Contacts of the strand formed by residues 152 - 159 (chain B) in PDB entry 1VCA
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 LYS 152 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114B SER* 3.4 1.5 - - - -
115B VAL 3.0 30.4 + - - -
118B VAL* 5.7 0.2 - - + -
121B PHE* 3.9 40.3 - - + -
124B LEU* 3.9 24.2 - - + -
126B ILE* 3.9 4.9 - - - +
140B PHE* 3.5 40.1 - - + -
150B GLU* 4.0 16.5 + - + +
151B THR* 1.3 88.3 - - - +
153B SER* 1.3 64.7 + - - +
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Residues in contact with SER 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B LYS* 3.6 24.7 - - - +
113B CYS 3.0 17.0 - - - -
114B SER* 3.7 14.1 - - - -
126B ILE* 4.2 6.3 - - - -
138B GLN* 4.1 15.8 - - - +
140B PHE* 4.2 5.8 - - - -
151B THR* 5.9 0.7 - - - -
152B LYS* 1.3 77.1 - - - +
154B LEU* 1.3 62.5 + - - +
155B GLU* 5.5 0.7 - - - +
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Residues in contact with LEU 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B VAL 5.1 0.4 - - - +
112B LYS* 3.4 3.8 - - - +
113B CYS* 2.8 40.0 + - + +
126B ILE* 3.3 40.4 - - + +
128B LEU* 3.7 35.4 - - + +
136B LYS* 3.9 34.8 - - + +
138B GLN* 3.7 24.5 - - + +
153B SER* 1.3 73.9 - - - +
155B GLU* 1.3 72.5 + - - +
156B VAL* 4.6 0.9 - - + +
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Residues in contact with GLU 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B THR* 3.9 18.2 - - + +
111B VAL 3.3 5.6 - - - +
112B LYS* 3.4 48.7 + - + +
136B LYS* 3.0 27.7 + - - +
153B SER* 5.5 1.1 - - - +
154B LEU* 1.3 74.3 - - - +
156B VAL* 1.3 63.3 + - - +
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Residues in contact with VAL 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B ILE 4.0 0.3 - - - +
110B THR* 3.4 2.3 - - - -
111B VAL* 2.8 42.2 + - + +
128B LEU* 3.4 33.4 - - + -
135B MET* 4.6 24.7 - - + +
136B LYS* 4.5 20.2 - - + +
154B LEU* 4.7 1.3 - - + -
155B GLU* 1.3 76.2 - - - +
157B THR* 1.3 73.8 + - - +
158B PHE* 4.8 3.1 - - + -
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Residues in contact with THR 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B PRO* 4.3 19.3 - - + -
109B ILE 3.2 14.6 - - - +
110B THR* 3.1 24.3 + - - +
156B VAL* 1.3 83.1 - - - +
158B PHE* 1.3 67.6 + - - +
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Residues in contact with PHE 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B LEU* 6.2 0.9 - - + -
103B LEU* 4.5 13.9 - - + -
108B PRO* 3.5 2.1 - - - +
109B ILE* 2.9 61.5 + - + +
111B VAL* 3.5 24.9 - - + -
130B LYS* 3.7 35.9 - - + -
135B MET* 4.4 25.8 - - + -
156B VAL* 4.8 4.3 - - + -
157B THR* 1.3 78.4 - - - +
159B THR* 1.3 72.9 + - - +
160B PRO* 4.3 15.3 - - + -
164B ASP* 4.3 2.9 - - - -
169B LEU* 5.4 4.9 - - + -
193B LEU* 5.1 3.8 - - + -
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Residues in contact with THR 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B GLY* 3.5 40.8 - - - +
107B LYS 4.0 2.0 - - - +
108B PRO* 4.0 15.6 - - - +
158B PHE* 1.3 83.6 + - - +
160B PRO* 1.3 66.8 - - - +
161B VAL* 3.7 9.2 + - + +
164B ASP* 4.6 0.7 - - - +
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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