Contacts of the strand formed by residues 678 - 681 (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 ASN 678 (chain V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163V SER* 5.1 2.8 + - - -
169V GLU* 3.8 15.8 - - - +
170V ASP 2.8 11.4 + - - +
171V GLN* 3.1 35.6 + - - +
172V SER* 2.6 29.8 + - - -
677V THR* 1.3 75.6 - - - +
679V PRO* 1.3 81.9 + - - +
680V ASN* 2.8 10.6 + - - +
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Residues in contact with PRO 679 (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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172V SER* 3.0 14.5 - - - +
174V LEU* 4.0 10.8 - - + -
492V LEU* 6.0 2.5 - - + -
496V THR* 4.4 22.0 - - + -
674V LEU 5.0 4.0 - - - +
677V THR* 3.5 8.7 - - - +
678V ASN* 1.3 98.2 + - - +
680V ASN* 1.3 67.6 + - - +
681V PHE* 3.9 27.9 - - + -
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Residues in contact with ASN 680 (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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156V ILE* 4.4 14.1 - - + +
159V THR* 5.3 4.5 - - - +
160V ALA* 3.8 24.1 + - - +
171V GLN* 3.4 18.2 + - - +
172V SER 2.6 27.9 + - - +
173V ILE* 3.1 16.3 - - + +
174V LEU* 2.9 23.5 + - - +
678V ASN* 2.8 20.0 + - - +
679V PRO* 1.3 75.1 + - - +
681V PHE* 1.3 62.6 + - - +
682V VAL* 3.8 1.6 + - - -
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Residues in contact with PHE 681 (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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120V PHE* 3.6 21.9 - - + +
121V CYS* 3.4 22.0 + - - +
156V ILE* 5.6 1.0 - - - +
174V LEU* 3.2 42.6 - - + -
176V THR* 4.1 11.2 - - + -
489V LEU* 4.2 11.9 - - + -
492V LEU* 4.5 4.3 - - + -
493V PHE* 3.4 57.9 - + + -
496V THR* 4.3 10.8 - - - -
497V MET* 5.0 6.3 - - - -
679V PRO* 3.9 21.1 - - + -
680V ASN* 1.3 73.0 - - - +
682V VAL* 1.3 64.1 + - - +
683V ARG* 3.6 6.1 - - - +
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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