Contacts of the strand formed by residues 584 - 592 (chain B) in PDB entry 2JJD
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 VAL 584 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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515B TRP* 4.3 0.2 - - - -
570B LEU* 3.6 28.7 - - + -
571B VAL 3.4 7.9 - - - +
572B THR* 3.5 24.9 - - + -
581B GLY 5.1 0.2 - - - +
582B GLU 3.6 3.5 + - - -
583B GLN* 1.3 80.9 + - + +
585B ARG* 1.3 70.9 + - - +
264F GLU* 5.0 11.4 - - + +
265F ASP* 6.2 1.6 - - + -
276F LYS* 3.7 37.4 - - + -
292F LEU* 3.4 17.7 - - + +
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Residues in contact with ARG 585 (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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514B ILE 4.9 1.8 + - - -
515B TRP* 3.0 80.0 + - + +
518B LYS* 4.5 12.2 - - - +
519B SER 4.8 2.0 + - - -
520B HIS* 3.1 35.6 + - + +
570B LEU* 3.3 8.5 - - - +
571B VAL* 2.8 39.3 + - + +
582B GLU* 4.4 9.3 + - - +
584B VAL* 1.3 79.3 + - - +
586B VAL* 1.3 63.7 + - - +
587B VAL* 4.0 4.0 - - + -
292F LEU* 3.5 11.2 - - - -
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Residues in contact with VAL 586 (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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520B HIS* 4.1 19.1 - - - +
568B ASP* 4.8 4.5 - - - +
569B PHE 3.2 11.7 - - - +
570B LEU* 4.4 10.1 - - + -
585B ARG* 1.3 75.0 - - - +
587B VAL* 1.3 70.4 + - - +
588B ARG* 5.4 3.5 - - + +
617B GLN* 5.5 5.0 + - - +
278F CYS* 4.9 1.6 - - - -
289F ALA* 5.7 2.2 - - + -
290F PRO* 3.6 50.5 - - + +
291F ARG* 4.6 2.0 - - - +
292F LEU* 3.9 23.9 - - + +
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Residues in contact with VAL 587 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511B TRP* 4.5 7.9 - - + -
514B ILE* 4.4 9.9 - - + -
519B SER 3.9 19.3 - - - +
520B HIS* 3.5 10.8 - - + +
522B ILE* 3.8 33.0 - - + -
568B ASP* 3.7 1.7 - - - -
569B PHE* 2.8 41.2 + - + +
571B VAL* 3.5 30.1 - - + -
585B ARG* 3.9 9.5 + - + -
586B VAL* 1.3 79.3 - - - +
588B ARG* 1.3 65.4 + - - +
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Residues in contact with ARG 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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520B HIS 3.0 8.2 + - - +
521B THR* 3.5 5.0 - - - +
522B ILE 3.0 24.6 + - - +
566B ILE* 3.6 30.8 - - + +
567B ARG 3.5 2.7 - - - -
568B ASP* 2.9 37.9 + - - +
586B VAL* 5.4 2.5 - - + +
587B VAL* 1.3 77.6 - - - +
589B GLN* 1.3 59.8 + - - +
590B PHE* 3.8 21.8 + - + -
617B GLN* 3.2 46.3 + - + +
288F LYS* 4.3 11.7 - - - +
289F ALA* 3.4 32.0 - - - +
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Residues in contact with GLN 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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522B ILE* 3.3 23.6 - - + +
524B MET* 2.8 30.0 - - + +
539B TYR* 3.0 19.0 + - + -
540B TRP* 3.3 16.1 - - - -
565B SER 3.4 5.9 - - - +
566B ILE* 3.5 1.8 - - - -
567B ARG* 2.8 69.5 + - - +
569B PHE* 3.6 25.4 - - + -
587B VAL 4.3 0.4 - - - -
588B ARG* 1.3 73.1 - - - +
590B PHE* 1.3 67.4 + - - +
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Residues in contact with PHE 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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521B THR* 3.8 20.4 - - + -
522B ILE 2.7 12.1 + - - +
523B VAL* 3.4 4.3 - - + +
524B MET* 2.8 33.3 + - - +
564B ILE* 4.2 4.3 - - + -
565B SER 4.0 2.2 - - - -
566B ILE* 3.7 29.4 - - + +
588B ARG* 3.8 28.3 - - + -
589B GLN* 1.3 73.1 - - - +
591B HIS* 1.3 54.5 + - - +
592B PHE 3.8 0.8 + - - -
610B LEU* 3.8 20.9 - - + -
613B ALA* 3.5 42.8 - - + -
614B VAL* 3.5 25.6 - - + -
617B GLN* 3.9 12.6 - - + -
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Residues in contact with HIS 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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524B MET* 3.2 35.3 - - + +
526B THR 3.1 27.5 + - - -
527B GLU* 4.3 8.2 - - + -
528B VAL* 5.3 2.7 - - + -
540B TRP* 4.0 9.9 - + - -
564B ILE* 3.6 4.0 - - - +
565B SER* 3.0 43.8 + - - +
567B ARG* 3.0 35.8 + - - +
589B GLN* 3.6 1.1 + - - +
590B PHE* 1.3 71.0 - - - +
592B PHE* 1.3 66.1 + - - +
593B HIS* 3.5 27.4 + + - -
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Residues in contact with PHE 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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523B VAL* 5.8 0.4 - - + -
524B MET 2.9 20.8 + - - +
525B LEU* 4.0 36.8 - - + +
526B THR 4.4 2.6 - - - +
563B ALA* 4.6 5.8 - - + -
564B ILE* 3.6 27.3 - - + +
590B PHE 3.8 1.2 + - - -
591B HIS* 1.3 75.9 - - - +
593B HIS* 1.3 63.9 + - - +
594B GLY* 3.8 29.2 - - - -
595B TRP* 4.1 14.8 + + + -
601B PRO* 4.9 3.8 - - + -
606B GLY* 3.7 21.3 - - - -
607B MET* 3.4 43.3 - - + -
610B LEU* 4.0 16.4 - - + -
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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