Contacts of the helix formed by residues 624 - 644 (chain A) in PDB entry 2HX4
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 LEU 624 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621A THR 2.8 18.4 + - - +
622A SER* 4.5 0.4 - - - -
623A SER* 1.3 82.2 - - - +
625A TRP* 1.3 59.2 + - - +
626A LYS 3.3 1.6 - - - -
627A ASP* 3.2 21.4 + - + +
628A GLN* 2.9 27.9 + - - +
631B VAL* 3.9 6.5 - - + +
634B ASN* 3.6 33.9 - - + -
635B ILE* 3.6 22.9 - - + +
638B LEU* 3.5 25.6 - - + -
650B ASP* 4.5 2.0 - - + -
651B HIS* 3.6 26.9 - - + -
652B HIS* 4.2 5.4 - - + -
683B MET* 4.8 1.8 - - + -
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Residues in contact with TRP 625 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607A LEU* 4.2 3.6 - - + -
608A GLU* 4.0 23.8 - - + -
611A ALA* 3.3 27.8 - - + -
616A LEU* 3.8 26.2 - - + +
617A ASP 3.6 2.2 - - - +
618A MET* 3.4 56.0 + - + +
620A LYS 3.8 10.0 + - - -
621A THR* 4.3 15.0 - - + +
623A SER* 3.1 26.0 - - - +
624A LEU* 1.3 73.7 - - - +
626A LYS* 1.3 120.3 + - + +
628A GLN* 3.8 12.0 - - - +
629A ALA* 3.0 27.6 + - + +
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Residues in contact with LYS 626 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601A ASN* 5.0 14.5 + - - +
607A LEU* 3.6 34.4 - - + +
608A GLU* 6.0 0.4 - - - -
621A THR* 6.4 3.1 - - + -
624A LEU 3.3 0.8 - - - -
625A TRP* 1.3 124.9 - - + +
627A ASP* 1.3 63.0 + - - +
629A ALA* 4.7 0.2 - - - -
630A LEU* 2.9 29.6 + - - +
652B HIS* 4.2 21.2 + - + +
687B ILE* 4.2 19.2 + - + +
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Residues in contact with ASP 627 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624A LEU* 3.4 23.9 - - + +
625A TRP 3.1 0.2 - - - -
626A LYS* 1.3 74.7 - - - +
628A GLN* 1.3 66.4 + - - +
630A LEU* 3.3 3.7 + - - +
631A VAL* 3.0 27.0 + - - +
631B VAL* 4.0 20.0 - - + -
651B HIS* 2.9 22.4 + - - -
652B HIS* 2.6 28.0 + - - -
683B MET* 3.6 7.1 - - + +
684B SER* 2.5 30.6 + - - +
687B ILE* 4.2 3.6 - - - -
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Residues in contact with GLN 628 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614A MET* 4.6 8.8 - - + +
616A LEU* 3.7 29.0 - - + +
623A SER* 4.0 8.3 - - - +
624A LEU 2.9 12.6 + - - +
625A TRP* 3.3 9.8 + - - +
627A ASP* 1.3 73.5 - - - +
629A ALA* 1.3 65.9 + - - +
631A VAL* 3.1 15.2 + - - +
632A GLU* 3.2 15.1 + - - +
550B LYS* 6.0 4.5 - - - +
631B VAL* 3.3 26.4 - - + +
632B GLU* 2.9 25.9 + - - +
635B ILE* 3.5 16.1 - - + +
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Residues in contact with ALA 629 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607A LEU* 4.2 13.5 - - + +
610A VAL* 4.1 18.2 - - + -
611A ALA* 4.3 14.8 - - + +
614A MET* 3.8 18.2 - - - -
616A LEU* 4.3 1.2 - - + +
625A TRP 3.0 14.5 + - - +
626A LYS* 3.9 3.6 - - - +
628A GLN* 1.3 80.0 - - - +
630A LEU* 1.3 63.6 + - - +
632A GLU* 3.0 4.4 + - - +
633A ILE* 2.9 28.2 + - - +
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Residues in contact with LEU 630 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595A VAL* 4.0 16.6 - - + -
599A CYS* 3.7 30.5 - - + -
607A LEU* 3.9 6.4 - - + +
626A LYS 2.9 19.5 + - - +
627A ASP* 3.5 5.6 - - - +
629A ALA* 1.3 76.8 - - - +
631A VAL* 1.3 65.6 + - - +
633A ILE* 3.4 3.3 + - - +
634A ASN* 3.0 45.9 + - - +
683A MET* 3.9 31.4 - - + -
684B SER* 4.2 9.9 - - - +
687B ILE* 3.8 29.6 - - + -
