Contacts of the strand formed by residues 117 - 125 (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 PHE 117 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111A ARG* 3.5 0.8 - - - -
112A GLU* 2.9 29.6 + - - +
115A ASN* 3.1 12.5 - - + +
116A LYS* 1.3 75.5 - - - +
118A ILE* 1.3 70.6 - - - +
119A MET* 3.7 11.8 + - + +
157A TYR* 3.6 41.3 - + - -
814D GLN* 3.4 37.7 - - + -
818D PRO* 6.0 0.7 - - + -
819D ILE* 3.7 32.3 - - + -
821D VAL* 4.1 9.6 - - + -
825D TYR* 3.3 32.5 - + - +
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Residues in contact with ILE 118 (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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109A LEU* 3.6 29.6 - - + -
110A ALA 3.4 5.6 - - - +
111A ARG* 4.0 19.7 - - + -
116A LYS 4.6 2.7 - - - +
117A PHE* 1.3 78.8 - - - +
119A MET* 1.3 64.3 + - - +
157A TYR* 5.2 0.5 + - - -
172A PHE* 4.1 8.6 + - + +
801D TRP* 4.0 18.2 - - + +
807D LEU* 3.8 18.6 - - + -
810D ALA* 3.8 29.6 - - + -
811D ILE* 3.9 18.6 - - + -
814D GLN* 2.8 36.0 + - - +
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Residues in contact with MET 119 (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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93A PHE* 3.8 22.2 - - + -
109A LEU* 3.8 7.4 - - - +
110A ALA* 2.8 38.2 + - + +
112A GLU* 4.3 6.5 - - + -
117A PHE* 3.7 14.6 - - + +
118A ILE* 1.3 75.2 - - - +
120A ALA* 1.3 65.5 + - - +
121A LEU* 5.0 1.1 - - + -
157A TYR* 3.8 21.3 - - + -
169A MET* 3.7 37.5 - - + -
170A LEU 3.3 11.2 - - - +
172A PHE* 3.9 13.0 - - - +
825D TYR* 3.6 32.5 - - + +
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Residues in contact with ALA 120 (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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99A LEU* 4.2 7.0 - - + -
107A VAL* 4.0 9.0 - - + -
108A TYR 3.3 9.0 - - - +
109A LEU* 4.8 0.2 - - - +
119A MET* 1.3 77.2 - - - +
121A LEU* 1.3 63.4 + - - +
122A LYS 4.1 0.4 - - - -
168A LEU 3.5 0.9 - - - +
169A MET* 3.7 2.4 - - - -
170A LEU* 2.8 36.6 + - - +
171A GLU 4.3 1.1 - - - +
172A PHE* 4.1 3.3 - - - +
1357A AD5 3.5 40.8 - - + +
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Residues in contact with LEU 121 (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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90A ILE* 3.7 30.7 - - + -
93A PHE* 3.9 24.2 - - + -
95A ILE* 4.0 6.3 - - + -
106A ASN 3.7 1.6 - - - +
107A VAL* 3.3 4.4 - - - -
108A TYR* 2.8 46.1 + - + +
110A ALA* 4.0 18.8 - - + +
119A MET* 4.3 1.5 - - + -
120A ALA* 1.3 72.3 - - - +
122A LYS* 1.3 59.7 + - - +
123A VAL* 3.8 8.4 + - + -
160A PHE* 4.2 13.0 - - + -
167A TYR* 4.4 8.3 - - + -
168A LEU 3.4 8.5 - - - +
169A MET* 3.7 31.6 - - + -
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Residues in contact with LYS 122 (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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105A GLY 6.5 0.7 - - - -
106A ASN 3.5 4.9 - - - +
107A VAL* 3.9 23.3 - - + +
120A ALA 4.1 0.8 - - - -
121A LEU* 1.3 72.0 - - - +
123A VAL* 1.3 61.7 + - - +
124A LEU* 4.0 25.8 - - + -
141A GLU* 5.9 0.8 + - - -
166A ILE 3.5 1.7 - - - +
167A TYR* 3.3 4.9 - - - -
168A LEU* 2.8 59.8 + - + +
170A LEU* 3.9 24.0 - - + +
234A ASP* 5.1 8.5 + - - -
1357A AD5 5.6 7.3 - - - +
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Residues in contact with VAL 123 (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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90A ILE* 5.7 1.1 - - + -
105A GLY* 3.0 26.2 - - - -
106A ASN* 2.7 17.7 + - - +
108A TYR* 3.9 30.5 - - + -
121A LEU* 4.1 9.0 - - + +
122A LYS* 1.3 76.7 - - - +
124A LEU* 1.3 64.5 + - - +
125A PHE* 4.9 6.3 - - + -
165A ARG* 3.6 38.4 - - + +
166A ILE 3.5 2.7 - - - -
167A TYR* 3.7 27.1 - - + -
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Residues in contact with LEU 124 (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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104A PHE* 3.5 24.7 - - + +
105A GLY* 4.2 2.9 - - - +
122A LYS* 4.0 29.4 - - + +
123A VAL* 1.3 84.5 - - - +
125A PHE* 1.3 63.6 + - - +
129A LEU* 3.9 19.5 - - + -
138A LEU* 3.5 40.4 - - + -
165A ARG* 3.2 6.7 - - - +
166A ILE* 2.8 42.3 + - + +
168A LEU* 4.5 13.5 - - + -
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Residues in contact with PHE 125 (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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104A PHE 3.2 19.0 + - - +
105A GLY* 4.5 12.8 - - - -
106A ASN* 4.9 9.4 - - - -
123A VAL* 5.0 6.3 - - + -
124A LEU* 1.3 73.4 - - - +
126A LYS* 1.3 66.1 + - - +
127A SER* 3.3 3.0 + - - +
128A GLN* 3.3 22.5 + - + +
129A LEU* 3.2 24.3 + - - +
164A LYS* 3.7 11.0 - - + -
165A ARG* 3.3 52.5 - - + -
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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