Contacts of the strand formed by residues 495 - 503 (chain B) in PDB entry 1M2V
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 ILE 495 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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432B TYR* 3.7 30.1 - - + -
435B ILE* 3.5 23.8 - - + -
436B GLY* 3.7 6.7 - - - -
440B GLY 3.5 16.2 - - - +
442B ILE* 3.9 22.4 - - + +
490B CYS* 2.9 38.9 + - + +
493B VAL* 3.4 23.8 - - + +
494B GLN* 1.3 75.9 - - - +
496B THR* 1.3 76.7 + - - +
497B VAL* 4.6 0.4 - - + -
519B THR* 3.8 5.5 - - - +
586B SER* 3.2 13.3 + - - -
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Residues in contact with THR 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440B GLY 3.0 6.0 + - - -
441B LYS* 3.5 9.1 - - + -
442B ILE 2.8 26.0 + - - -
495B ILE* 1.3 77.6 - - - +
497B VAL* 1.3 69.0 + - - +
498B ASP* 4.3 3.6 - - - +
519B THR* 2.7 29.1 + - - +
520B ALA 3.8 2.5 - - - +
521B GLY* 3.4 24.9 - - - +
586B SER* 3.3 3.1 - - - -
587B THR* 3.1 44.3 + - - +
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Residues in contact with VAL 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428B LEU* 5.0 2.5 - - + -
442B ILE* 3.3 19.1 - - + +
444B VAL* 4.3 9.6 - - + -
486B PHE* 4.0 27.8 - - + -
490B CYS* 4.6 4.7 - - - -
495B ILE* 4.6 3.4 - - + -
496B THR* 1.3 82.9 - - - +
498B ASP* 1.3 68.9 + - - +
499B LEU* 3.4 23.3 - - + -
515B LEU* 3.9 25.4 - - + +
516B SER* 3.1 25.1 - - - -
519B THR* 3.0 11.6 + - + +
521B GLY* 3.3 5.7 - - - -
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Residues in contact with ASP 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441B LYS* 2.7 41.1 - - - +
442B ILE 2.9 10.1 + - - +
443B ILE* 4.4 10.2 - - + +
444B VAL* 2.7 34.2 + - - +
496B THR* 4.7 0.2 - - - -
497B VAL* 1.3 72.1 - - - +
499B LEU* 1.3 60.1 + - - +
500B PHE* 4.7 3.4 - - + -
521B GLY* 2.9 12.1 - - - -
522B GLN* 2.7 34.3 + - - +
547B HIS* 2.9 28.6 + - + +
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Residues in contact with LEU 499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424B LEU* 5.4 2.0 - - + -
444B VAL* 3.4 16.8 - - + +
497B VAL* 3.4 20.4 - - + -
498B ASP* 1.3 84.6 - - - +
500B PHE* 1.3 63.6 + - - +
501B LEU* 3.8 25.4 - - + -
512B LEU* 3.8 34.1 - - + +
515B LEU* 4.0 19.7 - - + -
516B SER* 4.0 17.7 - - - -
522B GLN 2.9 9.3 + - - +
523B THR* 3.6 10.9 - - + +
524B HIS* 2.7 34.7 + - - +
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Residues in contact with PHE 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443B ILE* 3.8 13.0 - - + -
444B VAL 2.7 18.3 + - - +
445B VAL* 3.6 5.0 - - + +
446B SER 2.9 27.2 + - - +
498B ASP* 4.7 3.1 - - + -
499B LEU* 1.3 75.8 - - - +
501B LEU* 1.3 63.0 + - - +
502B ALA* 3.5 2.6 + - - +
524B HIS* 3.5 28.3 - + + -
526B TYR* 3.4 32.8 - + - -
540B PHE* 3.7 21.1 - + + -
543B GLU 4.6 1.3 - - - -
544B PHE* 3.7 39.9 - + + -
547B HIS* 3.6 41.3 - + + -
866B ILE* 4.6 0.7 - - + -
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Residues in contact with LEU 501 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444B VAL* 5.3 3.4 - - + -
446B SER* 3.4 17.0 - - - +
499B LEU* 4.0 20.4 - - + -
500B PHE* 1.3 74.3 - - - +
502B ALA* 1.3 58.6 + - - +
507B MET* 3.7 26.0 - - + -
509B VAL* 3.8 30.3 - - + -
512B LEU* 4.1 32.1 - - + -
523B THR* 4.0 15.9 - - + -
524B HIS 2.8 14.0 + - - +
525B PHE* 3.1 12.6 - - + -
526B TYR* 3.0 22.6 + - - -
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Residues in contact with ALA 502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319B SER* 5.1 2.3 + - - -
321B LEU* 3.5 30.9 - - + +
446B SER 2.9 8.5 + - - -
447B GLY* 3.2 14.4 - - - -
500B PHE 3.5 0.8 + - - +
501B LEU* 1.3 70.4 - - - +
503B SER* 1.3 64.5 + - - +
526B TYR* 3.7 22.9 - - + -
529B PHE* 3.8 18.5 - - + +
540B PHE* 4.0 13.5 - - + -
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Residues in contact with SER 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315B SER* 4.7 1.8 + - - -
319B SER* 6.1 1.8 - - - -
447B GLY* 3.4 24.3 + - - -
501B LEU 4.0 2.0 + - - -
502B ALA* 1.3 76.5 - - - +
504B GLU* 1.3 63.5 + - - +
505B ASP* 2.8 29.9 + - - +
507B MET* 3.6 17.5 - - - +
525B PHE* 4.4 7.0 - - - -
526B TYR 3.3 9.2 + - - +
527B PRO* 3.9 3.6 - - - +
528B GLY 3.3 12.6 + - - -
529B PHE* 3.8 13.0 - - - +
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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