Contacts of the helix formed by residues 743 - 761 (chain D) in PDB entry 2HHW
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 PHE 743 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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668D ASP* 2.9 27.6 - - - +
670D ASN* 4.1 6.5 - - + -
671D LEU* 3.8 40.8 - - + -
674D ALA* 5.4 1.6 - - + -
681D ILE* 4.8 17.5 - - + -
739D TYR* 3.1 57.2 + + + +
740D PHE* 3.3 11.2 - - + +
741D GLU 3.4 0.2 - - - -
742D SER* 1.3 99.2 - - - +
744D PRO* 1.3 61.4 - - - +
746D VAL* 3.1 26.3 + - + +
747D LYS 3.4 7.1 + - - -
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Residues in contact with PRO 744 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668D ASP* 3.9 2.7 - - - +
670D ASN* 4.7 5.6 - - - +
740D PHE 3.1 12.1 - - - +
741D GLU* 3.6 11.2 - - - +
742D SER 3.3 9.6 - - - +
743D PHE* 1.3 89.1 - - - +
745D GLY* 1.3 57.6 + - - +
747D LYS* 3.3 7.8 + - + +
748D ARG* 2.9 39.6 + - - +
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Residues in contact with GLY 745 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
666D ALA* 3.9 7.5 - - - +
668D ASP* 2.6 32.2 + - - -
744D PRO* 1.3 79.2 - - - +
746D VAL* 1.3 55.0 + - - -
748D ARG* 3.2 27.1 + - - +
749D TYR* 2.8 29.6 + - - +
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Residues in contact with VAL 746 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662D LEU* 3.8 33.7 - - + -
666D ALA* 4.1 8.3 - - + -
668D ASP* 3.0 22.4 + - + +
671D LEU* 4.1 18.4 - - + -
713D VAL* 4.6 9.2 - - + -
739D TYR* 6.3 0.2 - - + -
740D PHE* 4.1 16.4 - - + -
743D PHE* 3.1 20.6 + - + +
745D GLY* 1.3 73.4 - - - +
747D LYS* 1.3 60.0 + - - +
749D TYR* 3.1 2.6 + - - +
750D MET* 2.9 38.7 + - + +
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Residues in contact with LYS 747 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
740D PHE* 3.8 43.7 - - + +
743D PHE 3.4 2.6 + - - -
744D PRO* 3.3 12.0 + - + +
746D VAL* 1.3 79.3 - - - +
748D ARG* 1.3 62.3 + - - +
750D MET* 3.3 6.6 + - - +
751D GLU* 3.1 50.3 + - + +
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Residues in contact with ARG 748 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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666D ALA 5.3 4.2 + - - -
667D GLU 4.9 7.1 + - - -
668D ASP* 5.4 0.6 - - - +
669D ASP* 5.7 3.2 + - - +
744D PRO* 2.9 22.5 + - - +
745D GLY* 3.2 26.6 + - - +
747D LYS* 1.3 77.0 - - - +
749D TYR* 1.3 58.0 + - - +
751D GLU* 3.2 15.4 + - - +
752D ASN* 2.9 54.4 + - - +
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Residues in contact with TYR 749 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662D LEU* 4.0 8.7 - - + -
665D ILE* 3.5 27.3 - - + +
666D ALA* 3.5 25.1 - - + +
745D GLY 2.8 15.2 + - - +
746D VAL 3.3 6.7 - - - +
748D ARG* 1.3 79.2 - - - +
750D MET* 1.3 89.4 + - + +
752D ASN* 3.1 7.1 + - + +
753D ILE* 2.8 59.6 + - + +
792D MET 4.6 2.2 - - - -
795D PRO* 3.6 26.5 - - - +
796D ILE* 4.0 13.1 - - + +
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Residues in contact with MET 750 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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662D LEU* 3.9 29.4 - - + -
713D VAL 3.1 28.7 - - - +
714D TYR* 4.5 6.7 - - + -
740D PHE* 5.6 4.9 - - + -
746D VAL* 2.9 29.0 + - + +
747D LYS* 3.3 7.2 + - - +
749D TYR* 1.3 86.7 - - + +
751D GLU* 1.3 60.7 + - + +
753D ILE* 3.5 6.3 - - - +
754D VAL* 3.4 24.3 - - - +
792D MET* 3.4 58.7 - - + +
796D ILE* 4.8 0.2 - - + -
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Residues in contact with GLU 751 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747D LYS* 3.1 46.6 + - + +
748D ARG* 3.5 14.1 - - - +
749D TYR 3.1 0.2 - - - -
750D MET* 1.3 78.0 - - + +
752D ASN* 1.3 64.3 + - - +
754D VAL* 3.4 7.1 + - - +
755D GLN* 3.3 26.1 + - - +
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Residues in contact with ASN 752 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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748D ARG* 2.9 44.5 + - - +
