Contacts of the helix formed by residues 782 - 796 (chain K) in PDB entry 6D6Q
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 TYR 782 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513K ILE* 5.3 3.1 - - + -
520K ASP* 2.4 49.5 + - - -
523K SER* 4.0 22.9 - - - +
524K ALA* 4.2 21.2 - - + +
527K GLY* 4.0 10.4 + - - +
539K MET* 4.0 11.1 - - - +
781K ARG* 1.3 71.8 - - - +
783K ALA* 1.3 63.2 + - - +
784K ASP 3.1 1.6 - - - -
785K VAL* 2.9 35.3 + - + +
786K ILE* 3.0 38.7 + - + +
789K ARG* 4.3 7.4 + - - -
813K ILE* 4.5 13.0 - - + -
817K LEU* 4.3 13.4 - - + +
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Residues in contact with ALA 783 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687K LEU* 4.0 24.6 - - + +
753K TYR* 3.9 31.9 - - + +
773K THR* 6.0 0.7 - - - +
774K HIS* 4.4 2.9 - - + +
781K ARG* 5.4 2.0 - - + -
782K TYR* 1.3 78.0 - - - +
784K ASP* 1.3 57.4 + - - +
786K ILE* 3.2 2.5 + - - +
787K VAL* 2.9 37.0 + - + +
817K LEU* 3.5 23.7 - - + +
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Residues in contact with ASP 784 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
774K HIS* 2.6 46.5 - - - +
775K PHE* 2.8 7.3 + - - +
777K SER 2.4 36.5 + - - +
778K PRO* 3.5 24.2 - - + -
781K ARG* 2.9 23.8 + - - +
782K TYR 3.1 1.0 - - - +
783K ALA* 1.3 77.7 - - - +
785K VAL* 1.3 56.4 + - - +
787K VAL* 3.3 3.2 + - - +
788K HIS* 2.7 33.6 + - - -
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Residues in contact with VAL 785 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509K VAL* 4.9 7.2 - - + -
510K SER* 4.9 13.2 - - - +
513K ILE* 4.7 18.6 - - + -
523K SER* 6.1 0.2 - - - +
539K MET* 5.4 1.3 - - + -
778K PRO* 3.4 28.5 - - + +
781K ARG 3.8 10.3 - - - +
782K TYR* 2.9 26.9 + - + +
784K ASP* 1.3 73.2 - - - +
786K ILE* 1.3 66.8 + - + +
788K HIS* 3.1 10.3 + - + +
789K ARG* 3.0 47.9 + - + +
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Residues in contact with ILE 786 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687K LEU* 3.3 37.9 - - + -
782K TYR* 3.0 42.7 + - + +
783K ALA* 3.8 1.8 - - - +
785K VAL* 1.3 76.5 - - + +
787K VAL* 1.3 57.4 + - - +
789K ARG* 3.2 15.6 + - - +
790K LEU* 2.9 40.8 + - + +
801K TYR* 5.6 3.6 - - - +
804K LEU* 4.8 10.5 - - + -
810K LEU* 5.0 7.4 - - + -
813K ILE* 3.5 31.0 - - + -
817K LEU* 6.0 0.9 - - + -
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Residues in contact with VAL 787 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674K VAL* 3.7 18.8 - - + -
678K ILE* 4.2 14.1 - - + -
687K LEU* 4.2 16.2 - - + +
773K THR* 3.6 23.6 - - + +
774K HIS 3.6 10.8 - - - +
775K PHE* 3.3 24.5 - - + -
783K ALA* 2.9 21.6 + - + +
784K ASP 3.5 4.7 - - - +
786K ILE* 1.3 75.4 - - - +
788K HIS* 1.3 65.6 + - - +
790K LEU* 3.9 6.8 - - + +
791K LEU* 2.9 23.9 + - - +
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Residues in contact with HIS 788 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506K ILE* 3.6 24.2 - - + -
507K ALA 4.4 6.5 + - - -
508K ASP* 5.3 2.9 - - - +
509K VAL 5.5 2.9 - - - -
510K SER* 4.5 18.8 - - - -
560K PHE* 4.5 13.5 - - + +
775K PHE* 3.0 48.6 + + - -
778K PRO* 3.5 25.9 - - + +
784K ASP 2.7 33.9 + - - -
785K VAL* 3.1 12.8 + - + +
787K VAL* 1.3 75.8 - - - +
789K ARG* 1.3 57.6 + - - +
791K LEU* 3.8 1.8 - - - +
792K ALA* 2.9 33.1 + - - +
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Residues in contact with ARG 789 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510K SER* 3.5 19.4 + - - +
513K ILE* 3.0 33.1 + - - +
514K ARG 3.7 1.0 - - - -
