Contacts of the strand formed by residues 156 - 161 (chain A) in PDB entry 2VGO
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 MET 156 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141A GLU 5.0 1.1 - - - +
142A ILE* 4.0 33.2 - - + +
145A GLN* 4.0 31.5 + - + +
146A SER* 4.0 35.4 - - - +
154A LEU 3.7 2.6 + - - -
155A ARG* 1.3 83.5 + - - +
157A TYR* 1.3 64.9 + - - +
158A ASN* 3.6 13.1 + - - +
159A TYR* 4.1 7.6 - - + -
168A LEU* 3.8 27.1 - - + -
169A MET 3.4 14.1 - - - +
170A LEU* 3.8 21.8 - - + -
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Residues in contact with TYR 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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117A PHE* 3.6 30.2 - + - -
118A ILE 5.2 0.5 + - - -
119A MET* 3.8 19.9 - - + +
155A ARG* 3.5 30.3 + - + +
156A MET* 1.3 74.0 - - - +
158A ASN* 1.3 64.0 + - - +
169A MET* 2.8 20.2 + - + +
170A LEU 3.5 15.3 - - - -
171A GLU* 3.4 41.6 - - + +
172A PHE 4.6 0.9 + - - -
821D VAL* 3.9 35.0 - - + -
825D TYR* 3.9 33.3 - + + +
826D GLY* 4.4 4.9 + - - -
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Residues in contact with ASN 158 (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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88A PHE* 4.2 7.2 - - + -
146A SER* 6.5 0.2 - - - -
156A MET* 3.4 7.0 - - - +
157A TYR* 1.3 78.4 + - - +
159A TYR* 1.3 93.3 + - - +
169A MET* 2.9 46.7 + - + +
825D TYR* 2.9 25.9 + - + +
826D GLY* 5.2 0.4 - - - -
828D ILE* 3.1 29.9 + - - +
829D ASP 4.0 1.3 + - - +
830D SER* 2.7 25.9 + - - -
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Residues in contact with TYR 159 (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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88A PHE* 5.6 1.2 - - - +
142A ILE* 3.6 22.7 - - + -
143A GLU* 4.3 7.6 + - - -
146A SER* 4.1 16.6 + - - -
156A MET* 4.1 8.1 - - - -
158A ASN* 1.3 98.2 + - - +
160A PHE* 1.3 72.2 + - - +
166A ILE* 5.6 1.1 - - + -
167A TYR 3.2 15.0 - - - +
168A LEU* 3.9 14.6 - - + -
169A MET* 4.3 0.6 - - - +
829D ASP 5.0 1.0 - - - +
830D SER* 3.8 19.7 - - - -
831D PRO* 3.4 45.0 + - + +
833D LEU* 3.6 30.6 + - + +
836D LEU* 4.5 9.6 - - + -
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Residues in contact with PHE 160 (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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87A LYS* 5.8 2.2 - - + -
88A PHE* 3.3 40.2 - - + +
89A THR* 3.5 5.2 - - - -
90A ILE* 3.4 22.4 - - + -
93A PHE* 3.6 34.3 - + - -
121A LEU* 4.2 3.4 - - + -
159A TYR* 1.3 79.1 - - - +
161A HIS* 1.3 69.7 + - - +
162A ASP* 6.0 0.7 - - + -
166A ILE* 3.7 4.3 - - - +
167A TYR* 2.8 74.6 + + + +
169A MET* 3.9 19.5 - - + -
831D PRO* 4.0 13.7 - - + -
836D LEU* 4.8 1.3 - - - -
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Residues in contact with HIS 161 (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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87A LYS* 5.0 5.0 + - - -
88A PHE 5.3 1.6 - - - +
89A THR* 6.1 0.7 - - - +
126A LYS* 2.8 29.4 + - - -
160A PHE* 1.3 81.5 - - - +
162A ASP* 1.3 61.2 + - - +
165A ARG 3.2 13.9 - - - +
166A ILE* 4.2 2.9 - - + -
167A TYR* 4.3 4.7 - - - -
831D PRO* 3.5 33.5 - - + +
835D GLU* 3.6 21.9 + - - +
836D LEU* 3.8 16.1 + - + -
839D LYS 3.4 25.6 + - - -
840D SER* 3.6 18.4 - - - -
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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