Contacts of the strand formed by residues 164 - 169 (chain P) 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 P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158P PHE* 3.5 8.5 - - - -
159P ASP* 3.1 49.4 + - + +
163P LYS* 1.3 90.8 - - + +
165P LEU* 1.3 60.5 + - - +
176P LEU* 4.0 17.7 - - + -
177P TRP 3.3 11.0 - - - +
178P ASP* 4.7 1.3 - - + -
179P PHE* 5.3 0.7 - - - -
185P ILE* 4.0 23.3 - - + -
200P ILE* 3.8 4.2 - - + +
204P GLY 5.2 7.2 - - - +
221P VAL* 4.5 19.5 - - + -
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Residues in contact with LEU 165 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124P VAL* 4.3 5.2 - - + -
132P ILE* 4.2 24.7 - - + -
146P LEU* 4.4 9.0 - - + -
156P ILE* 3.1 36.8 - - + -
157P SER 3.4 17.3 - - - +
158P PHE* 3.6 22.2 - - + +
164P LEU* 1.3 75.3 - - - +
166P ALA* 1.3 61.6 + - - +
167P SER* 5.6 0.4 - - - -
176P LEU* 3.6 3.5 - - - -
177P TRP* 2.7 52.0 + - + -
179P PHE* 3.8 26.0 - - + -
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Residues in contact with ALA 166 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156P ILE* 3.2 9.2 - - - +
157P SER* 2.9 37.2 + - - +
165P LEU* 1.3 73.6 - - - +
167P SER* 1.3 62.8 + - - +
174P ILE* 4.7 1.8 - - + -
175P LYS 3.5 6.3 - - - +
176P LEU* 4.6 2.7 - - + +
198P VAL* 3.9 24.9 - - + -
200P ILE* 3.9 20.3 - - + +
207P ILE* 4.3 13.0 - - + -
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Residues in contact with SER 167 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132P ILE* 3.5 28.0 - - - -
149P HIS* 2.4 36.9 + - - -
153P VAL* 4.1 2.2 - - - -
155P ASP 3.5 9.2 - - - -
156P ILE* 5.0 1.3 - - - -
165P LEU* 4.1 0.9 + - - -
166P ALA* 1.3 75.3 - - - +
168P CYS* 1.3 62.4 + - - +
174P ILE* 3.3 30.0 - - - +
175P LYS 2.8 10.0 + - - -
177P TRP* 3.5 11.9 + - - -
198P VAL* 4.1 2.1 - - - +
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Residues in contact with CYS 168 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149P HIS* 4.2 1.8 - - - -
153P VAL* 3.1 11.2 - - - +
154P GLN 2.8 21.2 + - - -
155P ASP* 3.1 26.6 + - + +
167P SER* 1.3 76.6 + - - +
169P SER* 1.3 62.0 + - - +
173P THR 4.2 2.9 - - - -
174P ILE* 4.8 1.6 - - - -
195P VAL* 3.6 33.7 - - - +
197P SER 3.5 17.5 - - - -
198P VAL* 3.4 28.9 - - - -
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Residues in contact with SER 169 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149P HIS* 3.4 20.1 + - - -
152P SER 2.7 20.4 - - - -
154P GLN* 3.7 8.5 - - - -
168P CYS* 1.3 76.0 - - - +
170P ALA* 1.3 57.6 + - - +
171P ASP* 2.5 47.9 + - - +
172P MET 3.6 0.7 + - - -
173P THR 3.8 8.3 + - - -
195P VAL* 3.1 33.5 + - - +
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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