Contacts of the strand formed by residues 164 - 169 (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 LEU 164 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158S PHE* 3.6 8.0 - - - -
159S ASP* 2.9 48.9 + - + +
163S LYS* 1.3 93.1 - - + +
165S LEU* 1.3 59.8 + - - +
176S LEU* 4.1 11.0 - - + -
177S TRP 3.3 11.0 - - - +
178S ASP* 4.6 2.7 - - + +
179S PHE* 5.5 0.7 - - - -
185S ILE* 4.0 22.0 - - + -
200S ILE* 3.9 7.6 - - + +
204S GLY 5.2 4.9 - - - +
221S VAL* 4.1 26.2 - - + -
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Residues in contact with LEU 165 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115S ILE* 4.9 0.4 - - + -
124S VAL* 4.4 4.9 - - + -
132S ILE* 4.1 15.7 - - + -
146S LEU* 4.3 13.7 - - + -
156S ILE* 3.8 40.4 - - + -
157S SER 3.7 11.9 - - - +
158S PHE* 3.8 42.4 - - + -
164S LEU* 1.3 74.5 - - - +
166S ALA* 1.3 59.6 + - - +
176S LEU* 3.7 2.2 - - - -
177S TRP* 2.7 56.6 + - + +
179S PHE* 4.6 12.5 - - + -
200S ILE* 4.5 1.1 - - - -
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Residues in contact with ALA 166 (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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156S ILE* 3.3 10.9 - - - +
157S SER* 2.9 37.0 + - - +
165S LEU* 1.3 75.0 - - - +
167S SER* 1.3 60.3 + - - +
174S ILE* 4.9 2.0 - - + -
175S LYS 3.5 6.1 - - - +
176S LEU* 4.7 2.2 - - + +
198S VAL* 3.8 21.3 - - + -
200S ILE* 3.8 16.9 - - + +
207S ILE* 4.2 19.1 - - + -
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Residues in contact with SER 167 (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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132S ILE* 3.7 16.4 - - - -
149S HIS* 2.4 32.5 + - - -
153S VAL* 4.1 2.5 - - - -
155S ASP 3.4 8.3 - - - -
156S ILE* 4.4 2.9 - - - -
166S ALA* 1.3 74.8 - - - +
168S CYS* 1.3 62.1 + - - +
174S ILE* 3.3 30.7 - - - +
175S LYS 2.9 11.0 + - - -
177S TRP* 2.9 24.2 + - - -
198S VAL* 4.2 2.5 - - - -
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Residues in contact with CYS 168 (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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149S HIS* 4.7 0.7 - - - -
153S VAL* 3.0 11.1 - - - +
154S GLN 2.7 22.1 + - - -
155S ASP* 3.1 28.3 + - + +
167S SER* 1.3 77.1 - - - +
169S SER* 1.3 60.0 + - - +
173S THR 4.2 4.0 - - - -
174S ILE* 5.2 0.4 - - - -
195S VAL* 3.2 44.9 - - - +
197S SER 3.4 28.0 - - - -
198S VAL* 3.7 9.4 - - + -
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Residues in contact with SER 169 (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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149S HIS* 3.0 16.9 + - - -
152S SER 2.7 19.5 - - - -
154S GLN* 4.0 1.8 - - - +
168S CYS* 1.3 76.4 - - - +
170S ALA* 1.3 57.6 + - - +
171S ASP* 2.8 20.3 + - - -
172S MET 3.3 7.4 + - - -
173S THR* 2.5 36.6 + - - -
194S ASN* 4.0 5.4 - - - -
195S VAL* 3.1 26.4 + - - +
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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