Contacts of the helix formed by residues 631 - 651 (chain B) in PDB entry 2HRC
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 PRO 631 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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626B ILE* 5.1 1.1 - - + -
629B GLY 3.8 6.3 - - - +
630B SER* 1.3 85.1 - - - +
632B ILE* 1.3 64.1 + - - +
633B LYS 3.3 2.0 - - - -
634B ILE* 3.2 20.6 + - + +
635B TRP* 3.1 39.1 + - + +
840B ASP* 3.4 21.8 - - + +
841B HIS* 4.3 6.7 - - - -
845B LEU* 3.9 27.4 - - + -
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Residues in contact with ILE 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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575B ASN* 4.1 12.8 - - - +
577B GLY* 3.9 23.1 - - - +
578B GLY 4.7 3.6 - - - +
630B SER* 3.2 19.5 + - - +
631B PRO* 1.3 78.4 - - - +
633B LYS* 1.3 58.7 + - - +
635B TRP* 3.4 4.6 + - - +
636B THR* 2.7 44.1 + - - +
663B PHE* 3.8 20.2 - - + -
837B PHE* 4.1 17.9 - - + -
839B SER* 5.2 3.9 + - - -
840B ASP 3.9 6.5 - - - +
841B HIS* 3.6 24.0 - - + -
924B CL 3.6 15.7 - - + -
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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
----------------------------------------------------------
580B GLU* 3.8 26.4 + - + +
630B SER 4.8 3.7 + - - +
631B PRO 3.3 0.8 - - - -
632B ILE* 1.3 78.7 - - - +
634B ILE* 1.3 60.6 + - + +
636B THR* 3.8 1.2 - - - -
637B SER* 2.9 40.2 + - - +
661B ILE* 4.1 14.6 - - + -
663B PHE* 3.8 25.6 - - + -
667B HIS 4.6 5.8 + - - +
668B PRO* 4.0 28.1 - - + +
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Residues in contact with ILE 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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580B GLU* 6.4 3.1 - - + -
630B SER 5.6 1.6 - - - +
631B PRO* 3.2 20.7 + - + +
633B LYS* 1.3 78.0 - - + +
635B TRP* 1.3 69.7 + - + +
637B SER* 3.7 5.2 - - - -
638B LYS* 3.1 49.1 + - + +
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Residues in contact with TRP 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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631B PRO* 3.1 40.8 + - + +
632B ILE 3.9 1.1 - - - +
634B ILE* 1.3 77.8 - - + +
636B THR* 1.3 66.9 + - - +
638B LYS* 3.2 39.3 + - + +
639B GLN* 2.9 33.2 + - - +
839B SER* 3.7 25.4 - - - +
840B ASP* 4.1 10.5 + - - +
872B ASN* 3.5 48.2 + - + +
873B GLY* 3.4 22.7 - - - -
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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
----------------------------------------------------------
573B MET* 3.8 27.1 - - + +
575B ASN* 4.7 6.1 + - + +
632B ILE* 2.7 37.1 + - - +
633B LYS* 3.8 4.9 - - - -
635B TRP* 1.3 75.8 - - - +
637B SER* 1.3 52.8 + - - +
639B GLN* 3.4 11.9 + - - +
640B GLY* 2.8 32.4 + - - -
659B TYR* 4.8 0.2 - - - -
661B ILE* 3.7 33.2 - - + -
663B PHE* 4.1 5.6 - - + -
690B GLN* 5.4 6.1 - - + +
839B SER* 5.2 2.3 + - - -
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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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633B LYS* 2.9 31.0 + - - +
634B ILE* 3.7 6.5 - - - -
636B THR* 1.3 76.9 - - - +
638B LYS* 1.3 57.7 + - - +
640B GLY 3.2 0.2 + - - -
641B GLU* 2.9 42.6 + - - +
659B TYR* 3.6 22.6 + - - -
661B ILE* 3.5 14.4 - - - +
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Residues in contact with LYS 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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634B ILE* 3.1 37.1 + - + +
635B TRP* 3.6 44.6 - - + +
637B SER* 1.3 75.5 - - - +
639B GLN* 1.3 64.6 + - + +
641B GLU* 3.6 13.9 - - - +
642B GLY* 3.1 19.9 + - - -
873B GLY* 5.2 7.4 - - - -
878B SER* 4.6 1.4 + - - -
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Residues in contact with GLN 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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573B MET* 4.4 2.4 - - + +
635B TRP* 2.9 22.0 + - - +
636B THR* 3.7 13.3 + - - +
638B LYS* 1.3 75.8 - - + +
640B GLY* 1.3 58.9 + - - +
642B GLY* 3.4 1.2 + - - -
643B MET* 2.9 30.3 + - - +
690B GLN* 4.6 7.4 - - - +
838B THR* 3.7 6.6 + - - -
839B SER* 3.2 25.1 + - - -
872B ASN* 2.9 34.3 + - - +
873B GLY* 5.3 0.9 - - - -
877B PHE* 3.3 30.2 - - + -
878B SER* 4.1 12.3 + - - +
881B LEU* 3.8 19.6 - - + +
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Residues in contact with GLY 640 (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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573B MET* 3.6 22.4 - - - +
636B THR 2.8 21.8 + - - -
637B SER 3.7 0.9 - - - -
639B GLN* 1.3 73.4 - - - +
641B GLU* 1.3 61.2 + - - +
643B MET* 3.3 5.1 + - - +
644B VAL* 3.0 29.6 + - - +
659B TYR* 3.5 14.1 - - - -
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Residues in contact with GLU 641 (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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637B SER* 2.9 28.3 + - - +
