Contacts of the strand formed by residues 629 - 639 (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 ALA 629 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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622B PHE* 4.1 14.6 - - + +
623B ASP* 3.4 13.7 - - - +
625B THR* 5.0 4.0 - - - +
626B SER* 3.2 13.1 + - - -
628B PHE* 1.3 74.3 - - - +
630B ARG* 1.3 80.6 + - - +
649B SER* 3.5 8.3 - - - +
650B ARG 3.4 8.3 - - - +
659B MET* 3.3 33.3 - - + +
660B ILE* 4.4 2.5 - - + -
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Residues in contact with ARG 630 (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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619B LYS* 4.2 6.1 - - - +
623B ASP* 3.2 30.5 + - - +
626B SER 2.4 29.3 + - - -
627B ARG* 2.6 30.9 + - - +
628B PHE 3.3 10.7 + - - +
629B ALA* 1.3 85.8 + - - +
631B LEU* 1.3 66.0 + - - +
632B GLN* 3.2 6.6 + - - +
649B SER* 2.9 16.3 + - - -
650B ARG* 3.1 24.9 + - + +
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Residues in contact with LEU 631 (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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615B PHE* 3.8 21.0 - - + -
618B ILE* 4.0 13.7 - - + -
619B LYS* 3.1 48.0 + - + +
622B PHE* 3.9 18.5 - - + -
623B ASP* 2.8 17.6 + - - +
630B ARG* 1.3 68.7 - - - +
632B GLN* 1.3 60.5 + - - +
633B LYS 3.8 5.2 - - - +
634B LEU* 3.7 19.7 - - + -
647B PHE* 3.9 20.9 - - + -
648B GLN 3.4 33.2 - - - +
649B SER* 3.6 3.4 + - - -
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Residues in contact with GLN 632 (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 2.9 28.4 + - - +
587B GLY* 3.4 3.2 - - - -
615B PHE* 3.9 10.4 - - - -
630B ARG 3.7 8.7 - - - +
631B LEU* 1.3 75.3 - - - +
633B LYS* 1.3 68.5 + - + +
648B GLN* 2.8 30.4 + - - +
649B SER 2.9 7.8 - - - -
650B ARG* 2.8 42.1 + - + +
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Residues in contact with LYS 633 (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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615B PHE* 4.0 9.8 - - - -
631B LEU* 3.7 2.1 - - - +
632B GLN* 1.3 89.8 - - + +
634B LEU* 1.3 79.2 + - - +
635B HIS* 5.2 7.5 - - - +
646B ARG 3.8 0.3 - - - +
648B GLN* 3.0 57.9 + - + +
700B GLU* 4.9 17.2 + - - +
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Residues in contact with LEU 634 (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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609B LEU* 4.0 39.7 - - + +
615B PHE* 3.9 23.1 - - + -
618B ILE* 4.5 9.0 - - + -
631B LEU* 3.7 15.3 - - + -
633B LYS* 1.3 93.6 - - - +
635B HIS* 1.3 60.8 + - - +
636B THR* 3.9 8.0 + - + +
645B ILE* 3.9 17.0 - - + -
646B ARG 3.4 2.2 - - - -
647B PHE* 3.6 35.7 - - + -
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Residues in contact with HIS 635 (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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633B LYS* 5.2 8.1 - - - -
634B LEU* 1.3 74.8 - - - +
636B THR* 1.3 66.4 + - - +
637B SER* 5.0 0.4 - - - -
646B ARG* 2.8 46.5 + - + +
687B TYR* 3.0 36.9 + - - -
696B ILE* 3.9 2.6 - - - +
700B GLU* 3.0 39.9 + - - +
699C ILE* 3.2 30.6 + - + -
700C GLU* 4.4 9.3 + - + +
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Residues in contact with THR 636 (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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606B LYS* 3.2 28.9 + - + +
609B LEU* 3.9 34.5 - - + -
610B GLU* 3.2 25.1 + - + +
634B LEU* 3.9 10.5 + - + -
635B HIS* 1.3 85.0 + - - +
637B SER* 1.3 61.3 + - - +
643B LEU* 4.1 13.2 - - - -
644B TYR 3.4 3.4 - - - -
645B ILE* 4.1 16.2 - - + -
687B TYR* 4.7 0.7 - - - -
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Residues in contact with SER 637 (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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742A MET* 2.8 29.2 + - - +
606B LYS* 4.6 1.3 - - - +
635B HIS* 4.1 1.8 + - - -
636B THR* 1.3 73.8 - - - +
638B ILE* 1.3 61.9 + - - +
643B LEU* 3.7 1.7 - - - -
644B TYR* 2.8 45.1 + - - +
687B TYR* 3.0 35.2 + - - -
699C ILE 5.5 2.0 - - - -
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Residues in contact with ILE 638 (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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742A MET* 3.3 15.1 - - - +
602B SER* 3.4 37.9 - - - +
603B ALA* 3.5 13.5 - - + +
606B LYS* 3.8 23.0 - - + +
637B SER* 1.3 76.6 + - - +
639B ALA* 1.3 62.1 + - - +
640B GLY 3.6 18.6 - - - +
642B ASN 3.6 12.1 - - - +
643B LEU* 4.0 9.9 - - + -
584C LEU* 4.0 20.3 - - + +
707C VAL* 4.2 9.0 - - + -
796C THR* 3.2 29.9 - - + +
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Residues in contact with ALA 639 (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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738A VAL* 3.9 20.0 - - + -
742A MET* 4.1 10.8 - - - -
637B SER 4.3 0.2 + - - -
638B ILE* 1.3 73.3 - - - +
640B GLY* 1.3 63.6 + - - +
641B ARG 3.2 0.7 + - - -
642B ASN* 3.0 24.6 + - + +
644B TYR* 3.9 14.8 - - + -
778C ILE* 4.5 5.2 - - + -
780C LEU* 3.6 27.7 - - + +
796C THR* 3.6 7.4 - - - -
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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