Contacts of the helix formed by residues 791 - 807 (chain A) in PDB entry 2VZ9
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 ASP 791 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421A PRO* 4.9 2.4 - - - +
509A SER* 3.1 23.9 - - - -
512A ARG* 3.2 26.8 + - - -
789A HIS* 3.1 13.8 + - + +
790A ARG* 1.3 89.3 - - + +
792A ASN* 1.3 52.6 + - - +
793A LEU* 3.2 14.9 + - - +
794A GLU* 2.7 54.5 + - - +
795A PHE 3.4 5.9 + - - -
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Residues in contact with ASN 792 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A TRP* 3.3 35.0 - - - -
505A GLY 4.5 0.8 + - - -
507A GLY* 4.0 7.9 - - - +
508A LEU 5.2 0.2 - - - +
509A SER* 3.5 14.5 + - - +
510A LEU* 4.1 17.9 - - + +
784A LEU 4.8 0.3 - - - +
785A MET* 3.8 18.4 - - + +
786A LYS 3.1 33.0 + - - +
789A HIS* 3.8 8.5 + - - +
790A ARG 4.3 0.2 - - - -
791A ASP* 1.3 72.9 + - - +
793A LEU* 1.3 53.8 + - - +
794A GLU 3.1 0.2 - - - -
795A PHE* 3.6 7.0 - - - +
796A PHE* 2.7 38.0 + - - +
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Residues in contact with LEU 793 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A LEU* 4.5 11.7 - - + -
421A PRO* 3.6 23.3 - - + +
509A SER* 3.8 15.2 - - - +
510A LEU* 4.0 16.1 - - + +
512A ARG* 3.0 35.4 - - + +
513A LEU* 3.7 37.7 - - + +
791A ASP* 2.8 13.2 + - - +
792A ASN* 1.3 78.9 - - - +
794A GLU* 1.3 60.3 + - - +
796A PHE* 4.1 1.1 - - + +
797A LEU* 3.3 36.6 + - + +
816A PHE* 5.4 2.0 - - + -
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Residues in contact with GLU 794 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A PRO* 4.3 15.3 - - + +
472A VAL* 4.6 9.8 - - + +
475A GLY* 3.4 20.0 - - - -
476A GLU 3.4 5.5 + - - -
477A ALA* 3.4 36.3 + - + +
789A HIS* 4.9 5.9 - - + -
790A ARG* 3.6 25.1 + - - -
791A ASP* 2.7 29.3 + - - +
793A LEU* 1.3 76.5 - - - +
795A PHE* 1.3 62.0 + - - +
796A PHE 3.2 0.4 - - - -
797A LEU* 3.4 5.4 + - - +
798A SER* 2.8 32.7 + - - +
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Residues in contact with PHE 795 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
783A PRO* 3.9 17.7 - - + -
784A LEU 3.7 7.6 - - - -
785A MET* 3.8 5.6 - - - -
786A LYS* 3.6 47.6 - - + -
789A HIS* 3.9 37.4 - + + +
791A ASP 3.4 1.6 + - - -
792A ASN* 3.0 11.3 + - - +
794A GLU* 1.3 80.7 - - - +
796A PHE* 1.3 61.1 + - - +
798A SER* 3.5 8.6 - - - -
799A ASN* 2.9 47.5 + - - -
802A ARG* 6.2 1.6 - - - -
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Residues in contact with PHE 796 (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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510A LEU* 4.1 18.4 - - + -
513A LEU* 4.9 3.4 - - + -
563A LEU* 4.5 9.9 - - + -
566A LEU* 3.6 41.7 - - + -
567A LEU* 4.8 3.1 - - + -
570A LEU* 4.7 8.1 - - + -
784A LEU* 3.5 52.7 - - + +
792A ASN 2.7 19.3 + - - +
793A LEU 4.1 2.2 - - - +
795A PHE* 1.3 73.1 - - - +
797A LEU* 1.3 63.6 + - + +
799A ASN* 3.1 4.1 + - - +
800A VAL* 2.7 61.5 + - + +
815A LEU* 4.0 16.8 - - + -
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Residues in contact with LEU 797 (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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421A PRO* 3.2 38.1 - - + +
422A ARG 4.3 5.4 - - - +
423A LEU* 3.6 35.2 - - + +
472A VAL* 4.5 10.8 - - + -
793A LEU* 3.3 29.2 + - + +
794A GLU 3.9 3.4 - - - +
796A PHE* 1.3 80.5 - - + +
798A SER* 1.3 57.7 + - - +
800A VAL* 3.4 4.4 - - + +
801A GLY* 2.7 32.4 + - - -
815A LEU* 3.6 31.6 - - + -
816A PHE* 4.1 10.1 - - + -
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Residues in contact with SER 798 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470A TYR* 3.4 21.9 + - - -
472A VAL* 4.1 6.4 - - - +
477A ALA* 5.8 0.2 - - - +
479A SER* 3.4 23.0 + - - -
794A GLU 2.8 19.7 + - - -
795A PHE* 3.5 15.7 - - - -
797A LEU* 1.3 77.4 - - - +
799A ASN* 1.3 62.2 + - - -
801A GLY 3.3 0.7 + - - -
802A ARG* 3.0 30.7 + - - +
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Residues in contact with ASN 799 (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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782A ILE* 3.8 10.0 - - + +
783A PRO* 2.7 39.4 + - - +
784A LEU* 3.8 7.7 - - + +
795A PHE* 2.9 46.7 + - - +
796A PHE 3.1 5.4 + - - +
797A LEU 3.1 0.4 - - - -
798A SER* 1.3 76.8 - - - +
800A VAL* 1.3 66.8 + - - +
801A GLY 3.0 1.1 - - - -
