Contacts of the strand formed by residues 156 - 161 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B GLU* 4.9 2.2 - - + +
142B ILE* 4.0 26.5 - - - +
145B GLN* 3.8 41.5 + - + +
146B SER* 4.1 26.9 - - - +
154B LEU 3.6 2.6 + - - -
155B ARG* 1.3 80.4 + - - +
157B TYR* 1.3 62.3 + - - +
158B ASN* 3.8 12.0 - - - +
159B TYR* 4.0 23.1 - - + -
168B LEU* 4.0 29.6 - - + -
169B MET 3.4 13.9 - - - +
170B LEU* 3.8 13.2 - - + -
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Residues in contact with TYR 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B PHE* 3.5 23.6 - + - -
118B ILE 5.1 0.5 + - - -
119B MET* 3.7 25.4 - - + -
149B ARG* 5.7 0.7 + - - -
155B ARG* 3.6 28.7 + - + +
156B MET* 1.3 73.0 - - - +
158B ASN* 1.3 63.6 + - - +
169B MET* 2.8 29.0 + - + +
170B LEU 3.6 7.9 - - - -
171B GLU* 3.4 42.5 - - + +
172B PHE 4.6 0.9 + - - -
821C VAL* 4.0 35.2 - - + -
825C TYR* 3.7 34.4 - + + +
826C GLY* 4.2 5.7 + - - -
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Residues in contact with ASN 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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88B PHE* 4.1 5.8 - - + -
146B SER* 6.4 0.2 - - - -
156B MET* 3.4 7.2 - - - +
157B TYR* 1.3 79.4 + - - +
159B TYR* 1.3 91.8 + - - +
169B MET* 2.9 48.6 + - + +
825C TYR 2.9 24.0 + - - +
826C GLY 4.9 1.6 + - - -
828C ILE* 3.0 30.1 + - - +
829C ASP 3.8 3.4 + - - +
830C SER* 2.6 24.0 + - - -
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Residues in contact with TYR 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B PHE* 5.3 2.1 + - - +
142B ILE* 3.7 28.2 - - + +
146B SER* 4.0 19.3 + - - -
156B MET* 4.0 8.3 - - - -
158B ASN* 1.3 97.9 + - - +
160B PHE* 1.3 71.9 + - - +
166B ILE* 5.5 0.9 - - + -
167B TYR 3.2 15.3 - - - +
168B LEU* 3.8 15.9 - - + -
169B MET* 4.3 0.4 - - - +
829C ASP 4.9 1.0 - - - +
830C SER* 3.7 22.1 - - - -
831C PRO* 3.3 46.2 + - + +
833C LEU* 3.8 23.4 - - + +
836C LEU* 4.5 10.1 - - + -
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Residues in contact with PHE 160 (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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87B LYS* 5.0 3.6 - - + -
88B PHE* 3.1 40.6 - - + +
89B THR* 3.5 5.8 - - - -
90B ILE* 3.4 24.2 - - + -
93B PHE* 3.6 33.9 - + - -
121B LEU* 4.0 4.7 - - + -
159B TYR* 1.3 79.0 - - - +
161B HIS* 1.3 69.2 + - - +
166B ILE* 3.7 3.1 - - - +
167B TYR* 2.8 76.3 + + + +
169B MET* 3.9 16.6 - - + -
831C PRO* 3.9 15.0 - - + -
836C LEU* 4.7 1.1 - - - -
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Residues in contact with HIS 161 (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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87B LYS* 4.1 10.8 + - - +
126B LYS* 3.0 30.5 - - - +
160B PHE* 1.3 83.2 - - - +
162B ASP* 1.3 65.9 + - - +
165B ARG 3.3 15.0 - - - +
166B ILE* 4.1 3.6 - - - -
167B TYR* 4.1 5.6 - - - -
831C PRO* 3.5 30.9 - - + +
835C GLU* 3.6 37.2 + - + +
836C LEU* 3.6 16.8 - - + -
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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