Contacts of the strand formed by residues 492 - 497 (chain B) in PDB entry 5D3O
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 GLY 492 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287B PHE* 4.2 17.5 - - - -
288B CYS 5.7 0.6 + - - -
292B CYS* 3.7 16.1 - - - -
487B SER* 3.1 5.2 - - - -
488B GLY 3.0 27.3 + - - +
490B ALA* 3.8 1.4 - - - +
491B GLY* 1.3 79.5 - - - +
493B ILE* 1.3 65.5 + - - +
504B MET* 4.3 2.2 - - - -
505B CYS 3.3 7.4 - - - -
506B TRP* 4.0 1.4 - - - -
516B SER* 5.0 0.5 + - - -
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Residues in contact with ILE 493 (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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470B MET* 3.7 28.5 - - + -
485B ALA* 4.1 16.8 - - + -
486B LYS 3.4 6.5 - - - +
487B SER* 4.2 4.9 - - - +
492B GLY* 1.3 79.1 - - - +
494B LEU* 1.3 73.6 + - - +
495B LEU* 3.4 6.4 + - + +
504B MET* 3.5 4.1 - - - +
505B CYS* 2.8 37.9 + - + +
516B SER* 4.2 20.4 - - - +
519B GLY* 3.9 28.9 - - - +
520B ILE* 4.0 7.9 - - + +
523B CYS* 4.2 15.3 - - - -
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Residues in contact with LEU 494 (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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289B LEU* 5.3 5.8 - - + -
292B CYS* 4.3 19.6 - - + +
295B PRO* 5.2 3.8 - - + -
296B LEU* 4.6 14.4 - - + -
432B ALA* 3.8 25.8 - - + +
435B MET* 5.1 3.4 - - + -
436B ALA* 4.0 11.9 - - + +
439B LEU* 4.5 22.2 - - + -
465B MET* 4.0 11.1 - - + +
485B ALA* 3.0 6.6 - - - +
486B LYS* 2.8 43.2 + - + +
492B GLY 4.1 0.4 - - - -
493B ILE* 1.3 71.3 - - - +
495B LEU* 1.3 59.1 + - - +
496B VAL* 5.6 0.4 - - + -
503B MET 3.8 5.2 - - - +
504B MET* 3.8 26.0 - - + -
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Residues in contact with LEU 495 (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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436B ALA* 3.6 2.6 - - - +
477B PHE* 4.3 4.9 - - + -
483B LEU* 3.8 35.2 - - + -
484B PRO 3.8 1.6 - - - -
485B ALA* 3.9 18.2 - - + -
493B ILE* 3.4 5.6 + - + +
494B LEU* 1.3 76.0 - - - +
496B VAL* 1.3 65.1 + - - +
497B VAL* 4.3 5.6 - - + +
502B GLY* 3.5 1.9 - - - -
503B MET* 2.7 73.3 + - + +
505B CYS* 5.6 0.9 - - - -
523B CYS* 4.0 26.9 - - + -
526B LEU* 4.0 20.9 - - + -
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Residues in contact with VAL 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436B ALA* 3.5 26.7 - - + +
439B LEU* 3.8 19.3 - - + -
440B ALA* 3.7 26.9 - - + +
462B LEU* 3.8 25.8 - - + -
465B MET* 4.7 6.1 - - + -
483B LEU* 3.6 8.8 - - - +
484B PRO* 2.9 29.3 + - + +
494B LEU* 5.6 0.7 - - + -
495B LEU* 1.3 80.0 - - - +
497B VAL* 1.3 63.2 + - - +
498B PRO* 3.4 18.5 - - + +
501B MET 4.0 2.5 - - - -
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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
----------------------------------------------------------
440B ALA* 3.8 1.4 - - - +
483B LEU* 3.8 29.4 - - + -
495B LEU* 4.6 5.6 - - + -
496B VAL* 1.3 75.5 - - - +
498B PRO* 1.3 71.3 - - + +
499B ASN 3.4 0.2 + - - -
500B VAL* 3.0 27.3 + - + -
501B MET* 2.9 53.2 + - + +
503B MET* 5.9 0.2 - - + -
526B LEU* 4.8 0.2 - - + -
532B PHE* 3.9 35.7 - - + +
548B ARG* 5.6 0.7 - - - +
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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