802A ARG* 3.2 28.8 + - - +
803A LEU* 2.9 27.6 + - - +
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Residues in contact with VAL 800 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A LEU* 3.2 21.2 - - + +
567A LEU* 6.0 0.4 - - + -
570A LEU* 4.0 26.9 - - + -
784A LEU* 5.2 2.2 - - + +
796A PHE* 2.7 58.8 + - + +
797A LEU* 3.4 9.0 - - + +
799A ASN* 1.3 73.7 - - - +
801A GLY* 1.3 62.4 + - - +
803A LEU* 3.4 18.2 + - + +
804A HIS* 3.5 6.8 + - - +
810A VAL* 3.7 15.6 - - + +
812A PRO* 4.3 8.5 - - + -
815A LEU* 4.7 4.3 - - + -
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Residues in contact with GLY 801 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A LEU* 3.6 8.7 - - - +
425A GLN* 5.1 0.4 - - - -
470A TYR* 3.3 34.1 - - - +
797A LEU 2.7 13.0 + - - -
798A SER 3.5 5.2 - - - -
800A VAL* 1.3 75.8 - - - +
802A ARG* 1.3 58.7 + - - +
804A HIS* 2.9 28.8 + - - +
805A LEU* 3.2 4.5 + - - +
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Residues in contact with ARG 802 (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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470A TYR* 3.6 9.8 + - + -
481A GLU* 3.4 35.7 + - - +
780A THR* 5.8 1.6 - - + +
782A ILE* 3.9 17.6 - - + +
783A PRO* 6.1 2.6 - - - +
795A PHE* 6.2 1.6 - - - -
798A SER* 3.0 21.4 + - - +
799A ASN* 3.2 26.0 + - + +
801A GLY* 1.3 71.7 - - - +
803A LEU* 1.3 56.9 + - - +
804A HIS 2.9 5.3 + - - -
805A LEU* 3.0 9.2 + - + +
806A ALA* 2.9 29.3 + - - +
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Residues in contact with LEU 803 (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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492A VAL* 5.6 1.3 - - + -
567A LEU* 4.5 12.8 - - + -
570A LEU* 5.0 2.0 - - + -
572A LEU* 3.7 26.2 - - + -
757A VAL* 3.8 16.6 - - + -
759A VAL* 3.6 28.3 - - + -
782A ILE* 3.1 26.7 - - + -
784A LEU* 5.2 4.3 - - + -
799A ASN 2.9 13.7 + - - +
800A VAL* 3.6 16.4 - - + +
801A GLY 3.2 0.2 - - - -
802A ARG* 1.3 75.4 - - - +
804A HIS* 1.3 57.2 + - - +
806A ALA* 3.5 3.2 - - - +
808A VAL* 3.2 39.5 + - + +
810A VAL* 4.3 12.6 - - + -
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Residues in contact with HIS 804 (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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425A GLN* 3.2 49.5 + - + +
426A ALA 3.5 15.0 + - - -
427A SER* 3.6 1.2 + - - -
458A ALA* 3.9 15.9 - - + -
459A ALA* 5.1 2.5 - - - -
468A ARG* 3.0 71.8 + - + +
469A GLY 4.4 5.2 - - - -
800A VAL 3.5 3.4 + - - +
801A GLY 2.9 14.8 + - - +
802A ARG 2.9 0.6 - - - -
803A LEU* 1.3 76.5 - - - +
805A LEU* 1.3 53.2 + - + +
806A ALA 2.9 4.0 - - - -
807A GLY* 2.7 22.0 + - - -
808A VAL 4.1 6.5 + - - -
810A VAL* 4.3 6.9 + - + +
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Residues in contact with LEU 805 (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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468A ARG* 3.4 14.4 - - + +
469A GLY* 3.3 41.1 - - - +
470A TYR* 4.1 6.7 - - + +
481A GLU* 3.9 37.2 - - + +
482A VAL 4.4 0.2 - - - -
483A GLN* 3.7 37.0 - - + +
484A GLN 4.3 6.6 - - - +
485A VAL* 3.6 17.4 - - - +
486A PRO* 4.6 2.1 - - - +
801A GLY 3.2 10.1 + - - +
802A ARG* 3.0 10.9 + - + +
804A HIS* 1.3 80.5 - - + +
806A ALA* 1.3 61.9 + - - +
807A GLY* 4.4 0.2 - - - -
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Residues in contact with ALA 806 (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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485A VAL* 3.7 6.8 - - - +
486A PRO* 4.3 1.4 - - - +
490A ARG* 2.9 33.9 + - - +
757A VAL* 4.1 29.6 - - + -
780A THR* 4.8 10.8 - - + -
782A ILE* 4.7 3.1 - - + -
802A ARG 2.9 11.7 + - - +
803A LEU* 3.5 15.7 - - - +
804A HIS 2.9 0.6 - - - -
805A LEU* 1.3 80.4 - - - +
807A GLY* 1.3 57.8 + - - +
808A VAL* 3.7 3.4 - - + -
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Residues in contact with GLY 807 (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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462A PRO* 4.2 13.8 - - - +
468A ARG* 3.6 10.6 + - - -
485A VAL* 3.7 15.7 - - - -
486A PRO 5.5 0.9 - - - -
490A ARG* 4.8 8.7 - - - -
804A HIS 2.7 11.3 + - - -
806A ALA* 1.3 80.0 - - - +
808A VAL* 1.3 65.8 + - - +
809A SER* 3.9 2.8 + - - -
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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