515K PRO* 3.3 38.2 - - - +
520K ASP* 3.5 24.5 + - - -
782K TYR* 4.3 6.8 + - - -
785K VAL* 3.0 26.2 + - - +
786K ILE* 3.6 14.9 - - - +
787K VAL 3.2 0.2 - - - -
788K HIS* 1.3 76.9 - - - +
790K LEU* 1.3 62.9 + - - +
792K ALA* 3.2 3.4 + - - +
793K VAL* 2.9 26.6 + - - +
798K ASP* 4.2 17.5 - - - +
801K TYR* 3.1 33.0 + - + -
804K LEU* 4.7 12.3 - - + +
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Residues in contact with LEU 790 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678K ILE* 4.6 14.6 - - + -
682K PHE* 3.6 17.7 - - + -
685K HIS* 3.8 23.1 - - + +
686K ALA* 3.8 31.0 - - + -
687K LEU* 4.3 6.5 - - + +
786K ILE* 2.9 31.0 + - + +
787K VAL* 3.3 7.6 + - + +
789K ARG* 1.3 75.8 - - - +
791K LEU* 1.3 57.8 + - - +
793K VAL* 2.9 23.3 - - - +
794K ALA* 3.0 13.7 + - - +
804K LEU* 3.3 35.4 - - + +
810K LEU* 5.5 1.6 - - + -
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Residues in contact with LEU 791 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560K PHE* 3.2 35.9 - - + -
577K PHE* 4.1 7.0 - - + -
674K VAL* 3.8 17.7 - - + -
677K LYS* 3.6 36.1 - - + -
678K ILE* 3.7 23.5 - - + +
775K PHE* 3.6 23.3 - - + -
787K VAL 2.9 17.3 + - - +
788K HIS 3.9 2.7 - - - +
790K LEU* 1.3 77.8 - - - +
792K ALA* 1.3 58.4 + - - +
794K ALA* 3.2 5.7 + - + +
795K ILE* 2.9 32.8 + - + +
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Residues in contact with ALA 792 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510K SER* 6.0 2.7 - - - +
560K PHE* 5.4 4.9 - - + -
579K LYS* 3.5 35.9 - - - +
788K HIS 2.9 19.2 + - - +
789K ARG* 3.7 4.9 - - - +
791K LEU* 1.3 75.3 - - - +
793K VAL* 1.3 61.9 + - - +
795K ILE* 3.1 9.0 + - - +
796K GLY 2.7 23.0 + - - -
797K ALA 2.8 11.3 + - - -
798K ASP* 4.1 10.3 - - + +
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Residues in contact with VAL 793 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682K PHE* 3.7 20.4 - - + -
789K ARG 2.9 15.2 + - - +
790K LEU* 2.9 29.4 - - - +
792K ALA* 1.3 73.4 - - - +
794K ALA* 1.3 64.5 + - - +
796K GLY* 3.0 12.8 + - - +
798K ASP* 3.9 28.6 - - + +
799K CYS 5.4 0.7 - - - -
800K THR* 3.5 30.1 - - + -
804K LEU* 4.5 12.8 - - + -
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Residues in contact with ALA 794 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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677K LYS* 4.8 12.4 + - + -
678K ILE* 5.6 2.0 - - + -
681K GLU* 4.0 31.9 - - + +
682K PHE* 4.0 13.9 - - + -
790K LEU 3.0 14.6 + - - +
791K LEU* 3.2 12.3 + - + +
793K VAL* 1.3 80.6 - - - +
795K ILE* 1.3 62.0 + - - +
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Residues in contact with ILE 795 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560K PHE* 4.9 4.3 - - + -
577K PHE* 3.3 35.2 - - + +
578K THR* 5.6 2.0 - - - -
579K LYS* 5.8 6.3 - - + +
677K LYS* 3.5 33.2 - - - +
791K LEU* 2.9 23.5 + - + +
792K ALA* 3.1 11.0 + - - +
794K ALA* 1.3 76.3 - - - +
796K GLY* 1.3 58.0 + - - +
797K ALA* 4.6 11.2 - - + +
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Residues in contact with GLY 796 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466K ASN* 6.1 0.2 - - - -
792K ALA 2.7 5.9 + - - -
793K VAL* 3.0 15.5 + - - -
794K ALA 3.2 0.4 - - - -
795K ILE* 1.3 79.0 - - - +
797K ALA* 1.3 53.3 + - - -
798K ASP 3.3 13.0 + - - +
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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
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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