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Residues in contact with VAL 631 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
627A ASP 3.0 14.7 + - - +
628A GLN* 3.1 7.2 + - - +
630A LEU* 1.3 75.9 - - - +
632A GLU* 1.3 65.6 + - - +
634A ASN* 3.1 5.7 + - - +
635A ILE* 3.0 25.4 + - + +
683A MET* 4.0 22.2 - - + -
624B LEU* 4.0 2.8 - - + +
627B ASP* 3.7 15.0 - - + +
628B GLN* 3.1 41.5 - - + +
631B VAL* 3.5 23.6 - - + -
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Residues in contact with GLU 632 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A HIS* 2.6 45.5 + - + +
550A LYS* 4.7 3.2 + - - -
551A PHE* 3.8 18.4 - - + -
554A PHE* 5.4 1.3 - - + -
610A VAL* 5.3 2.7 - - + -
614A MET* 3.2 35.6 - - + +
628A GLN 3.2 5.8 + - - +
629A ALA 3.0 7.1 + - - +
631A VAL* 1.3 76.5 - - - +
633A ILE* 1.3 57.7 + - + +
635A ILE* 2.7 29.9 + - - +
636A ALA* 2.9 11.1 + - - +
628B GLN* 2.7 31.7 + - - +
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Residues in contact with ILE 633 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546A ILE* 6.4 0.2 - - + -
554A PHE* 4.2 17.5 - - + -
594A GLY* 3.7 20.2 - - - +
598A TYR* 4.0 22.7 - - + -
599A CYS* 3.4 25.1 - - - -
606A ILE* 4.0 9.0 - - + +
607A LEU* 4.2 9.4 - - + -
610A VAL* 3.6 39.7 - - + -
629A ALA 2.9 17.4 + - - +
630A LEU* 3.5 7.0 - - - +
632A GLU* 1.3 74.9 - - - +
634A ASN* 1.3 58.7 + - - +
636A ALA* 3.0 18.4 + - - +
637A VAL* 3.1 13.2 + - + +
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Residues in contact with ASN 634 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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590A GLY 4.0 1.6 - - - +
591A THR* 3.5 15.6 + - - +
594A GLY* 3.4 34.0 + - - -
595A VAL* 3.3 28.2 + - - +
630A LEU* 3.0 25.2 + - - +
631A VAL 3.1 5.3 + - - +
633A ILE* 1.3 76.9 - - - +
635A ILE* 1.3 65.7 + - - +
637A VAL* 3.9 6.5 - - - +
638A LEU* 3.3 29.8 + - + +
651A HIS* 5.5 0.9 - - + -
683A MET* 3.7 10.8 - - - +
624B LEU* 3.6 19.7 - - + -
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Residues in contact with ILE 635 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A HIS* 4.2 6.7 - - + +
549A PRO* 3.9 27.6 - - + -
631A VAL* 3.0 11.2 + - + +
632A GLU* 2.7 20.1 + - - +
634A ASN* 1.3 73.1 - - - +
636A ALA* 1.3 58.8 + - - +
638A LEU* 3.9 3.2 - - - +
639A TYR* 2.9 27.9 + - + +
622B SER 5.0 3.6 - - - +
623B SER* 3.1 31.6 - - - +
624B LEU* 3.5 18.6 - - + -
628B GLN* 3.4 39.7 - - + +
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Residues in contact with ALA 636 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546A ILE* 4.0 2.8 - - + +
547A ARG 3.2 19.2 - - - +
548A HIS* 4.2 11.0 - - + +
549A PRO* 4.6 0.2 - - - -
554A PHE* 3.7 31.2 - - + -
632A GLU 2.9 9.1 + - - +
633A ILE 3.0 11.9 + - - +
635A ILE* 1.3 76.7 - - - +
637A VAL* 1.3 61.8 + - - +
639A TYR* 4.2 2.2 - - - -
640A SER* 2.8 31.7 + - - -
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Residues in contact with VAL 637 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546A ILE* 4.4 13.2 - - + -
590A GLY* 4.1 17.0 - - - +
593A ILE* 4.1 15.9 - - + -
594A GLY* 3.9 15.9 - - - +
598A TYR* 3.8 29.2 - - + -
633A ILE* 3.1 13.6 + - + +
634A ASN* 4.1 6.3 - - - +
635A ILE 3.4 0.2 - - - -
636A ALA* 1.3 74.6 - - - +
638A LEU* 1.3 65.4 + - + +
640A SER* 3.8 0.3 - - - -
641A PHE* 3.2 31.1 + - + -
648A ILE* 3.9 20.4 - - + -
