Contacts of the strand formed by residues 201 - 205 (chain Y) in PDB entry 1VQ9
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 201 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182Y PHE* 3.3 15.3 - - - -
183Y GLU* 3.3 21.8 - - + +
185Y VAL* 3.9 18.8 - - + +
195Y GLY 4.3 2.8 - - - +
196Y VAL* 3.4 20.8 - - + +
197Y ASP* 2.6 44.7 + - - +
198Y GLY* 3.6 10.6 - - - +
200Y THR* 1.3 96.4 - - + +
202Y ALA* 1.3 60.7 + - - +
226Y ILE* 4.1 5.4 - - - +
227Y ARG 4.7 0.9 + - - -
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Residues in contact with ALA 202 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182Y PHE* 3.5 25.9 - - + -
183Y GLU 3.2 6.8 + - - +
184Y GLU* 3.8 0.3 - - - -
185Y VAL* 3.1 26.9 + - - +
196Y VAL* 5.3 0.9 - - - -
201Y GLU* 1.3 75.8 - - - +
203Y VAL* 1.3 62.2 + - - +
226Y ILE* 4.3 3.4 - - - -
227Y ARG* 3.5 15.9 - - + +
229Y LEU* 3.6 33.0 - - + -
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Residues in contact with VAL 203 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185Y VAL* 3.3 23.8 - - + +
187Y VAL* 3.3 32.8 - - + -
192Y ASP 5.6 0.2 - - - +
193Y LEU* 3.9 19.1 - - + -
196Y VAL* 5.3 4.5 - - + -
202Y ALA* 1.3 74.6 - - - +
204Y ARG* 1.3 59.5 + - - +
205Y ILE* 4.6 1.8 - - + -
217Y ILE* 5.5 0.4 - - + -
221Y ALA* 4.8 0.2 - - + -
226Y ILE* 4.0 14.1 - - + +
227Y ARG 2.8 13.0 + - - +
228Y VAL* 3.4 32.8 - - + +
229Y LEU* 2.9 27.7 + - - +
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Residues in contact with ARG 204 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5520 A 2.7 20.2 + - - -
5530 G 2.5 35.2 + - - -
13240 G 3.2 19.0 - - - +
13250 G 5.0 4.8 + - - -
13330 U 3.7 16.8 - - - +
13340 C 3.5 31.1 + - - -
178Y HIS* 4.1 0.6 - - - -
184Y GLU* 2.5 48.8 + - + +
185Y VAL 2.9 15.2 + - - +
186Y ARG* 3.6 11.2 - - - +
187Y VAL* 2.9 25.5 + - - -
203Y VAL* 1.3 72.3 - - - +
205Y ILE* 1.3 62.2 + - - +
206Y ALA 3.5 1.2 + - - -
229Y LEU* 3.9 16.2 + - + +
230Y ASN* 3.6 8.6 - - - +
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Residues in contact with ILE 205 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13340 C 3.8 5.4 - - - +
187Y VAL* 3.3 25.6 - - + +
203Y VAL* 4.6 2.0 - - + -
204Y ARG* 1.3 71.5 - - - +
206Y ALA* 1.3 78.2 + - - +
207Y SER 3.6 0.5 + - - -
209Y VAL* 3.8 24.7 - - + -
214Y ARG* 3.4 30.5 - - + +
217Y ILE* 3.6 29.8 - - + -
218Y GLU* 4.1 14.8 - - + -
228Y VAL* 4.0 21.3 - - + -
230Y ASN* 2.8 31.0 + - - +
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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