Contacts of the strand formed by residues 118 - 124 (chain V) in PDB entry 4UJ3
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 VAL 118 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85V VAL 3.2 7.6 + - - +
86V GLY* 3.4 0.9 - - - -
87V ALA 2.9 26.7 + - - +
116V ASN 3.3 1.5 + - - +
117V ILE* 1.3 69.9 - - - +
119V ILE* 1.3 67.1 + - - +
149V SER* 5.0 0.4 - - - +
168V ILE* 3.9 20.5 - - + +
171V GLU* 3.6 29.8 - - + +
172V ILE* 3.2 40.8 - - + +
175V ILE* 4.2 22.0 - - + -
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Residues in contact with ILE 119 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87V ALA* 3.7 7.2 - - + +
89V LEU* 4.5 11.0 - - + -
106V LEU* 3.8 20.4 - - + -
109V LEU* 3.2 39.7 - - + -
110V ARG* 5.9 3.1 - - + -
117V ILE* 3.3 23.6 + - + +
118V VAL* 1.3 78.1 - - - +
120V MET* 1.3 69.4 + - - +
147V GLY 4.7 1.8 + - - +
148V LEU* 3.2 31.5 - - + +
149V SER* 3.4 21.0 + - - -
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Residues in contact with MET 120 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87V ALA 3.1 7.1 + - - -
88V LEU* 3.2 38.7 - - + -
89V LEU* 2.8 28.9 + - - +
118V VAL 4.2 0.4 - - - -
119V ILE* 1.3 77.6 - - - +
121V LEU* 1.3 69.6 + - - +
122V VAL* 3.6 11.6 + - + +
149V SER* 3.3 31.0 - - - +
150V PHE 4.3 0.9 - - - +
151V ILE* 4.0 13.0 - - + -
164V ALA* 3.4 45.5 - - + +
167V THR* 4.6 10.3 - - - -
168V ILE* 4.2 13.0 - - + +
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Residues in contact with LEU 121 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89V LEU* 3.4 26.0 - - + +
91V TYR* 4.1 25.4 - - + -
99V TYR* 4.5 8.1 - - + -
102V VAL* 3.8 23.8 - - + -
119V ILE 4.2 0.4 - - - -
120V MET* 1.3 73.4 - - - +
122V VAL* 1.3 62.7 + - - +
139V ALA 4.2 13.7 - - - +
142V PHE* 4.0 26.9 - - + -
143V ALA* 4.4 4.5 - - + -
148V LEU* 4.4 13.9 - - + +
149V SER 2.9 14.3 + - - +
150V PHE* 3.4 16.2 - - + -
151V ILE 3.3 22.7 + - - -
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Residues in contact with VAL 122 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27V LEU* 4.4 12.8 - - + -
88V LEU* 4.2 9.9 - - + -
89V LEU 2.8 12.5 + - - +
90V VAL* 3.5 14.0 - - + +
91V TYR* 3.0 33.7 + - - +
120V MET* 3.6 36.3 - - + +
121V LEU* 1.3 80.9 - - - +
123V GLY* 1.3 63.9 + - - +
124V ASN 3.8 1.0 + - - +
151V ILE* 3.4 5.4 - - + +
153V THR* 3.5 39.3 - - + +
164V ALA* 5.2 0.9 - - + -
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Residues in contact with GLY 123 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91V TYR* 3.5 18.0 - - - -
93V ILE* 3.0 27.7 - - - +
121V LEU 4.3 0.4 - - - -
122V VAL* 1.3 72.3 - - - +
124V ASN* 1.3 52.8 + - - -
150V PHE* 4.5 1.2 - - - -
151V ILE 3.1 11.0 + - - -
152V GLU* 3.1 6.5 - - - +
153V THR 2.5 34.8 + - - +
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Residues in contact with ASN 124 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22V VAL 3.1 26.8 + - - +
23V GLY* 3.8 9.3 + - - -
27V LEU* 3.4 11.9 - - + +
90V VAL* 4.1 9.6 - - + -
91V TYR 3.1 12.3 + - - +
92V ASP* 4.0 0.5 - - - +
93V ILE* 3.1 21.1 + - - +
122V VAL* 3.8 0.4 + - + -
123V GLY* 1.3 72.7 - - - -
125V LYS* 1.3 79.2 + - - +
126V SER 3.2 2.2 - - - -
153V THR* 2.8 24.4 + - - +
155V ALA* 3.2 20.0 + - - +
200V GNP 3.2 28.4 + - - -
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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