Contacts of the strand formed by residues 132 - 136 (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 ILE 132 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124P VAL* 3.3 32.5 - - + -
125P SER 3.3 4.7 - - - +
126P ALA* 4.6 0.4 - - + -
131P THR* 1.3 75.0 - - - +
133P LYS* 1.3 58.9 + - - +
134P VAL* 5.1 0.9 - - + -
145P THR* 3.6 2.9 - - - +
146P LEU* 2.7 61.9 + - + +
149P HIS* 4.6 3.6 - - + -
153P VAL* 4.1 17.3 - - + -
156P ILE* 4.4 11.7 - - + -
165P LEU* 4.2 6.5 - - + -
167P SER* 3.5 32.1 - - - +
177P TRP* 3.7 28.0 - - + +
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Residues in contact with LYS 133 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106P GLY 3.9 20.5 + - - -
107P HIS* 3.5 36.3 - - + +
124P VAL* 3.4 4.9 - - - +
125P SER* 2.8 39.0 + - - +
129P ASP* 4.1 13.7 - - - -
131P THR* 4.0 5.1 + - - -
132P ILE* 1.3 72.4 - - - +
134P VAL* 1.3 62.7 + - - +
135P TRP* 3.7 20.2 + - + +
142P PHE* 4.7 14.6 - - + +
144P ARG 3.7 5.4 - - - +
145P THR* 3.2 42.8 + - + +
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Residues in contact with VAL 134 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122P VAL* 3.5 30.7 - - + -
123P MET 3.7 4.0 - - - +
124P VAL* 3.7 18.4 - - + -
132P ILE* 5.1 0.4 - - + -
133P LYS* 1.3 75.4 - - - +
135P TRP* 1.3 61.9 + - - +
142P PHE 3.4 5.9 - - - -
143P GLU* 2.9 47.2 + - + +
144P ARG* 3.0 33.5 + - + +
146P LEU* 5.0 11.9 - - + -
179P PHE* 4.1 17.5 - - + -
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Residues in contact with TRP 135 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104P LEU* 3.5 54.3 - - + -
105P SER 3.6 29.8 - - - -
106P GLY* 4.3 3.1 - - - -
107P HIS* 4.0 22.9 - + - -
122P VAL* 3.4 5.8 - - - +
123P MET* 2.5 70.3 + - + +
125P SER* 3.1 19.2 + - - -
133P LYS* 3.7 19.2 + - + -
134P VAL* 1.3 74.7 - - - +
136P ASP* 1.3 61.4 + - - +
141P ASP* 3.6 13.9 - - - +
142P PHE* 4.1 36.8 - + - -
143P GLU* 4.4 0.2 - - - -
404P VAL* 4.7 3.5 - - + +
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Residues in contact with ASP 136 (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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121P SER* 3.2 28.6 + - - +
122P VAL* 3.2 15.1 - - - +
135P TRP* 1.3 66.3 + - - +
137P TYR* 1.3 57.7 + - - +
138P GLU* 3.2 12.0 - - - +
139P THR* 3.1 32.8 + - - -
140P GLY* 2.4 42.6 + - - +
141P ASP* 4.3 13.7 - - + +
143P GLU* 3.8 23.3 - - + +
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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