Contacts of the helix formed by residues 781 - 795 (chain J) in PDB entry 6H25
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 ARG 781 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527J GLY 3.4 5.4 - - - +
528J THR* 4.7 8.5 + - - +
539J MET* 3.6 4.9 - - - +
753J TYR* 4.4 6.2 + - - +
774J HIS* 3.0 51.6 + - - +
775J PHE 5.5 0.2 - - - +
776J THR* 5.4 2.2 + - - -
777J SER* 3.3 20.9 + - - +
778J PRO 3.6 4.7 - - - +
779J ILE 3.5 1.2 - - - -
780J ARG* 1.3 117.9 - - + +
782J TYR* 1.3 62.4 + - - +
783J ALA* 4.2 4.9 - - + +
784J ASP* 3.4 27.5 + - - +
785J VAL* 3.4 20.8 + - - +
821J HIS* 6.1 4.0 - - - -
42R U 3.9 10.7 + - - -
43R U 4.4 9.1 + - - -
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Residues in contact with TYR 782 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513J ILE* 6.0 0.4 - - + -
520J ASP* 2.6 38.1 + - - -
523J SER* 3.3 39.0 - - - +
524J ALA* 3.7 31.8 - - + +
527J GLY* 2.8 20.6 + - - +
539J MET* 3.7 3.5 - - - -
781J ARG* 1.3 71.0 - - - +
783J ALA* 1.3 64.7 + - - +
784J ASP 3.2 0.4 - - - -
785J VAL* 3.0 21.5 + - + +
786J ILE* 3.0 39.6 + - + +
789J ARG* 4.0 5.0 + - - -
813J ILE* 4.4 18.8 - - + +
817J LEU* 4.0 19.3 - - + -
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Residues in contact with ALA 783 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527J GLY 4.8 0.6 + - - -
687J LEU* 3.7 19.1 - - + -
753J TYR* 4.1 30.7 - - + +
781J ARG* 3.3 4.7 - - + +
782J TYR* 1.3 76.9 - - - +
784J ASP* 1.3 61.1 - - - +
786J ILE* 2.9 22.6 - - - +
787J VAL* 2.8 23.0 + - + +
817J LEU* 4.0 13.7 - - + +
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Residues in contact with ASP 784 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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774J HIS* 2.9 31.1 - - - +
775J PHE 3.8 18.1 - - - +
776J THR 3.8 0.5 + - - -
777J SER* 2.9 47.1 + - - +
778J PRO* 3.7 4.3 - - + -
781J ARG* 3.4 24.0 + - - +
782J TYR 3.2 0.6 - - - -
783J ALA* 1.3 76.3 - - - +
785J VAL* 1.3 59.6 + - - +
787J VAL* 3.5 5.5 - - - +
788J HIS* 2.9 36.7 + - - -
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Residues in contact with VAL 785 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509J VAL* 4.1 15.3 - - + -
510J SER* 4.5 10.7 - - - +
513J ILE* 5.3 9.6 - - + -
520J ASP* 5.1 0.2 - - - +
523J SER* 5.8 1.3 - - - -
539J MET* 4.7 4.0 - - + -
778J PRO* 3.5 21.3 - - + +
781J ARG 3.4 16.5 + - - +
782J TYR* 3.0 32.2 + - + +
784J ASP* 1.3 78.4 - - - +
786J ILE* 1.3 57.8 + - - +
788J HIS* 3.3 7.0 + - - +
789J ARG* 3.0 49.6 + - + +
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Residues in contact with ILE 786 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687J LEU* 2.7 43.3 - - + -
782J TYR* 3.0 35.7 + - + +
783J ALA* 2.9 27.4 - - - +
785J VAL* 1.3 73.4 - - - +
787J VAL* 1.3 60.6 + - - +
789J ARG* 3.7 15.0 - - - +
790J LEU* 2.9 40.7 + - + +
810J LEU* 5.6 12.6 - - + -
813J ILE* 4.8 19.3 - - + -
814J CYS* 5.9 0.9 - - - -
817J LEU* 4.9 0.7 - - + -
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Residues in contact with VAL 787 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674J VAL* 5.3 3.1 - - + -
678J ILE* 5.5 12.4 - - + +
687J LEU* 4.8 11.4 - - + +
773J THR* 4.2 17.9 - - + +
774J HIS 3.3 22.0 - - - +
775J PHE* 2.8 36.6 - - + -
783J ALA* 2.8 29.3 + - + +
784J ASP* 3.5 7.0 - - - +
785J VAL 3.2 0.2 - - - -
786J ILE* 1.3 81.0 - - + +
788J HIS* 1.3 56.8 + - - +
790J LEU* 3.4 6.0 + - - +
791J LEU* 2.9 30.2 + - + +
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Residues in contact with HIS 788 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506J ILE* 3.7 16.1 - - + +
