Contacts of the strand formed by residues 580 - 590 (chain B) in PDB entry 1DQA
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 SER 580 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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546B LEU* 4.4 1.8 - - - -
547B ASP* 3.3 9.6 + - - -
578B GLY 5.4 0.3 + - - -
579B ALA* 1.3 76.4 + - - +
581B SER* 1.3 60.7 + - - +
582B ARG* 4.8 1.1 - - - -
708B CYS* 3.2 2.4 - - - +
709B GLU* 2.9 42.4 + - - +
598C ARG* 5.7 4.2 + - - -
600C CYS* 3.7 26.1 - - - -
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Residues in contact with SER 581 (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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546B LEU* 3.8 8.2 - - - +
547B ASP* 2.7 33.1 + - - +
580B SER* 1.3 74.8 - - - +
582B ARG* 1.3 86.7 + - - +
706B VAL* 4.7 2.9 - - - -
707B VAL* 3.1 13.9 - - - -
708B CYS* 3.8 11.4 - - - -
840B ARG* 3.2 34.9 + - - +
600C CYS* 5.0 0.7 - - - -
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Residues in contact with ARG 582 (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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547B ASP* 4.0 10.7 + - - -
580B SER* 4.8 1.4 - - - -
581B SER* 1.3 91.5 + - - +
583B VAL* 1.3 66.5 + - - +
584B LEU* 3.7 3.3 + - + -
706B VAL* 3.4 7.1 - - - +
707B VAL* 2.9 44.5 + - + +
840B ARG* 4.9 2.2 - - - +
600C CYS* 3.5 44.6 + - - +
603C ALA* 4.0 24.2 - - + -
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Residues in contact with VAL 583 (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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582B ARG* 1.3 75.2 - - - +
584B LEU* 1.3 63.4 + - - +
585B ALA 3.6 22.9 - - - +
586B ASP* 4.9 0.9 - - + -
704B LYS* 4.6 7.6 - - + -
705B SER 3.6 5.8 - - - +
706B VAL* 4.4 8.5 - - + +
836B ARG* 4.0 41.7 - - + +
839B ALA* 5.3 0.9 - - + -
840B ARG* 3.7 32.4 - - + +
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Residues in contact with LEU 584 (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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582B ARG* 4.1 6.7 - - + +
583B VAL* 1.3 78.3 - - - +
585B ALA* 1.3 60.1 + - + +
705B SER* 2.7 26.6 + - - +
706B VAL 4.3 7.6 - - - +
707B VAL* 4.0 20.4 - - + -
796B THR* 4.7 5.8 - - + -
603C ALA* 3.7 34.8 - - + +
606C LYS* 4.4 29.3 + - + +
610C GLU* 4.8 6.4 - - - +
638C ILE* 4.1 32.8 - - + +
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Residues in contact with ALA 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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583B VAL* 3.6 9.4 - - - +
584B LEU* 1.3 82.8 - - + +
586B ASP* 1.3 65.1 + - - +
587B GLY 5.5 0.2 - - - +
648B GLN* 5.9 4.3 - - - +
700B GLU 5.9 2.9 - - - +
703B GLY 4.1 1.6 - - - +
704B LYS* 3.3 4.0 - - - -
705B SER* 2.9 40.6 + - - +
606C LYS* 5.6 4.3 - - - +
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Residues in contact with ASP 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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583B VAL* 4.9 2.0 - - + -
585B ALA* 1.3 79.1 - - - +
587B GLY* 1.3 62.7 + - - +
588B MET 5.0 0.5 + - - -
632B GLN* 2.9 22.3 + - - +
648B GLN* 5.0 1.1 - - - -
650B ARG* 3.0 34.0 + - - +
651B SER* 5.3 3.5 + - - -
652B GLY 4.8 5.4 - - - +
703B GLY 3.3 4.9 - - - +
704B LYS* 2.8 41.3 + - + +
836B ARG* 2.9 34.9 + - - +
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Residues in contact with GLY 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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586B ASP* 1.3 79.3 + - - +
588B MET* 1.3 66.4 + - - -
589B THR* 3.7 2.4 - - - +
632B GLN* 3.4 16.8 - - - -
648B GLN* 3.1 26.1 + - - +
649B SER 3.4 2.5 - - - -
703B GLY* 2.8 29.7 + - - -
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Residues in contact with MET 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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586B ASP* 5.0 1.4 + - - -
587B GLY* 1.3 72.7 - - - +
589B THR* 1.3 74.5 + - - +
647B PHE 3.7 0.2 - - - +
649B SER* 3.0 32.6 + - - +
651B SER* 4.6 5.3 + - - +
655B MET* 3.5 47.8 - - + +
656B GLY 3.9 7.4 - - - -
657B MET* 4.0 8.7 - - - +
660B ILE* 3.5 29.6 - - + +
702B ARG* 3.4 28.9 - - - +
703B GLY* 4.1 14.6 - - - +
801B GLU* 3.9 25.6 - - + -
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Residues in contact with THR 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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587B GLY 3.7 11.0 - - - +
588B MET* 1.3 86.2 - - - +
590B ARG* 1.3 60.6 + - - +
646B ARG* 3.7 30.5 - - + +
647B PHE 3.0 13.2 - - - +
648B GLN* 3.7 15.7 - - + +
657B MET* 3.2 9.0 - - - +
660B ILE* 3.8 5.2 - - - -
688B CYS* 2.6 26.7 + - - -
702B ARG* 2.8 40.2 + - + +
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Residues in contact with ARG 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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201A MAH 3.0 38.2 + - - -
862A LEU* 4.2 10.5 - - - +
2B NAP 2.7 29.5 + - - -
589B THR* 1.3 74.8 - - - +
591B GLY* 1.3 58.2 + - - +
592B PRO* 3.3 5.2 - - + +
645B ILE 3.3 2.8 - - - +
646B ARG* 4.5 0.7 - - - -
647B PHE* 2.9 29.8 + - + +
657B MET* 3.5 11.3 - - + +
660B ILE* 3.5 11.1 - - + +
661B SER* 3.0 24.0 + - - -
664B THR* 3.5 27.1 - - + +
683B VAL* 3.4 28.0 - - - +
684B SER* 3.6 8.0 + - - -
688B CYS* 3.3 26.0 - - - -
690B ASP* 3.7 8.9 - - - +
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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