Contacts of the strand formed by residues 111 - 116 (chain B) in PDB entry 6VMS
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 TYR 111 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105B TYR* 4.9 0.2 - - - -
106B ALA* 3.1 30.2 + - + +
109B GLY 3.4 1.6 - - - -
110B ASN* 1.3 101.6 + - + +
112B VAL* 1.3 67.9 + - - +
123B ILE* 4.1 13.9 - - + -
124B TYR 3.4 10.5 - - - +
125B ASN* 4.1 27.8 + - + -
136B SER* 4.7 8.7 - - - -
151B PHE* 4.0 19.9 - + + -
154B ASP* 3.8 44.4 - - + -
171B ILE* 6.0 6.3 - - + -
172B GLU* 4.8 9.8 + - - -
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Residues in contact with VAL 112 (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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71B VAL* 4.1 7.4 - - + -
79B LEU* 3.9 29.4 - - + -
81B ILE* 4.0 7.6 - - + -
93B ILE* 5.2 0.7 - - + -
104B ALA 3.2 16.4 - - - +
105B TYR* 4.1 11.4 - - + -
111B TYR* 1.3 78.6 - - - +
113B ALA* 1.3 65.4 + - - +
122B SER 3.7 1.2 - - - +
123B ILE* 3.3 3.6 - - - -
124B TYR* 2.8 43.3 + - + +
126B LEU* 3.4 37.5 - - + -
151B PHE* 4.3 3.4 - - - -
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Residues in contact with ALA 113 (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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103B CYS* 3.2 2.9 - - - +
104B ALA* 2.9 32.5 + - + +
112B VAL* 1.3 77.0 - - - +
114B CYS* 1.3 66.0 + - - +
121B CYS* 4.3 0.2 - - - -
122B SER 3.7 0.4 - - - -
123B ILE* 3.2 25.8 - - + -
149B CYS* 3.3 28.9 - - - -
151B PHE* 3.3 16.8 - - + -
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Residues in contact with CYS 114 (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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79B LEU* 3.4 20.2 - - + -
95B LEU* 3.5 24.5 - - - -
100B VAL* 4.0 4.3 - - + -
102B THR* 3.4 20.9 - - - +
113B ALA* 1.3 78.1 - - - +
115B GLY* 1.3 60.7 + - - +
121B CYS* 3.5 6.7 - - - -
122B SER* 2.8 37.1 + - - +
124B TYR* 3.5 31.4 - - - -
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Residues in contact with GLY 115 (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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100B VAL* 3.1 11.7 - - - +
101B MET 2.9 19.9 + - - -
102B THR* 3.2 19.4 + - - +
114B CYS* 1.3 79.7 - - - +
116B GLY* 1.3 58.3 + - - -
118B ASP* 4.4 3.8 - - - -
120B ILE 3.8 9.4 - - - -
122B SER* 5.9 0.4 - - - -
146B LEU* 3.8 11.9 - - - -
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Residues in contact with GLY 116 (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 TRP 3.2 9.8 + - - -
101B MET* 3.9 9.0 - - - -
115B GLY* 1.3 75.1 - - - -
117B LEU* 1.3 56.1 + - - -
118B ASP* 2.8 28.1 + - - +
119B ASN 3.4 4.0 + - - -
145B TYR* 3.9 0.8 - - - -
146B LEU* 3.3 37.5 + - - +
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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