 2.0 + - - -
127B VAL* 1.3 73.9 - - - +
129B ILE* 1.3 74.2 + - - +
130B ALA* 3.9 20.0 - - + -
156B TRP* 5.2 1.4 + - - -
169B VAL* 3.4 29.4 - - + -
171B GLY* 3.4 17.2 - - - -
201B HIS* 2.6 38.6 - + - -
202B ARG* 4.0 12.9 + - - +
264B MG 4.2 7.0 - - - -
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Residues in contact with ILE 129 (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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103B ASN* 5.0 0.2 - - - -
127B VAL* 4.0 7.0 - - + -
128B TYR* 1.3 77.6 - - - +
130B ALA* 1.3 65.5 + - - +
131B ALA* 3.8 1.0 + - + -
140B VAL* 4.0 12.8 - - + -
153B LEU* 3.6 24.0 - - + -
156B TRP* 3.7 37.2 - - + +
157B VAL* 3.9 26.2 - - + -
160B VAL* 4.5 5.2 - - + -
168B ILE* 3.7 32.8 - - + -
169B VAL 2.7 12.1 + - - +
170B LEU* 3.7 6.7 - - + +
171B GLY 2.8 26.5 + - - +
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Residues in contact with ALA 130 (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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103B ASN* 4.2 9.6 + - - +
128B TYR* 3.7 20.2 + - + -
129B ILE* 1.3 71.6 - - - +
131B ALA* 1.3 59.7 + - - +
140B VAL* 3.5 7.4 - - - +
141B PHE 2.9 43.7 + - - +
145B GLY* 4.8 7.2 - - - +
171B GLY 3.4 5.4 - - - +
173B ILE* 3.7 19.7 - - + -
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Residues in contact with ALA 131 (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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129B ILE* 3.8 3.6 + - + +
130B ALA* 1.3 75.6 - - - +
132B LYS* 1.3 61.4 + - - +
138B PHE* 4.9 0.4 - - + -
139B MET 3.2 15.9 - - - +
153B LEU* 4.0 32.1 - - + -
170B LEU* 4.9 0.2 - - + -
171B GLY 2.9 8.1 + - - +
172B SER* 3.7 0.2 - - - -
173B ILE* 3.0 27.4 + - - +
174B ASP 4.2 0.3 + - - -
186B MET* 3.4 29.3 - - + +
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Residues in contact with LYS 132 (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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131B ALA* 1.3 77.5 - - - +
133B ARG* 1.3 77.5 + - - +
134B VAL* 3.4 6.1 + - + +
138B PHE* 4.4 4.0 - - - -
139B MET* 2.9 30.1 + - - +
141B PHE* 3.7 35.9 - - + -
145B GLY 5.7 0.2 - - - +
173B ILE* 4.1 24.4 - - + +
174B ASP* 3.4 25.4 - - - +
186B MET* 4.8 0.9 - - - -
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Residues in contact with ARG 133 (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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132B LYS* 1.3 83.6 - - - +
134B VAL* 1.3 65.3 + - - +
135B ASP 4.2 0.7 - - - -
136B GLY* 5.3 5.4 - - - +
137B GLU 3.4 11.7 - - - +
138B PHE* 3.4 29.8 - - + +
174B ASP* 2.9 39.9 + - - +
175B ARG* 5.4 4.5 - - - +
183B ASP* 2.8 43.2 + - - -
185B GLU* 2.9 34.9 + - - +
186B MET* 4.5 0.4 - - - +
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Residues in contact with VAL 134 (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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132B LYS* 3.8 9.4 - - + +
133B ARG* 1.3 78.9 - - - +
135B ASP* 1.3 82.8 + - + +
137B GLU* 2.9 26.0 + - - +
139B MET* 3.8 14.1 - - + +
141B PHE* 3.7 35.4 - - + -
148B ASN* 3.9 17.0 - - - +
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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