Contacts of the strand formed by residues 206 - 211 (chain T) in PDB entry 1VYH
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 HIS 206 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200T ILE* 3.9 1.4 - - - +
201T MET* 3.1 39.1 + - + +
203T ASN* 3.9 11.0 + - - -
204T GLY 5.1 0.3 - - - -
205T ASP* 1.3 107.2 + - + +
207T ILE* 1.3 68.4 + - - +
218T MET* 3.9 27.2 - - + +
219T TRP 3.2 7.2 + - - +
220T GLU* 3.7 32.8 + - + -
221T VAL* 3.5 6.4 - - - +
227T VAL* 5.1 10.1 - - + +
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Residues in contact with ILE 207 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166T ALA* 4.3 14.4 - - + -
174T ILE* 4.4 10.1 - - + -
176T LEU* 3.8 24.0 - - + -
188T MET* 4.4 7.0 - - + -
198T VAL* 3.9 20.9 - - + -
199T SER 3.4 10.3 - - - +
200T ILE* 3.8 19.5 - - + -
206T HIS* 1.3 77.6 - - - +
208T VAL* 1.3 64.9 + - - +
209T SER* 4.6 0.2 - - - +
218T MET* 3.1 8.1 - - - +
219T TRP* 2.7 62.6 + - + +
221T VAL* 3.6 22.4 - - + -
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Residues in contact with VAL 208 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198T VAL* 3.2 6.2 - - - +
199T SER* 2.8 49.3 + - - +
201T MET* 3.0 35.0 - - - -
207T ILE* 1.3 75.0 - - - +
209T SER* 1.3 65.8 + - - +
216T ILE* 3.6 26.5 - - + -
217T LYS 3.4 4.5 - - - +
218T MET* 4.1 8.3 - - + -
230T PHE* 5.5 0.4 - - + -
240T VAL* 3.8 18.8 - - + +
242T PRO* 5.1 0.2 - - + -
249T ILE* 4.1 20.0 - - + -
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Residues in contact with SER 209 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174T ILE* 4.2 12.6 - - - -
191T HIS* 3.5 18.7 + - - -
195T VAL* 4.4 5.4 - - - -
197T SER 3.1 11.7 - - - -
198T VAL* 4.8 3.4 - - - -
207T ILE* 5.1 0.2 - - - -
208T VAL* 1.3 74.3 - - - +
210T ALA* 1.3 61.7 + - - +
216T ILE* 3.2 12.5 - - - +
217T LYS 3.0 25.2 + - - -
219T TRP* 2.5 36.2 + - - -
240T VAL* 3.8 3.6 - - - -
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Residues in contact with ALA 210 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191T HIS* 4.4 0.9 - - - -
195T VAL* 3.5 6.1 - - - +
196T SER 2.8 25.2 + - - -
197T SER* 3.0 16.6 + - - -
209T SER* 1.3 76.6 - - - +
211T SER* 1.3 61.8 + - - +
215T THR 3.4 6.5 - - - -
237T VAL* 3.6 33.2 - - + +
239T MET 4.3 2.7 - - - -
240T VAL* 3.8 19.3 - - + -
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Residues in contact with SER 211 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191T HIS* 3.1 32.8 + - - -
193T HIS 3.6 7.3 + - - -
194T ASN 3.1 16.9 + - - -
195T VAL* 4.3 0.2 - - - -
196T SER 4.4 1.1 - - - +
210T ALA* 1.3 75.9 - - - +
212T ARG* 1.3 58.2 + - - +
213T ASP* 2.6 34.9 + - - +
214T LYS 3.0 15.6 + - - -
215T THR 3.1 6.5 + - - -
236T TRP* 4.0 0.2 - - - -
237T VAL* 3.1 25.3 + - - +
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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
------------------------------------------------------------
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