Contacts of the strand formed by residues 167 - 172 (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 GLU 167 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B ARG* 3.0 30.5 + - - -
78B THR* 4.9 1.2 + - - -
99B LYS* 2.6 30.7 + - + -
123B GLN 5.9 0.4 - - - +
125B VAL 3.3 2.4 + - - +
126B VAL* 3.5 28.6 - - + +
127B VAL 3.1 23.4 + - - -
165B ALA* 3.7 3.1 - - - +
166B GLY* 1.3 79.5 - - - +
168B ILE* 1.3 66.9 + - - +
169B VAL 4.2 0.2 - - - -
196B LEU* 4.3 3.6 - - - -
197B PRO* 3.6 26.1 - - + +
199B ILE* 3.5 19.8 - - + +
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Residues in contact with ILE 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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127B VAL 3.3 5.8 - - - +
129B ILE* 3.7 23.6 - - + -
157B VAL* 4.1 30.1 - - + +
160B VAL* 4.0 24.9 - - + -
167B GLU* 1.3 77.9 - - - +
169B VAL* 1.3 74.5 + - - +
170B LEU* 3.8 10.0 + - + +
190B VAL* 5.4 3.4 - - + -
194B THR* 4.3 11.4 - - + +
196B LEU* 4.0 20.2 - - + -
197B PRO 3.0 10.7 + - - +
198B ILE* 3.4 9.8 - - + -
199B ILE* 2.8 30.4 + - - +
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Residues in contact with VAL 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B GLU* 5.0 2.0 - - - -
126B VAL* 3.6 25.8 - - + -
127B VAL 2.9 7.9 + - - -
128B TYR* 3.4 39.0 - - + -
129B ILE* 2.7 33.1 + - - +
167B GLU 4.2 0.2 - - - -
168B ILE* 1.3 74.3 - - - +
170B LEU* 1.3 61.5 + - - +
171B GLY 3.6 0.3 + - - -
199B ILE* 3.4 23.8 - - + +
201B HIS* 3.8 16.6 - - + -
222B LYS* 3.8 26.0 - - - +
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Residues in contact with LEU 170 (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* 3.7 13.2 - - + +
131B ALA* 4.9 0.9 - - + -
153B LEU* 3.9 25.8 - - + -
168B ILE* 3.8 6.7 + - + -
169B VAL* 1.3 73.2 - - - +
171B GLY* 1.3 57.2 + - - +
172B SER 3.9 0.7 + - - -
186B MET* 3.7 39.4 - - + +
187B ILE* 3.9 19.4 - - + +
190B VAL* 3.7 31.9 - - + -
198B ILE* 4.2 19.1 - - + -
199B ILE 2.7 13.3 + - - +
200B ALA* 3.9 2.5 - - - -
201B HIS 3.1 24.5 + - - +
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Residues in contact with GLY 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B TYR* 3.4 27.9 - - - -
129B ILE 2.8 14.9 + - - -
130B ALA* 3.4 3.7 - - - +
131B ALA* 2.9 28.8 + - - -
169B VAL 3.6 2.0 + - - -
170B LEU* 1.3 71.8 - - - +
172B SER* 1.3 61.4 + - - -
173B ILE* 3.3 2.7 + - - -
186B MET* 4.4 3.4 - - - +
201B HIS* 3.6 6.7 - - - -
202B ARG* 4.2 2.0 - - - -
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Residues in contact with SER 172 (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 3.7 4.3 - - - -
170B LEU 3.9 2.0 + - - -
171B GLY* 1.3 70.1 - - - -
173B ILE* 1.3 57.0 + - - +
174B ASP* 3.4 16.8 + - - +
175B ARG* 2.9 25.7 + - - +
176B LEU 3.5 1.2 + - - -
183B ASP* 2.7 45.2 + - - +
186B MET* 3.6 10.7 - - - +
201B HIS 3.2 12.9 + - - -
202B ARG* 3.3 18.7 - - - +
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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