Contacts of the helix formed by residues 635 - 648 (chain E) in PDB entry 3HR4
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 CYS 635 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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592E THR* 3.5 11.9 - - - -
625E GLY 3.4 28.9 - - - -
626E LEU 3.8 14.4 - - - -
627E GLY 3.8 3.4 - - - -
633E ARG 3.2 0.2 + - - -
634E PHE* 1.3 91.1 - - - +
636E ALA* 1.3 62.5 + - - +
637E PHE 3.5 0.2 - - - -
638E ALA* 4.0 7.6 - - + -
639E HIS* 3.2 22.9 + - - -
656E MET* 4.0 17.0 - - + -
658E GLU* 4.0 16.6 - - - +
659E GLY 4.3 1.1 - - - -
999E FMN 2.9 15.1 + - - -
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Residues in contact with ALA 636 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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592E THR* 3.2 3.8 + - + -
596E GLY* 3.1 31.6 - - - -
633E ARG* 3.2 28.3 + - + +
634E PHE 3.1 2.8 + - - -
635E CYS* 1.3 74.1 - - - +
637E PHE* 1.3 64.4 + - - +
638E ALA 3.1 2.0 - - - -
639E HIS* 3.3 5.1 + - - +
640E ASP* 2.8 33.1 + - - +
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Residues in contact with PHE 637 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544E ALA* 4.4 0.4 - - + -
572E MET* 3.9 26.0 - - + -
590E THR* 3.4 30.7 - - + -
591E SER 4.4 0.4 - - - +
592E THR* 2.7 21.0 + - + +
596E GLY* 4.2 4.9 - - - +
597E ASP 3.9 15.5 - - - +
598E CYS* 3.3 29.4 - - + -
599E PRO* 3.8 3.1 - - + -
602E GLY* 4.6 0.9 - - - -
606E LYS* 3.3 50.3 - - + -
610E PHE* 4.3 0.2 - + - -
636E ALA* 1.3 74.7 - - - +
638E ALA* 1.3 60.4 + - - +
640E ASP* 3.8 4.5 - - + -
641E ILE* 3.2 45.5 + - + +
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Residues in contact with ALA 638 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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590E THR* 4.1 12.4 - - + +
592E THR* 3.8 2.9 + - - +
623E VAL* 4.4 3.6 - - + -
625E GLY* 3.4 33.4 - - - +
635E CYS* 3.6 7.1 + - + +
636E ALA 3.1 0.6 - - - -
637E PHE* 1.3 75.5 - - - +
639E HIS* 1.3 64.5 + - - +
640E ASP 3.1 1.8 - - - -
641E ILE* 3.3 11.5 - - - +
642E ASP* 3.0 25.8 + - - +
656E MET* 3.4 19.5 - - + +
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Residues in contact with HIS 639 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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634E PHE 4.0 7.2 - - - -
635E CYS 3.2 16.3 + - - +
636E ALA* 3.3 6.0 + - - +
638E ALA* 1.3 78.9 - - - +
640E ASP* 1.3 60.6 + - - +
642E ASP* 3.5 4.1 + - - -
643E GLN* 2.9 52.8 + - - +
656E MET* 3.2 30.5 - - + +
658E GLU* 2.6 33.1 + - - -
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Residues in contact with ASP 640 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596E GLY 5.2 1.5 - - - +
606E LYS* 4.3 12.6 + - - +
610E PHE* 3.5 28.4 - - + -
636E ALA* 2.8 30.6 + - - +
637E PHE* 3.6 11.0 - - + +
638E ALA 3.1 0.2 - - - -
639E HIS* 1.3 76.9 - - - +
641E ILE* 1.3 61.5 + - - +
642E ASP 3.0 1.1 - - - -
643E GLN* 2.7 22.4 + - - +
644E LYS 2.9 13.7 + - - -
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Residues in contact with ILE 641 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572E MET* 5.4 5.6 - - + -