749D TYR* 3.8 7.8 - - + +
751D GLU* 1.3 79.0 - - - +
753D ILE* 1.3 60.4 + - - +
755D GLN* 3.3 9.2 + - - +
756D GLU* 2.9 28.5 + - - +
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Residues in contact with ILE 753 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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749D TYR* 2.8 49.8 + - + +
750D MET* 3.5 19.1 - - - +
752D ASN* 1.3 72.7 - - - +
754D VAL* 1.3 62.8 + - + +
756D GLU* 3.3 22.6 + - + +
757D ALA* 3.0 28.1 + - - +
763D VAL* 4.4 10.5 - - + -
764D THR 5.9 1.3 - - - +
791D ALA* 3.5 34.0 - - - +
792D MET* 4.1 7.6 - - - +
795D PRO* 4.2 10.8 - - + -
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Residues in contact with VAL 754 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
750D MET 3.4 15.3 - - - +
751D GLU* 3.4 9.8 + - - +
752D ASN 3.2 0.4 - - - -
753D ILE* 1.3 84.6 - - + +
755D GLN* 1.3 66.5 + - - +
757D ALA* 3.3 3.1 + - - +
758D LYS* 3.1 50.6 + - - +
776D ILE* 3.7 7.1 - - + +
788D GLU* 3.8 46.4 - - + +
791D ALA* 4.2 4.5 - - + -
792D MET* 4.2 9.9 - - + -
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Residues in contact with GLN 755 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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751D GLU 3.3 13.2 + - - +
752D ASN* 3.3 10.9 + - - +
753D ILE 3.3 0.4 - - - -
754D VAL* 1.3 83.5 - - - +
756D GLU* 1.3 61.2 + - - +
758D LYS* 3.4 33.5 + - - +
759D GLN* 3.1 21.8 + - - +
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Residues in contact with GLU 756 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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759A GLN* 5.1 8.2 + - - -
752D ASN 2.9 17.4 + - - +
753D ILE* 3.7 24.3 - - + +
754D VAL 3.3 0.2 - - - -
755D GLN* 1.3 77.8 - - - +
757D ALA* 1.3 57.5 + - - +
759D GLN* 3.3 8.0 + - - +
760D LYS* 2.9 64.6 + - + +
762D TYR 4.6 3.0 - - - +
764D THR* 5.7 0.9 + - - -
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Residues in contact with ALA 757 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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753D ILE 3.0 16.3 + - - +
756D GLU* 1.3 75.2 - - - +
758D LYS* 1.3 57.7 + - - +
761D GLY* 2.7 34.7 + - - -
762D TYR 3.6 12.8 - - - +
763D VAL* 3.6 22.2 - - + +
773D LEU* 4.5 4.9 - - + -
776D ILE* 3.4 31.1 - - + +
791D ALA* 4.1 2.9 - - + -
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Residues in contact with LYS 758 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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754D VAL* 3.1 33.8 + - - +
755D GLN* 3.7 30.1 - - - +
756D GLU 3.3 0.2 - - - -
757D ALA* 1.3 76.9 - - - +
759D GLN* 1.3 62.2 + - - +
761D GLY* 4.1 3.3 + - - -
776D ILE* 2.9 52.1 + - + +
777D THR* 4.2 18.3 - - + +
784D ARG* 3.8 8.5 - - - +
788D GLU* 3.2 21.5 + - - -
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Residues in contact with GLN 759 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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755D GLN 3.1 16.4 + - - +
756D GLU* 3.7 8.0 - - - +
757D ALA 3.2 0.2 - - - -
758D LYS* 1.3 79.2 - - - +
760D LYS* 1.3 96.2 + - - +
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Residues in contact with LYS 760 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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759A GLN* 6.1 2.2 - - - +
756D GLU* 2.9 48.0 + - + +
759D GLN* 1.3 103.2 + - - +
761D GLY* 1.3 57.6 + - - +
762D TYR* 3.3 54.5 - - + +
772D TYR* 5.5 0.7 - - - -
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Residues in contact with GLY 761 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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757D ALA 2.7 20.9 + - - -
758D LYS 4.1 3.1 + - - -
759D GLN 3.5 1.4 - - - -
760D LYS* 1.3 73.7 - - - +
762D TYR* 1.3 61.6 + - - +
772D TYR* 3.5 11.8 - - - +
773D LEU* 2.9 29.8 + - - -
774D PRO* 4.4 1.8 - - - +
776D ILE* 5.8 1.3 - - - -
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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