Contacts of the strand formed by residues 152 - 157 (chain A) in PDB entry 2VGM
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 ALA 152 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145A VAL* 4.6 4.0 - - + -
146A VAL 3.1 6.1 - - - +
147A LEU* 3.8 7.6 - - + -
151A ILE* 1.3 76.1 - - - +
153A HIS* 1.3 72.0 + - - +
154A VAL 4.2 0.7 - - - +
167A LYS* 3.8 0.3 - - - -
168A ILE* 2.9 34.5 + - + +
191A PHE* 3.6 7.2 - - + -
195A ILE* 3.1 42.0 - - + -
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Residues in contact with HIS 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A VAL* 3.1 24.6 - - - -
146A VAL* 2.8 30.1 + - + +
151A ILE* 3.4 35.8 - - + +
152A ALA* 1.3 83.1 + - - +
154A VAL* 1.3 62.2 + - - +
155A CYS* 3.4 6.9 + - - -
164A LEU* 3.5 18.7 - - + +
166A GLN 3.8 4.5 - - - -
167A LYS* 4.0 21.8 - - + +
254A GLY 3.4 26.3 + - - -
255A TYR* 3.7 19.2 - + - -
256A LEU* 4.0 19.3 - - + +
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Residues in contact with VAL 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A ALA 3.9 4.3 - - - +
145A VAL* 4.4 2.6 - - + +
152A ALA* 4.2 0.8 - - - +
153A HIS* 1.3 70.7 - - - +
155A CYS* 1.3 61.1 + - - +
164A LEU* 2.9 23.0 - - - +
165A LYS* 3.0 29.9 + - + -
166A GLN* 3.4 16.7 + - + +
168A ILE* 4.9 3.1 - - + +
195A ILE* 4.2 10.1 - - + +
198A ALA* 4.1 23.8 - - + +
199A MET* 3.5 26.9 - - + +
202A ASP* 4.3 5.6 - - + -
203A LEU* 3.8 30.1 - - + -
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Residues in contact with CYS 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A ALA* 3.7 1.4 - - - +
144A ALA* 2.9 40.7 + - + +
146A VAL* 4.7 3.6 - - - -
153A HIS* 4.1 9.4 - - - +
154A VAL* 1.3 81.0 - - - +
156A LEU* 1.3 64.9 + - - +
162A THR* 4.2 11.2 - - + -
163A ILE 3.7 4.5 - - - -
164A LEU* 3.9 20.0 - - - -
165A LYS* 4.2 4.0 - - - -
203A LEU* 3.5 18.5 - - - +
256A LEU* 3.4 34.1 - - - -
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Residues in contact with LEU 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A ILE 5.3 4.0 - - - +
137A GLU* 5.3 8.7 - - + +
140A SER* 3.7 30.3 - - - +
142A THR 4.0 12.6 - - - +
143A ALA* 4.3 4.0 - - + -
155A CYS* 1.3 81.1 - - - +
157A VAL* 1.3 62.4 - - - +
158A THR* 3.3 12.8 + - + +
162A THR 4.6 1.3 - - - -
163A ILE* 2.9 37.7 + - + +
165A LYS* 3.8 27.4 - - - +
203A LEU* 4.5 9.9 - - + -
204A ASN 6.2 0.4 - - - +
208A LEU* 4.2 20.2 - - + -
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Residues in contact with VAL 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A SER* 3.6 16.3 - - - -
141A ASP 4.7 0.2 + - - -
142A THR* 2.9 47.6 + - + +
144A ALA* 4.5 11.2 - - + -
156A LEU* 1.3 69.8 - - - +
158A THR* 1.3 70.9 + - - +
161A SER 3.9 3.8 - - - +
162A THR* 4.4 12.6 - - + +
212A ILE* 5.8 0.4 - - + -
259A ILE* 3.9 24.9 - - + -
263A LEU* 4.4 21.3 - - + -
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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