Contacts of the strand formed by residues 117 - 125 (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 PHE 117 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B ARG* 3.4 0.8 - - - -
112B GLU* 2.8 32.0 + - - +
115B ASN* 4.0 10.5 - - + +
116B LYS* 1.3 73.5 - - - +
118B ILE* 1.3 71.4 + - - +
119B MET* 3.6 11.0 + - + +
157B TYR* 3.5 37.5 - + - -
814C GLN* 3.4 37.2 - - + -
818C PRO* 6.0 0.4 - - + -
819C ILE* 3.6 32.5 - - + -
821C VAL* 3.7 13.0 - - + -
825C TYR* 3.2 36.6 - + - +
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Residues in contact with ILE 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B LEU* 3.6 31.0 - - + -
110B ALA 3.3 7.2 - - - +
111B ARG* 4.3 12.8 - - + +
116B LYS 4.7 2.5 - - - +
117B PHE* 1.3 77.7 - - - +
119B MET* 1.3 65.4 + - - +
157B TYR* 5.1 0.7 + - - -
172B PHE* 4.3 9.0 + - + +
801C TRP* 4.2 19.1 - - + +
807C LEU* 4.0 12.8 - - + -
810C ALA* 3.7 29.6 - - + -
811C ILE* 3.7 29.6 - - + -
814C GLN* 2.9 36.9 + - - +
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Residues in contact with MET 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B PHE* 3.7 26.5 - - + -
109B LEU* 3.7 7.8 - - - +
110B ALA* 2.8 37.5 + - + +
112B GLU* 4.1 7.0 - - + -
117B PHE* 3.6 26.5 - - + +
118B ILE* 1.3 75.6 - - - +
120B ALA* 1.3 65.0 + - - +
121B LEU* 5.6 0.9 - - + -
157B TYR* 3.7 18.6 - - + -
169B MET* 3.9 29.2 - - + -
170B LEU 3.3 11.9 - - - +
172B PHE* 4.0 13.5 - - - +
825C TYR* 3.7 25.8 - - + +
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Residues in contact with ALA 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B LEU* 4.0 10.5 - - + -
107B VAL* 3.8 22.9 - - + -
108B TYR 3.3 5.6 - - - +
119B MET* 1.3 77.9 - - - +
121B LEU* 1.3 60.9 + - - +
122B LYS 4.1 0.9 - - - -
168B LEU 3.6 0.7 - - - +
169B MET* 3.7 2.8 - - - -
170B LEU* 2.7 39.9 + - + +
171B GLU 4.4 1.1 - - - +
172B PHE* 4.2 2.9 - - - +
1359B AD5 3.8 23.6 - - + +
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Residues in contact with LEU 121 (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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90B ILE* 3.6 31.4 - - + -
93B PHE* 4.4 17.3 - - + -
95B ILE* 3.8 17.9 - - + -
106B ASN 3.7 0.5 - - - +
107B VAL* 3.5 3.1 - - - -
108B TYR* 2.8 45.4 + - + +
110B ALA* 4.1 10.1 - - + +
119B MET* 5.6 0.7 - - + -
120B ALA* 1.3 73.0 - - - +
122B LYS* 1.3 62.4 + - - +
123B VAL* 3.7 7.3 + - + +
160B PHE* 4.0 15.5 - - + -
167B TYR* 4.3 14.4 - - + -
168B LEU 3.4 8.3 - - - +
169B MET* 3.8 29.6 - - + -
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Residues in contact with LYS 122 (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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102B GLY* 5.2 0.2 - - - -
103B LYS* 3.4 38.7 + - - +
104B PHE* 5.0 3.0 - - - -
105B GLY 4.4 5.4 - - - +
106B ASN 3.5 5.6 - - - +
107B VAL* 3.8 27.1 - - + +
120B ALA 4.1 0.8 - - - -
121B LEU* 1.3 71.6 - - - +
123B VAL* 1.3 60.7 + - - +
124B LEU* 3.5 16.1 - - + +
138B LEU* 5.7 0.6 - - - +
141B GLU* 4.0 18.2 + - - -
166B ILE 3.5 2.1 - - - +
167B TYR* 3.4 5.7 - - - -
168B LEU* 2.9 58.8 + - + +
170B LEU* 4.0 25.6 - - + +
234B ASP* 5.7 0.6 + - - -
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Residues in contact with VAL 123 (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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90B ILE* 5.8 0.9 - - + -
105B GLY* 3.2 22.3 - - - -
106B ASN* 2.9 16.5 + - + +
108B TYR* 3.7 30.3 - - + -
121B LEU* 4.1 9.0 - - + +
122B LYS* 1.3 74.5 - - - +
124B LEU* 1.3 62.5 + - - +
125B PHE* 4.2 17.4 + - + -
165B ARG* 3.9 33.0 - - + -
166B ILE 3.7 2.2 - - - -
167B TYR* 3.9 26.0 - - + -
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Residues in contact with LEU 124 (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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104B PHE* 3.7 39.5 - - + +
122B LYS* 3.5 34.3 - - + +
123B VAL* 1.3 75.4 - - - +
125B PHE* 1.3 64.2 + - - +
126B LYS 3.6 0.2 + - - -
129B LEU* 3.8 13.7 - - + -
138B LEU* 3.7 36.1 - - + -
165B ARG* 3.2 5.5 - - - -
166B ILE* 2.8 52.3 + - + +
168B LEU* 3.9 17.5 - - + -
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Residues in contact with PHE 125 (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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104B PHE 4.6 5.2 + - - +
106B ASN* 5.5 6.7 - - - -
123B VAL* 4.4 17.9 - - + -
124B LEU* 1.3 73.2 - - - +
126B LYS* 1.3 66.3 + - - +
127B SER* 4.4 8.1 - - - +
128B GLN* 3.0 30.2 + - + +
129B LEU* 3.0 15.3 + - - +
164B LYS* 3.5 34.8 - - + -
165B ARG* 3.7 27.6 - - + -
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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