Contacts of the helix formed by residues 194 - 200 (chain B) in PDB entry 1V1A
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 194 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193B SER* 1.3 70.3 - - - +
195B GLU* 1.3 69.1 + - + +
197B ALA* 3.1 13.7 + - - +
198B GLU* 3.2 19.9 + - - +
204B VAL* 4.5 12.0 - - + +
218B LEU* 3.8 20.5 - - + +
219B LYS 2.9 20.0 + - - +
220B ARG* 2.8 63.9 + - + +
223B LYS* 4.2 12.3 + - - -
226B TRP* 4.7 2.9 - - - -
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Residues in contact with GLU 195 (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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193B SER* 3.4 9.0 + - - +
194B GLU* 1.3 76.7 - - + +
196B GLU* 1.3 54.2 + - + +
198B GLU* 3.0 9.6 + - - +
199B LEU* 2.8 42.4 + - + +
1303B ADP 4.7 16.6 + - - -
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Residues in contact with GLU 196 (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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163B ASP* 4.8 0.9 - - - +
164B VAL* 3.4 20.5 - - + +
165B ASN* 3.0 14.0 + - - +
166B TYR* 3.0 47.9 + - + +
167B ARG* 4.4 3.8 + - - -
192B LEU* 3.5 7.8 - - + +
193B SER* 2.8 41.0 + - - +
195B GLU* 1.3 80.1 - - + +
197B ALA* 1.3 61.8 + - - +
199B LEU* 3.0 6.5 + - - -
200B LEU* 3.0 34.5 + - + +
1303B ADP 4.7 5.0 + - - -
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Residues in contact with ALA 197 (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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192B LEU* 3.5 18.1 - - + +
193B SER 3.1 10.1 + - - +
194B GLU* 3.1 11.0 + - - +
196B GLU* 1.3 79.1 - - - +
198B GLU* 1.3 58.9 + - - +
201B PHE* 3.1 33.9 + - - +
202B GLY 3.4 0.7 + - - -
203B ARG 4.2 1.9 - - - +
204B VAL* 3.8 21.3 - - + -
207B ALA* 3.6 22.5 - - + +
218B LEU* 4.6 0.2 - - + -
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Residues in contact with GLU 198 (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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194B GLU* 3.2 9.5 + - - +
195B GLU* 3.0 10.1 + - - +
197B ALA* 1.3 75.5 - - - +
199B LEU* 1.3 59.1 + - - +
202B GLY* 3.1 39.2 - - - +
203B ARG* 4.3 17.2 + - - +
204B VAL* 3.6 33.4 - - + +
205B GLU* 5.4 0.7 - - - +
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Residues in contact with LEU 199 (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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166B TYR* 3.3 38.8 - - + +
168B GLN* 5.2 10.5 - - + +
173B PRO* 4.0 19.8 - - + +
177B ARG* 4.5 1.9 + - - -
195B GLU* 2.8 20.4 + - + +
196B GLU* 3.8 6.1 - - - +
198B GLU* 1.3 79.5 - - - +
200B LEU* 1.3 59.3 + - + +
201B PHE 3.6 0.2 - - - -
202B GLY 4.6 0.7 - - - -
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Residues in contact with LEU 200 (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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164B VAL* 4.4 11.2 - - + -
166B TYR* 3.6 48.0 - - + -
173B PRO* 3.1 41.1 - - + +
176B ALA* 3.8 12.3 - - + -
177B ARG* 2.5 38.5 + - + +
180B LEU* 4.4 15.5 - - + -
192B LEU* 6.1 0.9 - - + -
196B GLU 3.0 15.7 + - - +
199B LEU* 1.3 75.7 - - - +
201B PHE* 1.3 79.3 + - + +
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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