638B LYS* 3.6 10.9 + - - +
639B GLN 3.3 0.2 - - - -
640B GLY* 1.3 76.5 - - - +
642B GLY* 1.3 63.9 + - - +
644B VAL* 3.4 4.2 + - - +
645B LYS* 3.1 23.2 + - - +
659B TYR* 3.6 24.6 + - + +
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Residues in contact with GLY 642 (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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638B LYS 3.1 10.7 + - - -
639B GLN 3.8 2.0 - - - -
641B GLU* 1.3 79.8 - - - +
643B MET* 1.3 62.9 + - - +
645B LYS* 3.4 8.5 + - - +
646B LEU* 3.2 27.7 + - - +
878B SER* 4.1 17.3 - - - -
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Residues in contact with MET 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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571B ILE* 3.5 43.5 - - + -
573B MET* 4.2 11.4 - - - +
639B GLN 2.9 17.2 + - - +
640B GLY 3.5 4.7 - - - +
642B GLY* 1.3 77.4 - - - +
644B VAL* 1.3 60.7 + - + +
646B LEU* 3.2 4.9 + - - +
647B LEU* 2.9 39.8 + - + +
659B TYR* 3.9 20.9 - - + -
688B PHE* 4.1 11.7 - - - -
878B SER* 4.1 11.5 - - - +
881B LEU* 3.9 25.6 - - + -
882B ALA* 3.9 15.4 - - - +
885B VAL* 4.1 6.1 - - - -
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Residues in contact with VAL 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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571B ILE* 5.5 0.2 - - + -
640B GLY 3.0 20.5 + - - +
641B GLU* 3.8 5.2 - - - +
643B MET* 1.3 78.8 - - + +
645B LYS* 1.3 67.9 + - - +
647B LEU* 3.2 7.0 + - + +
648B ASP* 3.0 33.5 + - - +
657B HIS* 3.2 29.8 - - + +
658B LYS* 4.1 4.7 - - - -
659B TYR* 3.7 37.5 - - + +
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Residues in contact with LYS 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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641B GLU 3.1 16.5 + - - +
642B GLY* 3.7 8.7 - - - +
644B VAL* 1.3 79.9 - - - +
646B LEU* 1.3 68.8 + - + +
648B ASP* 3.7 8.3 + - - +
649B GLU* 3.6 20.3 + - + +
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Residues in contact with LEU 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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642B GLY 3.2 13.1 + - - +
643B MET 3.6 6.1 - - - +
644B VAL 3.2 0.8 - - - -
645B LYS* 1.3 81.5 - - + +
647B LEU* 1.3 60.3 + - - +
649B GLU* 3.0 9.3 + - + +
650B LEU* 2.8 37.1 + - + +
875B PRO 5.1 1.1 - - - +
878B SER* 3.8 10.1 - - - +
879B LYS* 3.5 44.2 - - + +
882B ALA* 3.7 10.3 - - + -
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Residues in contact with LEU 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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571B ILE* 4.2 11.4 - - + -
643B MET* 2.9 37.9 + - + +
644B VAL* 3.2 6.0 + - - +
646B LEU* 1.3 77.8 - - - +
648B ASP* 1.3 57.6 + - - +
650B LEU* 4.1 6.3 - - + -
651B SER* 2.8 31.3 + - - -
657B HIS* 3.3 37.9 - - + +
882B ALA* 3.5 29.2 - - + +
885B VAL* 3.8 29.4 - - + -
886B HIS* 4.1 11.7 - - + +
889B ILE* 5.3 0.7 - - + -
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Residues in contact with ASP 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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565B ARG* 3.5 33.7 + - - +
644B VAL* 3.0 28.4 + - - +
645B LYS* 4.0 7.8 - - - +
646B LEU 3.3 0.4 - - - -
647B LEU* 1.3 75.2 - - - +
649B GLU* 1.3 70.5 + - - +
651B SER 4.5 0.2 - - - -
652B PRO* 4.1 18.2 - - - +
655B ALA* 4.2 6.6 - - + +
656B PRO* 3.6 3.3 - - - +
657B HIS* 2.8 43.0 + - - +
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Residues in contact with GLU 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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645B LYS* 3.6 16.8 - - + +
646B LEU* 3.0 7.1 + - + +
647B LEU 3.0 0.8 - - - -
648B ASP* 1.3 90.7 - - - +
650B LEU* 1.3 65.4 + - + +
651B SER 3.5 0.4 - - - -
652B PRO* 3.7 10.0 - - - +
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Residues in contact with LEU 650 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646B LEU* 2.8 25.4 + - + +
647B LEU* 4.0 5.8 - - + +
649B GLU* 1.3 79.5 - - + +
651B SER* 1.3 57.5 + - - +
652B PRO* 3.5 6.1 - - - +
879B LYS* 6.3 0.7 - - + -
882B ALA* 3.7 36.1 - - + +
883B ASP* 3.9 19.5 - - - +
886B HIS* 3.5 37.6 + - + +
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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
----------------------------------------------------------
647B LEU* 2.8 21.4 + - - -
648B ASP 4.4 0.2 - - - -
650B LEU* 1.3 76.2 - - - +
652B PRO* 1.3 64.5 - - - +
653B ASN* 3.1 4.1 + - - +
654B THR* 2.7 38.3 + - - +
655B ALA 3.3 0.2 + - - -
657B HIS* 3.2 18.7 - - - -
886B HIS* 4.0 20.2 + - - -
889B ILE* 4.5 10.3 - - - +
890B GLN* 6.0 0.3 - - - +
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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
------------------------------------------------------------
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