507J ALA 4.3 5.4 - - - -
508J ASP* 4.3 5.1 + - - -
509J VAL 5.6 0.2 - - - -
510J SER* 3.6 22.4 + - - +
560J PHE* 3.9 33.1 - - + +
775J PHE* 3.3 42.3 + + - -
778J PRO* 3.5 31.6 - - + +
784J ASP 2.9 27.2 + - - +
785J VAL* 3.7 5.4 - - - +
787J VAL* 1.3 77.0 - - - +
789J ARG* 1.3 55.9 + - - +
791J LEU* 3.8 2.2 - - - +
792J ALA* 2.9 31.2 + - - +
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Residues in contact with ARG 789 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510J SER* 4.3 13.8 + - - +
513J ILE* 2.7 37.6 + - - +
514J ARG* 3.2 14.9 + - - +
515J PRO* 3.4 37.3 - - + +
520J ASP* 2.9 31.3 + - - -
782J TYR* 4.0 6.7 + - - -
785J VAL* 3.0 30.4 + - - +
786J ILE* 3.7 14.3 - - - +
788J HIS* 1.3 76.0 - - - +
790J LEU* 1.3 59.2 + - + +
792J ALA* 3.4 5.4 + - - +
793J VAL* 2.9 29.8 + - - +
804J LEU* 4.1 21.2 - - + +
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Residues in contact with LEU 790 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678J ILE* 5.7 6.7 - - + -
682J PHE* 4.8 13.9 - - + -
685J HIS* 3.7 22.2 - - + +
686J ALA* 3.9 17.5 - - + -
687J LEU* 4.2 11.0 - - + +
786J ILE* 2.9 29.0 + - + +
787J VAL* 4.1 5.4 - - - +
789J ARG* 1.3 76.3 - - + +
791J LEU* 1.3 56.5 - - - +
793J VAL* 3.7 6.8 - - + +
794J ALA* 2.9 29.6 + - - +
800J THR* 6.3 0.7 - - - -
804J LEU* 3.6 35.7 - - + +
805J THR* 5.4 4.0 - - + -
810J LEU* 5.0 8.3 - - + -
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Residues in contact with LEU 791 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560J PHE* 3.6 28.3 - - + -
577J PHE* 4.4 20.4 - - + -
674J VAL* 4.5 9.4 - - + -
677J LYS* 4.1 26.0 - - + -
678J ILE* 4.4 14.6 - - + +
775J PHE* 3.7 22.7 - - + -
787J VAL* 2.9 20.0 + - + +
788J HIS* 4.0 3.6 - - - +
790J LEU* 1.3 76.6 - - - +
792J ALA* 1.3 62.6 + - - +
794J ALA* 3.2 17.8 + - + +
795J ILE* 3.4 25.8 + - + +
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Residues in contact with ALA 792 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510J SER* 5.4 4.7 - - - +
560J PHE* 4.4 20.1 - - + -
788J HIS 2.9 18.8 + - - +
789J ARG* 3.8 4.9 - - - +
791J LEU* 1.3 77.7 - - - +
793J VAL* 1.3 58.4 + - - +
796J GLY 3.6 0.5 + - - -
797J ALA* 3.0 18.2 + - + -
798J ASP* 2.9 43.7 + - + +
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Residues in contact with VAL 793 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682J PHE* 4.5 8.7 - - + -
789J ARG 2.9 17.8 + - - +
790J LEU* 3.7 7.9 - - + +
792J ALA* 1.3 74.4 - - - +
794J ALA* 1.3 64.4 + - - +
795J ILE 3.6 0.2 - - - -
796J GLY* 3.6 8.9 + - - -
798J ASP* 3.3 8.2 + - - +
799J CYS 4.6 0.7 - - - +
800J THR* 2.4 56.7 - - + +
804J LEU* 5.3 2.5 - - + -
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Residues in contact with ALA 794 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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677J LYS* 5.5 3.4 - - + -
678J ILE* 5.7 3.6 - - + -
681J GLU* 4.5 12.4 - - + +
682J PHE* 3.6 28.7 - - + -
790J LEU 2.9 19.1 + - - +
791J LEU* 3.5 19.1 - - + +
792J ALA 3.2 0.6 - - - -
793J VAL* 1.3 79.9 - - - +
795J ILE* 1.3 62.3 + - + +
796J GLY 3.2 0.7 + - - -
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Residues in contact with ILE 795 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560J PHE* 4.8 10.3 - - + -
577J PHE* 4.2 30.1 - - + +
578J THR* 5.2 3.4 - - - +
579J LYS 5.9 0.4 - - - +
677J LYS* 4.1 27.1 - - - +
791J LEU* 3.6 22.0 - - + +
794J ALA* 1.3 77.8 - - + +
796J GLY* 1.3 61.1 + - - +
797J ALA* 3.8 25.1 - - + +
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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