Contacts of the strand formed by residues 586 - 592 (chain B) in PDB entry 4QDQ
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 ARG 586 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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368B ASN* 4.9 2.4 - - - +
464B ALA 3.6 17.9 - - - +
465B ALA* 3.2 7.0 - - - +
466B ARG 3.6 13.7 - - - +
467B LEU* 3.8 1.3 - - - -
468B VAL* 4.2 5.8 + - - +
470B SER* 3.0 38.3 + - - -
471B ARG* 4.9 0.8 - - - +
472B SER 3.5 13.6 + - - -
473B GLY* 3.9 2.9 - - - -
488B LEU* 5.4 0.4 - - - -
503B ILE* 3.8 4.9 - - - +
504B GLN* 2.9 69.1 + - + +
505B GLY 2.7 17.3 + - - +
507B ARG* 4.0 24.8 - - - +
555B TYR 3.0 28.1 + - - -
556B ASP* 4.1 6.7 + - - +
585B MET* 1.3 76.2 - - - +
587B LEU* 1.3 64.8 + - - +
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Residues in contact with LEU 587 (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 MET* 3.2 20.4 - - + +
465B ALA 2.8 9.2 + - - +
467B LEU* 3.2 20.2 + - - +
488B LEU* 3.9 27.8 - - + +
490B VAL* 4.1 22.2 - - + -
501B VAL* 4.1 11.7 - - + -
502B ILE 3.4 18.6 - - - +
503B ILE* 4.4 5.6 - - + -
524B PHE* 6.2 0.2 - - + -
571B VAL* 5.9 2.9 - - + +
573B VAL* 3.8 29.6 - - + -
585B MET* 3.8 18.6 - - + -
586B ARG* 1.3 76.7 - - - +
588B GLU* 1.3 73.3 + - - +
589B VAL* 4.8 4.9 - - + -
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Residues in contact with GLU 588 (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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437B MET* 3.5 36.5 - - + +
438B LEU* 3.8 2.0 - - - +
439B GLY* 3.4 6.2 + - - -
440B MET* 3.0 26.7 + - - +
441B LEU* 2.9 31.5 + - - +
442B SER 4.7 0.2 + - - -
467B LEU* 3.6 21.7 - - + +
501B VAL* 3.3 7.3 - - - +
502B ILE* 2.8 36.6 + - + +
587B LEU* 1.3 76.7 - - - +
589B VAL* 1.3 90.8 + - - +
590B LEU* 4.6 3.6 - - + -
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Residues in contact with VAL 589 (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 ASN 3.7 0.3 - - - +
437B MET* 3.7 0.2 - - - -
438B LEU* 2.9 45.3 + - + +
440B MET* 4.8 1.8 - - + -
445B ILE* 5.5 0.2 - - + -
490B VAL* 4.0 38.1 - - + -
492B LEU* 4.5 6.1 - - + -
498B VAL* 3.7 29.8 - - + -
500B GLY 3.8 4.3 - - - +
501B VAL* 4.4 4.7 - - + +
571B VAL* 4.3 17.7 - - + -
587B LEU* 4.8 6.7 - - + -
588B GLU* 1.3 87.8 + - - +
590B LEU* 1.3 64.7 + - - +
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Residues in contact with LEU 590 (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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429B VAL* 4.1 2.9 - - + -
435B SER* 4.0 22.4 - - - +
436B ASN 3.3 13.5 - - - +
437B MET* 3.7 25.6 - - + -
438B LEU* 3.9 4.1 - - - +
498B VAL* 3.5 8.5 - - - +
499B LYS* 2.9 22.3 + - + -
500B GLY* 2.7 34.4 + - - +
501B VAL 4.2 0.4 - - - +
502B ILE* 3.7 25.8 - - + -
560B ILE* 3.3 36.6 - - + -
562B ARG* 4.7 3.8 - - + +
588B GLU* 4.6 0.9 - - + -
589B VAL* 1.3 76.9 - - - +
591B GLY* 1.3 57.9 + - - +
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Residues in contact with GLY 591 (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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434B CYS* 3.4 19.3 + - - -
436B ASN* 2.8 35.6 + - - +
438B LEU* 3.7 8.1 - - - +
497B THR 3.0 13.9 - - - -
499B LYS 4.0 3.6 - - - -
590B LEU* 1.3 76.2 - - - +
592B CYS* 1.3 62.7 + - - +
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Residues in contact with CYS 592 (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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434B CYS* 2.0 51.9 - - + -
436B ASN* 4.2 14.4 - - - +
438B LEU* 4.0 6.1 - - - +
496B LYS* 3.7 4.7 - - - +
497B THR* 3.0 38.7 + - - +
591B GLY* 1.3 73.6 - - - +
593B ASP* 1.3 74.1 + - - +
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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