Contacts of the helix formed by residues 157 - 164 (chain B) in PDB entry 3V3H
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 LEU 157 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B PHE* 3.9 23.8 - - + -
148B LEU* 4.6 10.1 - - + -
154B LYS* 2.9 17.6 + - + +
156B GLY* 1.3 76.1 - - - +
158B GLN* 1.3 66.2 + - - +
159B LYS 3.2 2.7 - - - -
160B VAL* 3.0 34.2 + - + -
161B VAL* 3.1 26.0 + - + +
184B LEU* 3.9 17.0 - - + +
216B ILE* 5.6 1.3 - - + -
218B VAL* 3.6 33.9 - - + -
222B GLN* 4.0 11.0 - - + +
223B VAL* 5.8 0.4 - - - +
226B PHE* 4.5 5.4 - - + -
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Residues in contact with GLN 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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153B ALA* 5.4 2.3 - - - +
154B LYS 3.7 1.4 + - - -
155B PRO* 3.1 19.1 + - + +
157B LEU* 1.3 77.9 - - - +
159B LYS* 1.3 58.7 + - + +
161B VAL* 3.2 9.6 + - - +
162B ASP* 2.9 70.3 + - - +
222B GLN* 2.8 30.8 + - - +
225B LYS* 4.1 0.2 - - - +
302B CL 3.3 23.8 - - - +
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Residues in contact with LYS 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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155B PRO 4.8 2.8 + - - +
156B GLY* 4.6 10.5 + - - -
157B LEU 3.2 0.8 - - - -
158B GLN* 1.3 77.8 - - + +
160B VAL* 1.3 62.4 + - - +
162B ASP* 4.3 5.1 - - - +
163B VAL* 3.4 15.8 + - - +
176B PHE* 3.4 19.6 - - + -
177B THR 5.9 1.3 - - - +
178B ASN 4.2 17.0 - - - -
179B PHE* 3.7 35.4 - - + +
180B ASP 5.2 1.6 - - - +
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Residues in contact with VAL 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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59B ILE* 4.6 3.6 - - + -
66B PHE* 3.6 37.7 - - + -
68B VAL* 4.8 0.4 - - + -
93B PHE* 4.1 12.6 - - + -
95B PHE* 4.3 3.8 - - + -
157B LEU* 3.0 27.6 + - + +
159B LYS* 1.3 76.3 - - - +
161B VAL* 1.3 65.7 + - - +
163B VAL* 3.2 19.5 - - - +
164B LEU* 3.3 6.9 - - - +
176B PHE* 3.7 19.3 - - + -
179B PHE* 3.7 31.4 - - + -
226B PHE* 4.7 2.7 - - + -
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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 LEU* 3.1 26.1 + - + +
158B GLN* 3.4 33.2 - - - +
160B VAL* 1.3 75.7 - - - +
162B ASP* 1.3 65.6 + - - +
164B LEU* 3.3 22.6 + - - +
165B ASP 4.7 0.9 + - - -
222B GLN* 3.5 30.7 - - + +
225B LYS* 3.7 28.7 - - + +
226B PHE* 3.6 23.8 - - + -
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Residues in contact with ASP 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 GLN* 2.9 46.8 + - - +
159B LYS* 4.3 5.0 - - - +
161B VAL* 1.3 77.1 - - - +
163B VAL* 1.3 59.3 + - - +
164B LEU 3.5 0.3 + - - -
165B ASP* 4.2 11.0 + - - +
166B SER 5.3 0.2 + - - -
225B LYS* 2.8 28.5 + - - +
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Residues in contact with VAL 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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59B ILE* 3.6 30.1 - - + -
159B LYS 3.4 9.4 + - - +
160B VAL 3.2 16.1 + - - +
162B ASP* 1.3 75.3 - - - +
164B LEU* 1.3 65.4 + - - +
165B ASP 3.2 3.1 - - - -
166B SER* 2.8 37.9 + - - +
167B ILE* 3.6 4.4 + - + +
174B ALA* 4.0 18.4 - - + -
175B ASP 4.8 2.7 - - - +
176B PHE* 3.8 21.8 - - + -
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Residues in contact with LEU 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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59B ILE* 4.2 4.9 - - + -
66B PHE* 3.9 27.1 - - + -
160B VAL 3.3 15.9 - - - +
161B VAL* 3.5 15.5 - - - +
162B ASP 3.3 1.4 - - - -
163B VAL* 1.3 78.4 - - - +
165B ASP* 1.3 63.7 + - - +
167B ILE* 3.1 30.4 + - + +
168B LYS* 3.3 14.3 + - - -
225B LYS* 3.8 20.9 - - + +
226B PHE* 3.5 34.3 - - + -
229B LEU* 3.8 21.8 - - + +
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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