Contacts of the strand formed by residues 164 - 169 (chain L) 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 L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158L PHE* 3.5 7.1 - - - -
159L ASP* 3.0 46.3 + - + +
163L LYS* 1.3 90.4 - - + +
165L LEU* 1.3 59.6 + - - +
176L LEU* 3.7 17.9 - - + -
177L TRP 3.4 13.0 - - - +
178L ASP* 4.4 2.5 - - + +
185L ILE* 3.7 14.8 - - + -
200L ILE* 3.9 8.6 - - + +
204L GLY 5.2 5.6 - - - +
221L VAL* 3.8 28.5 - - + -
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Residues in contact with LEU 165 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124L VAL* 4.2 9.2 - - + -
132L ILE* 4.1 26.2 - - + -
146L LEU* 4.4 8.5 - - + -
156L ILE* 3.7 11.9 - - + -
157L SER 3.6 22.2 - - - +
158L PHE* 4.1 15.7 - - + +
164L LEU* 1.3 75.0 - - - +
166L ALA* 1.3 74.8 + - - +
176L LEU* 3.7 2.1 - - - -
177L TRP* 2.8 49.3 + - + +
179L PHE* 3.6 36.3 - - + -
200L ILE* 4.6 0.9 - - - -
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Residues in contact with ALA 166 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156L ILE* 3.3 4.9 - - - -
157L SER* 2.9 35.7 + - - +
165L LEU* 1.3 79.7 - - - +
167L SER* 1.3 62.0 + - - +
174L ILE* 4.9 2.5 - - + -
175L LYS 3.5 5.8 - - - +
176L LEU* 4.6 3.1 - - + +
198L VAL* 3.5 21.3 - - + -
200L ILE* 3.9 19.6 - - + +
207L ILE* 4.6 15.5 - - + -
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Residues in contact with SER 167 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132L ILE* 3.5 19.1 - - - -
149L HIS* 2.4 33.6 + - - -
153L VAL* 4.0 6.3 - - - -
155L ASP 3.5 7.2 - - - -
156L ILE* 4.6 1.1 - - - -
166L ALA* 1.3 75.0 - - - +
168L CYS* 1.3 61.2 + - - +
174L ILE* 3.2 30.1 - - - +
175L LYS* 2.8 10.2 + - - +
177L TRP* 3.3 18.9 + - - -
198L VAL* 4.3 1.8 - - - -
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Residues in contact with CYS 168 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149L HIS* 4.2 1.3 - - - -
153L VAL* 2.9 12.0 - - - +
154L GLN 2.7 25.6 + - - -
155L ASP 3.2 23.4 + - - +
167L SER* 1.3 75.1 - - - +
169L SER* 1.3 57.1 + - - +
173L THR 4.2 3.8 - - - -
174L ILE* 5.1 0.2 - - - -
195L VAL* 3.4 27.1 - - - +
197L SER 3.2 38.8 - - - -
198L VAL* 3.3 19.1 - - - -
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Residues in contact with SER 169 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149L HIS* 2.6 32.9 + - - -
152L SER 2.4 26.0 - - - -
154L GLN* 3.8 9.0 - - - -
168L CYS* 1.3 74.5 - - - +
170L ALA* 1.3 56.7 - - - +
171L ASP* 2.7 27.4 + - - +
172L MET* 3.3 9.9 + - - -
173L THR* 3.5 8.9 + - - -
195L VAL* 3.2 24.4 + - - +
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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