Contacts of the strand formed by residues 459 - 465 (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 SER 459 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164V MET* 3.8 28.4 - - - +
165V LEU* 5.7 1.6 - - - +
170V ASP* 3.1 10.1 - - - -
253V ARG* 5.7 0.2 - - - -
255V ASN* 3.3 8.1 - - - +
256V PHE* 2.7 45.5 + - - +
257V ASP 3.7 10.2 + - - -
458V ALA* 1.3 81.3 - - - +
460V PHE* 1.3 62.6 + - - +
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Residues in contact with PHE 460 (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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164V MET* 3.7 7.8 - - - +
170V ASP* 2.5 49.6 + - + +
171V GLN 3.5 15.7 + - - -
251V PHE* 4.5 8.5 - + - -
253V ARG* 3.0 53.2 - - + +
254V ILE 2.9 11.4 - - - +
255V ASN* 3.4 15.7 - - - +
256V PHE* 4.5 0.4 - - - -
459V SER* 1.3 75.3 - - - +
461V LEU* 1.3 64.1 + - - +
462V GLY* 4.3 12.3 - - - -
673V THR* 4.4 10.5 - - - -
676V ASN 5.9 0.2 - - - -
677V THR* 3.4 31.0 - - + -
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Residues in contact with LEU 461 (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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160V ALA* 4.4 7.9 - - + -
161V TYR* 3.8 31.2 - - + +
164V MET* 3.5 21.1 - - + -
171V GLN* 3.4 10.1 - - + +
173V ILE* 3.5 29.6 - - + -
190V VAL* 4.4 0.4 - - + -
194V LEU* 4.0 20.6 - - + -
252V ILE 3.7 1.2 - - - +
253V ARG* 3.6 4.9 - - - -
254V ILE* 2.7 33.4 + - + +
256V PHE* 3.7 17.6 - - + -
460V PHE* 1.3 75.9 - - - +
462V GLY* 1.3 61.6 + - - +
463V ILE* 4.0 17.7 + - + +
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Residues in contact with GLY 462 (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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171V GLN 2.5 17.6 + - - -
172V SER* 2.9 9.4 - - - -
173V ILE* 2.5 36.2 + - - +
251V PHE* 4.4 18.8 - - - -
252V ILE 3.8 5.2 - - - -
460V PHE* 4.1 5.7 - - - -
461V LEU* 1.3 75.5 - - - +
463V ILE* 1.3 57.2 + - - +
464V LEU* 4.1 0.4 - - - -
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Residues in contact with ILE 463 (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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173V ILE* 3.4 13.9 - - + +
175V CYS* 5.5 1.3 - - - -
187V THR* 3.2 37.9 - - + +
190V VAL* 3.9 23.3 - - + -
191V ILE* 3.8 30.1 - - + +
194V LEU* 5.9 0.2 - - + -
251V PHE* 3.6 3.9 - - - -
252V ILE* 3.0 43.8 + - + +
254V ILE* 4.2 18.8 - - + -
461V LEU* 4.2 15.9 - - + +
462V GLY* 1.3 75.5 - - - +
464V LEU* 1.3 61.0 + - - +
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Residues in contact with LEU 464 (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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173V ILE 3.0 11.3 + - - +
174V LEU* 3.9 25.6 - - + -
175V CYS* 3.3 29.6 + - - +
187V THR* 4.9 2.7 - - - -
250V LYS 3.4 17.3 - - - +
251V PHE* 3.6 26.9 - - + -
270V TYR* 4.5 6.3 - - + -
462V GLY 4.1 0.8 - - - -
463V ILE* 1.3 72.1 - - - +
465V ASP* 1.3 60.1 + - - +
466V ILE* 3.6 24.7 + - + -
489V LEU* 3.4 32.8 - - + -
670V LEU* 4.6 10.8 - - + -
671V MET* 6.0 0.7 - - + -
674V LEU* 4.2 12.3 - - + -
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Residues in contact with ASP 465 (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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183V LYS* 4.6 11.7 - - - +
184V THR* 3.9 18.2 + - - -
187V THR* 4.0 18.4 - - + +
246V SER* 4.1 12.8 + - - -
248V PHE 4.7 1.9 - - - +
249V GLY* 3.4 0.9 - - - -
250V LYS* 2.6 86.0 + - + +
252V ILE* 5.0 0.2 - - + -
463V ILE 3.9 0.8 + - - -
464V LEU* 1.3 71.6 - - - +
466V ILE* 1.3 64.9 + - - +
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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