Contacts of the strand formed by residues 195 - 200 (chain S) 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 VAL 195 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154S GLN* 3.4 12.3 - - - +
168S CYS* 3.2 30.3 - - - +
169S SER 3.1 12.3 + - - +
172S MET* 3.5 33.7 - - - -
173S THR 4.1 4.9 - - - +
174S ILE* 4.3 4.0 - - + -
191S HIS* 3.5 38.1 - - + +
193S HIS 3.6 4.0 - - - +
194S ASN* 1.3 81.1 + - - +
196S SER* 1.3 59.7 + - - +
209S SER* 3.9 10.3 - - - -
210S ALA 3.3 14.6 - - - +
211S SER* 4.3 0.2 - - - +
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Residues in contact with SER 196 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113S ARG* 3.6 21.8 + - - -
154S GLN* 3.7 20.6 - - - -
168S CYS* 4.1 1.3 - - - -
194S ASN* 3.9 7.5 + - - -
195S VAL* 1.3 73.5 - - - +
197S SER* 1.3 63.6 + - - +
210S ALA 2.8 7.2 + - - -
211S SER* 4.7 0.3 - - - -
236S TRP* 2.8 37.8 + - - -
237S VAL 3.4 9.0 + - - -
238S ARG* 3.4 16.7 - - - +
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Residues in contact with SER 197 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155S ASP* 2.9 8.7 + - - -
168S CYS* 3.4 10.3 - - - -
196S SER* 1.3 81.4 - - - +
198S VAL* 1.3 59.6 + - - +
209S SER* 3.1 6.2 - - - -
210S ALA* 3.0 27.8 + - - -
238S ARG 3.6 0.7 - - - -
239S MET* 3.3 34.1 - - - +
240S VAL* 3.4 13.4 + - - -
241S ARG* 2.9 28.9 + - - -
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Residues in contact with VAL 198 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155S ASP* 2.7 30.6 + - + +
156S ILE 4.3 0.2 - - - +
157S SER* 3.6 13.1 - - - +
166S ALA* 3.8 35.2 - - + +
167S SER 4.2 8.5 - - - -
168S CYS* 3.7 9.4 - - + -
174S ILE* 3.5 28.9 - - + -
197S SER* 1.3 75.6 - - - +
199S SER* 1.3 64.0 + - - +
207S ILE* 3.9 12.1 - - + -
208S VAL 3.1 16.4 - - - +
209S SER* 4.0 6.7 - - - -
240S VAL* 5.1 0.7 - - - -
241S ARG* 3.6 7.5 + - - -
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Residues in contact with SER 199 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157S SER* 3.4 8.5 - - - -
166S ALA* 5.4 0.2 - - - -
198S VAL* 1.3 81.1 - - - +
200S ILE* 1.3 64.6 + - - +
201S MET 3.7 0.3 + - - -
207S ILE* 3.4 6.1 - - - +
208S VAL* 2.8 55.8 + - - +
240S VAL* 3.8 14.9 + - - +
241S ARG* 4.3 7.0 - - - -
242S PRO* 4.1 23.8 - - - +
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Residues in contact with ILE 200 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157S SER* 2.8 38.5 + - - +
158S PHE 4.0 5.7 - - - +
159S ASP* 3.6 41.7 - - + +
160S HIS 4.8 0.4 - - - +
164S LEU* 3.9 11.0 - - + +
165S LEU 4.5 0.4 - - - -
166S ALA* 3.8 18.6 - - + +
176S LEU* 6.3 1.3 - - + -
199S SER* 1.3 78.2 - - - +
201S MET* 1.3 77.6 + - - +
202S PRO* 4.5 0.2 - - - +
204S GLY* 4.3 11.4 - - - -
206S HIS 3.7 4.9 - - - +
207S ILE* 3.5 24.5 - - + -
221S VAL* 5.1 4.3 - - + -
242S PRO* 4.3 6.8 - - - +
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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
------------------------------------------------------------
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