588E VAL* 3.7 14.6 - - + -
590E THR* 5.0 7.2 - - + -
606E LYS* 5.8 0.2 - - - -
609E LEU* 4.0 25.8 - - + +
610E PHE* 4.0 10.1 - - + -
623E VAL* 3.3 40.8 - - + -
637E PHE* 3.2 45.0 + - + +
638E ALA* 3.3 10.1 - - - +
640E ASP* 1.3 74.9 - - - +
642E ASP* 1.3 64.3 + - - +
644E LYS* 4.6 1.4 - - - +
645E LEU* 3.2 32.0 + - + +
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Residues in contact with ASP 642 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621E TYR* 3.1 38.3 + - - -
623E VAL* 3.8 14.3 + - + +
638E ALA 3.0 17.7 + - - +
639E HIS* 3.7 6.6 + - - +
641E ILE* 1.3 84.4 - - - +
643E GLN* 1.3 75.5 + - - +
645E LEU* 4.3 1.1 - - - -
646E SER* 3.7 3.5 + - - -
652E GLN* 3.6 17.5 - - - +
656E MET* 3.4 32.7 - - - +
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Residues in contact with GLN 643 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610E PHE* 5.9 0.4 - - + -
639E HIS* 2.9 42.5 + - - +
640E ASP* 2.7 9.2 + - - +
642E ASP* 1.3 90.6 + - - +
644E LYS* 1.3 66.4 + - - +
645E LEU 3.0 1.6 - - - -
646E SER* 2.9 21.2 + - - -
647E HIS* 3.0 36.7 + - + +
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Residues in contact with LYS 644 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609E LEU* 3.2 34.3 - - + +
610E PHE* 2.7 52.0 + - + -
612E LEU 2.7 30.4 + - - -
613E LYS* 4.9 1.4 - - - +
640E ASP 2.9 10.3 + - - +
641E ILE 4.6 1.6 - - - +
643E GLN* 1.3 72.7 - - - +
645E LEU* 1.3 59.4 + - - +
647E HIS* 3.6 15.6 + - + +
648E LEU* 3.0 44.5 + - + +
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Residues in contact with LEU 645 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580E LEU* 5.1 7.2 - - + -
586E LEU* 5.4 9.6 - - + -
588E VAL* 5.3 4.0 - - + -
609E LEU* 4.9 16.8 - - + -
619E PHE* 4.2 26.7 - - + -
621E TYR* 3.2 47.6 - - + +
623E VAL* 4.5 6.5 - - + -
641E ILE* 3.2 25.9 + - + +
642E ASP 4.1 0.4 - - - +
643E GLN 3.0 0.4 - - - -
644E LYS* 1.3 76.6 - - - +
646E SER* 1.3 62.1 + - - +
648E LEU* 2.8 34.4 + - + +
650E ALA* 3.4 12.9 + - + +
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Residues in contact with SER 646 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621E TYR* 3.4 17.8 + - - -
642E ASP 3.7 4.5 + - - -
643E GLN* 2.9 15.3 + - - -
645E LEU* 1.3 78.0 - - - +
647E HIS* 1.3 63.2 - - - +
649E GLY* 2.9 21.8 + - - -
650E ALA 3.9 12.5 + - - +
652E GLN* 6.0 0.5 - - - +
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Residues in contact with HIS 647 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643E GLN* 3.0 40.3 + - + +
644E LYS* 3.8 18.5 - - + +
646E SER* 1.3 80.3 - - - +
648E LEU* 1.3 57.9 + - + +
649E GLY 3.2 2.9 + - - -
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Residues in contact with LEU 648 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609E LEU* 4.1 6.7 - - + +
612E LEU* 3.8 26.9 - - + +
613E LYS* 3.6 32.1 - - - +
614E GLU 4.2 2.7 - - - +
615E LEU* 3.6 35.4 - - + +
618E LYS* 3.6 10.3 + - - +
644E LYS* 3.0 50.2 + - + +
645E LEU* 2.8 16.3 + - + +
647E HIS* 1.3 79.4 - - + +
649E GLY* 1.3 60.0 + - - +
650E ALA* 3.6 1.7 + - + +
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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