Contacts of the helix formed by residues 156 - 164 (chain B) in PDB entry 3V4V
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 156 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152B VAL 3.9 2.0 + - - -
154B GLN 2.9 9.1 + - - -
155B LEU* 1.3 80.3 - - - +
157B HIS* 1.3 63.3 + - - +
158B ALA 3.3 0.2 + - - -
159B LEU* 3.3 13.3 + - - +
160B LEU 4.2 1.2 + - - -
172B ILE* 4.2 12.0 - - - +
220B ALA* 4.3 4.3 - - - +
223B PHE* 3.3 34.3 - - - -
224B GLU* 3.7 8.0 - - - +
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Residues in contact with HIS 157 (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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156B GLY* 1.3 67.0 - - - +
158B ALA* 1.3 60.3 + - - +
159B LEU 2.9 11.8 + - - -
160B LEU* 3.2 14.8 + - + +
161B VAL* 3.5 27.8 + - + +
164B GLN* 6.2 0.2 - - - -
220B ALA* 3.7 29.4 + - + +
221B GLN* 6.1 0.2 - - - -
224B GLU* 2.9 26.7 + - - +
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Residues in contact with ALA 158 (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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154B GLN 4.8 2.2 + - - +
155B LEU* 4.0 34.7 - - + +
156B GLY 3.2 0.6 - - - -
157B HIS* 1.3 81.3 - - - +
159B LEU* 1.3 59.2 + - - +
161B VAL* 4.1 12.8 - - - +
162B ARG* 3.7 18.4 - - - +
224B GLU* 4.7 0.4 + - - -
360B VAL* 3.8 9.6 - - + +
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Residues in contact with LEU 159 (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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135B LEU* 3.7 24.9 - - + -
137B TYR* 5.7 6.7 - - + -
155B LEU 3.9 9.3 + - - +
156B GLY 3.3 11.6 + - - +
157B HIS 2.9 1.2 + - - -
158B ALA* 1.3 76.8 - - - +
160B LEU* 1.3 67.7 + - + +
161B VAL 3.2 2.0 - - - -
162B ARG* 3.1 5.2 + - + +
163B LEU* 3.0 34.0 + - + +
172B ILE* 4.6 11.4 - - + -
223B PHE* 6.2 3.6 - - + -
360B VAL* 4.2 23.8 - - + +
363B ILE* 4.3 17.9 - - + -
364B MET* 4.1 22.4 - - + -
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Residues in contact with LEU 160 (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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156B GLY 4.8 0.4 - - - +
157B HIS* 3.2 12.4 + - + +
159B LEU* 1.3 76.4 - - - +
161B VAL* 1.3 56.7 + - + +
163B LEU* 3.9 7.9 - - + -
164B GLN* 2.6 63.9 + - - +
170B VAL* 4.7 12.8 - - + +
172B ILE* 3.5 49.4 - - + +
218B GLY* 3.2 30.5 - - - +
219B ASP 4.9 0.2 - - - -
220B ALA* 3.8 19.7 - - + +
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Residues in contact with VAL 161 (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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157B HIS* 3.5 41.5 - - + +
158B ALA* 4.1 11.2 - - - +
160B LEU* 1.3 79.9 - - - +
162B ARG* 1.3 64.9 + - + +
164B GLN* 4.0 8.8 - - - +
165B GLU* 3.3 26.0 + - - +
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Residues in contact with ARG 162 (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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158B ALA 3.7 16.2 - - - +
159B LEU* 3.1 7.4 + - - +
161B VAL* 1.3 81.5 - - + +
163B LEU* 1.3 62.5 + - - +
165B GLU* 3.3 33.4 + - - +
166B VAL* 4.0 5.7 - - - +
360B VAL* 4.0 22.7 - - + +
361B GLN* 4.0 26.5 - - - +
364B MET* 3.7 52.0 - - + +
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Residues in contact with LEU 163 (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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133B VAL* 5.1 7.4 - - + -
135B LEU* 4.3 15.9 - - + -
159B LEU* 3.0 27.8 + - + +
160B LEU* 3.0 14.0 + - + +
162B ARG* 1.3 74.5 - - - +
164B GLN* 1.3 57.3 + - - +
165B GLU 2.9 4.9 - - - -
166B VAL* 3.0 20.0 + - + +
167B THR* 3.1 18.6 + - + +
170B VAL* 3.7 34.5 - - + -
172B ILE* 4.0 25.1 - - + -
264B LEU* 6.3 1.8 - - + -
363B ILE* 5.6 0.2 - - + -
364B MET* 3.5 26.9 - - + -
367B TYR* 6.0 4.9 - - + -
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Residues in contact with GLN 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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157B HIS* 6.2 0.3 - - - -
160B LEU* 2.6 54.8 + - - +
161B VAL* 4.0 7.4 - - - +
163B LEU* 1.3 68.6 - - - +
165B GLU* 1.3 55.7 + - - +
166B VAL 3.1 5.4 + - - -
167B THR 3.3 16.7 - - - +
168B HIS* 5.5 5.6 - - - -
169B SER* 5.6 1.6 - - - +
170B VAL* 3.5 20.8 + - + +
218B GLY 5.3 0.2 + - - -
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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