Contacts of the strand formed by residues 460 - 465 (chain C) in PDB entry 2V4M
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 460 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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431A ARG* 3.7 28.1 - - - +
377C HIS* 4.5 14.1 - - + +
380C GLU* 3.7 33.0 - - + +
381C ILE* 3.7 42.2 - - + +
384C CYS* 6.0 0.2 - - + -
431C ARG 4.4 0.6 + - - -
433C ASP 3.0 11.7 + - - +
434C VAL* 3.3 12.4 - - + +
435C CYS 2.9 24.9 + - - -
459C ALA* 1.3 71.3 - - - +
461C THR* 1.3 69.0 + - - +
462C VAL* 4.2 4.7 - - + -
477C ASP* 3.6 8.7 - - - +
478C CYS* 4.4 7.0 - - - -
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Residues in contact with THR 461 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435C CYS* 3.5 3.6 - - + -
437C PHE* 3.8 11.7 - - + -
451C LEU* 3.6 30.8 - - + +
454C CYS* 4.3 16.8 - - + -
455C LYS* 4.4 11.0 - - + +
459C ALA 3.8 11.0 - - - +
460C LEU* 1.3 75.6 - - - +
462C VAL* 1.3 66.6 + - - +
475C GLU 4.3 1.7 + - - -
476C THR* 3.4 7.4 - - - -
477C ASP* 2.8 56.2 + - - +
478C CYS* 3.4 8.3 + - - -
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Residues in contact with VAL 462 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374C LEU* 4.0 24.2 - - + -
381C ILE* 4.1 8.5 - - + -
434C VAL* 3.5 30.3 - - + -
435C CYS 2.9 8.9 + - - +
436C PHE* 3.4 29.7 - - + +
437C PHE* 3.0 27.2 + - - -
460C LEU* 4.2 1.8 - - + -
461C THR* 1.3 82.3 - - - +
463C GLY* 1.3 68.5 + - - +
464C ILE* 4.3 4.9 - - + -
476C THR* 3.8 4.2 - - - +
478C CYS* 3.3 17.7 - - - +
480C VAL* 5.1 0.2 - - + -
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Residues in contact with GLY 463 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437C PHE 3.7 4.9 - - - -
462C VAL* 1.3 72.8 - - - +
464C ILE* 1.3 61.1 + - - +
465C THR* 3.8 5.8 - - - -
472C ILE* 4.4 9.4 - - - -
473C SER* 5.5 2.2 - - - -
476C THR* 3.6 17.5 + - - -
478C CYS 3.0 12.5 + - - -
479C GLY* 3.1 3.4 - - - -
480C VAL 2.8 31.4 + - - -
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Residues in contact with ILE 464 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436C PHE* 4.1 25.8 - - + -
437C PHE 2.9 8.6 + - - +
438C LEU* 3.5 33.0 - - + -
439C SER 3.1 23.2 + - - +
462C VAL* 4.3 4.5 - - + +
463C GLY* 1.3 80.6 - - - +
465C THR* 1.3 59.5 + - - +
480C VAL* 3.5 27.1 - - + +
482C ILE* 3.6 22.3 - - + +
499C GLN* 4.4 16.3 + - + +
502C SER* 4.2 15.5 - - - +
503C LEU* 4.6 8.7 - - + -
506C PHE* 6.0 2.5 - - + -
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Residues in contact with THR 465 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437C PHE 4.5 0.2 - - - +
439C SER* 3.0 18.4 - - - +
440C GLN 4.3 0.7 - - - -
442C GLY* 4.3 4.7 - - - -
463C GLY* 4.4 2.8 - - - -
464C ILE* 1.3 83.7 - - - +
466C ASN* 1.3 59.7 + - - +
467C THR 3.6 10.6 + - - -
468C VAL* 5.5 0.2 - - - -
470C SER* 4.3 4.9 - - - -
472C ILE* 3.7 35.0 - - + -
473C SER* 3.9 23.7 + - - +
480C VAL 3.3 6.3 + - - -
481C HIS* 3.4 8.7 + - - +
482C ILE* 2.9 30.5 + - - +
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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