Contacts of the strand formed by residues 437 - 441 (chain V) in PDB entry 5IY8
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 LEU 437 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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354V ALA* 4.2 11.4 - - - +
357V VAL* 4.1 28.9 - - + -
359V LYS* 3.8 26.7 - - + +
360V ARG 3.1 6.0 + - - +
361V CYS* 3.4 28.0 - - + -
362V LEU* 3.1 30.9 + - - +
436V GLY* 1.3 78.2 - - - +
438V MET* 1.4 69.2 + - - +
439V ILE* 3.6 24.7 - - + -
462V CYS* 3.6 25.8 - - + +
463V LYS* 4.9 1.1 - - - +
464V LEU* 5.2 1.1 - - + +
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Residues in contact with MET 438 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362V LEU* 3.6 17.0 - - + -
364V LEU* 4.4 7.9 - - + -
427V MET* 4.0 42.6 - - + -
428V GLU* 5.1 2.0 - - - +
436V GLY 5.2 2.5 - - - +
437V LEU* 1.4 74.5 - - - +
439V ILE* 1.4 61.1 + - - +
440V LEU* 3.9 16.2 - - + +
455V LEU* 4.1 23.6 - - - -
458V VAL* 4.4 8.1 - - + -
460V ALA* 3.5 35.0 - - + -
462V CYS 2.8 16.6 + - - +
463V LYS* 3.4 6.8 - - + -
464V LEU 2.8 32.1 + - - +
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Residues in contact with ILE 439 (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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350V GLY* 4.4 14.8 - - - +
353V ALA* 4.2 16.8 - - + -
354V ALA* 4.4 9.6 - - + +
357V VAL* 5.5 1.8 - - + -
361V CYS* 3.7 24.7 - - - -
362V LEU 3.2 7.1 + - - +
363V VAL* 3.4 8.3 - - + +
364V LEU* 2.8 33.3 + - - +
374V TRP* 4.2 24.5 - - + -
437V LEU* 3.6 29.8 - - + -
438V MET* 1.4 74.2 - - - +
440V LEU* 1.3 56.2 + - - +
464V LEU* 3.4 22.2 - - + +
466V LEU* 4.5 9.6 - - + -
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Residues in contact with LEU 440 (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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364V LEU* 3.7 32.8 - - + -
410V TYR* 3.6 13.7 - - + +
438V MET* 3.9 24.5 - - + +
439V ILE* 1.3 78.5 - - - +
441V ASP* 1.3 59.7 + - - +
443V VAL* 4.1 14.1 - - + +
446V ILE* 4.1 17.7 - - + -
455V LEU* 4.4 7.9 - - + -
463V LYS* 5.1 0.7 - - + -
464V LEU 2.9 21.0 + - - +
465V GLY* 3.4 1.2 - - - -
466V LEU* 2.9 30.6 + - - +
484V ILE* 3.9 33.7 - - + -
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Residues in contact with ASP 441 (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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346V LYS* 2.7 43.0 + - - +
364V LEU 2.9 15.5 + - - +
365V GLY* 4.5 7.2 - - - -
366V ASN 5.6 0.2 + - - -
370V SER* 4.4 11.3 - - - -
374V TRP* 3.5 43.7 + - + -
410V TYR* 2.5 31.2 + - - -
439V ILE 4.0 0.8 - - - -
440V LEU* 1.3 72.7 - - - +
442V GLU* 1.3 80.2 + - + +
466V LEU* 3.9 4.3 - - - +
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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