Contacts of the strand formed by residues 120 - 124 (chain V) in PDB entry 1I84
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 120 (chain V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116V TYR* 4.2 0.9 - - - +
117V SER* 3.0 61.9 + - - +
118V GLY 4.0 0.5 - - - +
119V LEU* 1.3 82.7 - - + +
121V CYS* 1.3 59.9 + - - +
122V VAL* 5.3 0.2 - - + -
493V PHE* 4.1 17.0 - + + -
497V MET* 4.5 7.0 - - - -
681V PHE* 3.6 35.2 - - + +
683V ARG* 3.3 31.2 - - + -
710V VAL* 3.4 42.2 - - + -
713V GLY* 3.0 33.7 - - - -
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Residues in contact with CYS 121 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114V TYR* 4.8 4.7 - - - -
115V THR 3.2 15.3 - - - +
116V TYR* 3.5 24.5 - - + -
117V SER* 3.6 2.0 - - - -
119V LEU 5.0 0.9 - - - +
120V PHE* 1.3 78.8 - - - +
122V VAL* 1.3 71.4 + - - +
123V VAL* 3.7 10.7 - - - +
156V ILE* 3.5 32.1 - - + -
681V PHE 3.4 5.6 + - - +
682V VAL* 3.7 4.3 - - - -
683V ARG* 3.2 24.6 + - - -
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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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89V MET* 5.2 2.7 - - + -
104V LEU* 4.5 27.6 - - + -
113V ILE 4.4 1.1 - - - -
115V THR* 2.8 30.9 + - - +
117V SER* 3.4 22.0 - - - +
121V CYS* 1.3 70.3 - - - +
123V VAL* 1.3 82.6 + - - +
124V ILE* 4.6 6.5 - - + +
683V ARG* 3.8 10.8 - - + +
685V ILE* 3.5 35.7 - - + -
705V LEU* 4.4 5.2 - - + -
710V VAL* 4.6 16.6 - - + -
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Residues in contact with VAL 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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113V ILE* 3.6 13.0 - - + -
114V TYR* 3.7 39.3 - - + -
121V CYS* 3.7 12.6 - - - +
122V VAL* 1.3 93.1 - - - +
124V ILE* 1.3 62.6 + - - +
125V ASN* 3.2 4.4 + - - -
126V PRO* 6.4 0.2 - - + -
181V ALA 4.6 2.6 - - - +
186V ASN* 3.7 23.3 - - - +
682V VAL* 3.8 19.5 - - + +
683V ARG 3.6 4.9 + - - -
684V CYS* 4.2 11.5 - - - -
685V ILE 3.8 12.0 + - - -
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Residues in contact with ILE 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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104V LEU* 3.9 50.0 - - + +
108V TYR* 3.7 26.9 - - + -
113V ILE* 3.1 35.9 + - + +
115V THR* 5.3 0.7 - - - +
122V VAL* 4.6 3.4 - - + -
123V VAL* 1.3 69.7 - - - +
125V ASN* 1.3 78.5 + - - +
126V PRO* 3.2 0.7 - - - +
685V ILE* 3.4 28.5 - - + +
687V PRO* 3.8 21.1 - - + -
696V LEU* 5.4 4.5 - - + -
701V VAL* 5.0 7.6 - - + -
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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