Contacts of the strand formed by residues 206 - 211 (chain K) 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 K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200K ILE* 3.7 3.5 - - - +
201K MET* 3.1 35.9 + - + +
203K ASN* 3.8 10.1 + - - +
205K ASP* 1.3 90.0 + - + +
207K ILE* 1.3 66.1 + - - +
218K MET* 3.6 40.4 - - + +
219K TRP 3.2 14.5 + - - -
220K GLU* 3.6 26.8 - - + -
221K VAL* 3.3 5.2 - - - +
227K VAL* 4.5 9.9 - - + -
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Residues in contact with ILE 207 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166K ALA* 4.6 6.3 - - + -
174K ILE* 4.4 2.5 - - + -
176K LEU* 4.2 20.2 - - + -
188K MET* 4.0 27.4 - - + -
198K VAL* 3.9 23.6 - - + -
199K SER 3.4 4.3 - - - +
200K ILE* 3.7 22.0 - - + -
206K HIS* 1.3 76.3 - - - +
208K VAL* 1.3 65.9 + - - +
218K MET* 3.2 8.2 - - - +
219K TRP* 2.8 52.3 + - + +
221K VAL* 3.4 32.8 - - + -
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Residues in contact with VAL 208 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198K VAL* 3.2 5.5 - - - +
199K SER* 2.8 50.0 + - - +
201K MET* 3.3 37.5 - - + -
207K ILE* 1.3 74.4 - - - +
209K SER* 1.3 63.7 + - - +
216K ILE* 3.7 24.7 - - + -
217K LYS 3.4 4.9 - - - +
218K MET* 4.5 11.4 - - + -
230K PHE* 5.5 2.0 - - + -
240K VAL* 4.1 7.4 - - + +
249K ILE* 3.8 23.3 - - + -
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Residues in contact with SER 209 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174K ILE* 3.3 22.5 - - - +
191K HIS* 3.5 12.7 + - - -
195K VAL* 3.9 4.3 - - - -
197K SER 3.1 11.9 - - - -
198K VAL* 4.5 3.6 - - - -
208K VAL* 1.3 76.0 - - - +
210K ALA* 1.3 62.6 + - - +
216K ILE* 2.9 22.0 - - - +
217K LYS 3.0 14.8 + - - -
219K TRP* 2.7 31.1 + - - -
240K VAL* 3.8 3.6 - - - -
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Residues in contact with ALA 210 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191K HIS* 4.2 0.7 - - - -
195K VAL* 3.3 6.6 - - - +
196K SER 2.8 25.3 + - - -
197K SER* 3.0 10.6 + - - +
209K SER* 1.3 76.8 - - - +
211K SER* 1.3 62.0 + - - +
215K THR 3.4 9.0 - - - +
216K ILE* 4.6 0.4 - - + -
237K VAL* 3.9 25.6 - - + +
239K MET 4.4 7.4 - - - +
240K VAL* 3.8 25.4 - - + -
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Residues in contact with SER 211 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191K HIS* 3.0 33.0 - - - -
193K HIS 3.2 10.0 + - - -
194K ASN 2.4 26.0 + - - -
195K VAL* 4.2 0.2 - - - +
196K SER 4.4 0.9 - - - +
210K ALA* 1.3 75.7 - - - +
212K ARG* 1.3 63.5 + - - +
213K ASP* 2.8 19.3 + - - +
214K LYS* 3.1 11.8 + - - -
215K THR 3.1 7.7 + - - -
236K TRP* 3.9 0.4 - - - -
237K VAL* 3.0 29.9 + - - -
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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
------------------------------------------------------------
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