Contacts of the strand formed by residues 642 - 651 (chain B) in PDB entry 1DQ8
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 ASN 642 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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734A ASN* 2.8 30.6 + - - +
738A VAL* 4.3 5.7 - - - +
593B VAL* 4.6 2.5 - - - -
594B VAL 3.4 8.1 - - - +
595B ARG* 3.2 26.8 - - - +
638B ILE* 3.6 8.5 - - - +
639B ALA 3.0 36.2 + - - +
640B GLY 3.7 0.2 - - - +
641B ARG* 1.3 84.5 - - - +
643B LEU* 1.3 61.2 + - - +
644B TYR* 3.1 33.9 + - + -
780C LEU* 4.7 4.9 - - - +
782C GLU* 5.6 0.3 - - - +
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Residues in contact with LEU 643 (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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592B PRO 3.9 0.5 - - - +
593B VAL* 3.7 0.9 - - - -
594B VAL* 2.8 53.7 + - + +
596B LEU* 5.1 1.1 - - + -
602B SER* 4.3 9.2 - - - +
605B VAL* 3.5 37.2 - - + -
606B LYS* 4.2 7.2 - - + +
609B LEU* 4.1 5.4 - - + -
636B THR* 4.1 16.4 - - - -
637B SER 3.7 10.5 - - - +
638B ILE* 3.4 26.2 - - + -
641B ARG 3.9 0.4 + - - -
642B ASN* 1.3 74.3 - - - +
644B TYR* 1.3 67.5 + - - +
645B ILE* 3.8 23.7 + - + -
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Residues in contact with TYR 644 (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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734A ASN 2.8 25.6 + - - -
738A VAL* 3.1 20.3 - - + +
739A GLY* 3.5 15.3 - - - -
742A MET* 4.0 14.4 - - + -
592B PRO 3.5 3.6 - - - -
593B VAL* 3.4 29.0 - - + +
635B HIS 3.8 0.5 - - - +
636B THR* 3.2 5.4 - - - -
637B SER* 2.8 46.1 + - - +
639B ALA* 3.8 15.3 - - + -
642B ASN* 3.1 30.3 + - + -
643B LEU* 1.3 72.7 - - - +
645B ILE* 1.3 62.0 + - - +
646B ARG 4.0 0.7 - - - -
685B GLY 3.8 10.8 - - - -
687B TYR* 3.6 34.0 - + + -
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Residues in contact with ILE 645 (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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590B ARG 3.4 1.2 - - - +
591B GLY* 3.4 3.0 - - - -
592B PRO* 3.0 35.6 + - + +
594B VAL* 4.6 11.9 - - + -
609B LEU* 3.9 22.0 - - + -
634B LEU* 3.9 18.8 - - + -
635B HIS 3.8 1.6 - - - -
636B THR* 3.9 16.6 - - + -
643B LEU* 3.8 26.5 - - + +
644B TYR* 1.3 77.2 - - - +
646B ARG* 1.3 61.2 + - - +
647B PHE* 3.5 22.9 + - + -
668B LEU* 4.1 17.0 - - + -
671B LEU* 4.1 17.3 - - + -
687B TYR* 4.5 0.2 - - - -
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Residues in contact with ARG 646 (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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589B THR* 3.7 28.7 + - + +
590B ARG 3.6 4.5 - - - +
591B GLY* 4.2 1.8 - - - -
633B LYS* 3.8 0.9 - - - +
634B LEU* 3.4 7.8 - - - -
635B HIS* 2.7 54.2 + - + +
644B TYR 4.0 0.8 - - - -
645B ILE* 1.3 71.3 - - - +
647B PHE* 1.3 64.8 + - - +
648B GLN* 3.8 10.4 + - + +
687B TYR* 3.5 21.2 + - + +
688B CYS 2.7 27.7 + - - +
696B ILE* 3.5 28.5 + - - +
697B ASN* 3.2 15.8 + - - -
700B GLU* 3.4 27.8 + - - +
701B GLY 2.8 29.9 + - - -
702B ARG* 3.9 2.0 - - - +
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Residues in contact with PHE 647 (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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588B MET 3.8 0.3 - - - +
589B THR* 3.0 27.0 - - - -
590B ARG* 2.9 15.7 + - + +
592B PRO* 3.7 9.6 - - + -
609B LEU* 6.3 1.6 - - + -
618B ILE* 3.5 26.5 - - + -
622B PHE* 3.7 25.6 - + + -
631B LEU* 3.9 5.2 - - + -
633B LYS 4.1 2.7 - - - -
634B LEU* 3.7 12.8 - - + -
645B ILE* 3.5 32.3 - - + -
646B ARG* 1.3 71.0 - - - +
648B GLN* 1.3 60.1 + - - +
649B SER 4.2 0.2 - - - -
660B ILE* 4.6 1.8 - - + +
664B THR* 3.6 36.6 - - + +
667B ALA* 3.6 22.2 - - + -
668B LEU* 4.2 13.2 - - + -
671B LEU* 6.3 0.9 - - + -
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Residues in contact with GLN 648 (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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585B ALA* 5.8 5.5 - - - +
586B ASP 4.9 0.6 - - - -
587B GLY* 3.2 32.2 + - - +
588B MET 3.5 2.0 - - - -
589B THR* 3.9 14.2 - - + +
631B LEU* 3.4 4.0 - - - +
632B GLN* 2.8 41.2 + - - +
633B LYS* 3.1 50.3 + - + +
646B ARG* 3.8 11.7 + - + +
647B PHE* 1.3 73.9 - - - +
649B SER* 1.3 63.8 + - - +
700B GLU* 4.7 10.6 + - - +
701B GLY 4.4 11.9 + - - -
702B ARG* 4.8 0.2 - - - +
703B GLY 5.1 0.6 + - - -
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Residues in contact with SER 649 (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* 3.4 1.1 - - - -
588B MET* 3.0 32.0 + - - +
622B PHE* 3.4 30.6 - - - -
629B ALA 3.8 0.7 - - - -
630B ARG 3.2 24.3 + - - -
631B LEU* 3.8 0.9 - - - -
632B GLN* 3.8 8.1 - - - -
647B PHE 4.2 0.4 - - - -
648B GLN* 1.3 79.4 - - - +
650B ARG* 1.3 76.1 + - - +
651B SER* 4.6 0.3 - - - -
660B ILE* 3.6 13.3 - - - +
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Residues in contact with ARG 650 (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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585B ALA* 6.0 0.6 - - - +
586B ASP* 3.4 36.6 + - - +
587B GLY* 4.8 0.9 - - - -
628B PHE 3.3 15.9 - - - +
629B ALA* 3.5 4.0 - - - -
630B ARG* 3.2 22.1 + - + +
632B GLN* 2.9 30.8 - - + +
649B SER* 1.3 88.2 + - - +
651B SER* 1.3 63.2 + - - +
652B GLY 4.9 2.0 - - - +
660B ILE* 4.0 1.6 - - - +
836B ARG* 3.0 34.2 - - - +
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Residues in contact with SER 651 (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* 5.3 4.3 + - - -
588B MET* 4.7 3.4 + - - +
628B PHE* 3.5 11.9 - - - -
649B SER 4.6 1.5 + - - -
650B ARG* 1.3 77.9 - - - +
652B GLY* 1.3 71.5 + - - +
654B ALA* 2.7 41.8 + - - +
655B MET 3.7 7.0 + - - -
656B GLY* 3.9 14.6 - - - -
659B MET* 3.8 20.5 - - - +
660B ILE* 4.5 6.3 - - - -
704B LYS* 5.0 4.9 + - - -
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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