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Residues in contact with LEU 638 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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590A GLY* 3.5 33.0 - - - +
634A ASN* 3.3 20.7 + - + +
635A ILE 3.9 2.7 - - - +
637A VAL* 1.3 78.2 - - - +
639A TYR* 1.3 62.1 + - - +
641A PHE* 3.6 1.6 + - - +
642A GLN* 3.1 34.1 + - - +
648A ILE* 4.0 20.6 - - + -
649A VAL 4.3 0.4 - - - -
650A ASP* 3.6 32.8 - - + +
651A HIS* 5.4 2.7 - - + +
622B SER* 3.6 31.2 - - - +
624B LEU* 3.8 15.3 - - + -
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Residues in contact with TYR 639 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547A ARG* 3.5 39.0 - - + -
548A HIS 4.1 2.0 - - - -
549A PRO* 3.5 47.3 - - + +
635A ILE* 2.9 21.0 + - + +
636A ALA 3.7 2.7 - - - +
638A LEU* 1.3 76.8 - - - +
640A SER* 1.3 62.4 + - - +
642A GLN* 3.7 12.0 - - - +
643A SER* 2.7 46.0 + - - -
622B SER 5.5 0.2 + - - -
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Residues in contact with SER 640 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544A VAL* 3.5 12.1 - - - -
545A PRO 3.4 18.3 + - - -
546A ILE* 3.5 5.4 - - - -
547A ARG* 2.9 41.5 + - - +
636A ALA 2.8 17.6 + - - -
637A VAL 3.8 3.1 - - - -
639A TYR* 1.3 78.3 - - - +
641A PHE* 1.3 65.5 + - - +
643A SER* 2.9 5.4 + - - -
644A ASP* 2.9 24.4 + - - +
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Residues in contact with PHE 641 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544A VAL* 3.7 32.1 - - + -
546A ILE* 4.5 8.3 - - + -
561A TRP* 4.7 4.0 - - + -
562A TYR 3.9 13.9 - - - -
563A GLY* 3.9 21.3 - - - -
588A TYR* 4.6 3.6 - + + -
593A ILE* 3.8 27.8 - - + -
637A VAL* 3.2 23.3 + - + +
638A LEU 3.9 0.2 - - - +
640A SER* 1.3 78.1 - - - +
642A GLN* 1.3 60.8 + - - +
644A ASP 3.3 1.7 + - - -
645A LYS 3.0 3.8 + - - -
646A VAL* 2.8 45.1 + - + +
647A THR 3.7 10.8 - - - -
648A ILE* 3.4 42.4 - - + -
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Residues in contact with GLN 642 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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638A LEU* 3.1 30.3 + - - +
639A TYR* 3.7 10.9 - - + +
641A PHE* 1.3 72.4 - - - +
643A SER* 1.3 69.1 + - - +
645A LYS* 2.8 22.0 + - - +
646A VAL 4.6 3.1 - - - +
648A ILE* 4.2 14.8 - - + +
620B LYS* 4.7 11.8 - - - +
622B SER* 3.1 35.5 + - - -
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Residues in contact with SER 643 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547A ARG* 3.1 26.2 - - - -
639A TYR* 2.7 46.2 + - - -
640A SER 3.3 4.3 - - - -
642A GLN* 1.3 78.2 - - - +
644A ASP* 1.3 57.9 + - - +
645A LYS* 3.4 16.5 + - - +
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Residues in contact with ASP 644 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452A LYS 5.7 0.5 - - - +
453A GLY* 5.8 0.2 - - - -
542A LEU* 6.3 0.2 - - + -
543A GLU 4.7 2.0 - - - +
544A VAL* 4.0 7.5 - - + +
545A PRO* 3.5 18.2 - - - +
547A ARG* 2.6 43.5 + - - -
640A SER 2.9 11.7 + - - +
641A PHE 3.9 3.4 - - - +
642A GLN 3.1 0.2 - - - -
643A SER* 1.3 75.7 - - - +
645A LYS* 1.3 73.9 + - - +
646A VAL* 3.2 19.0 + - + +
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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
------------------------------------------------------------
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