Contacts of the helix formed by residues 781 - 796 (chain u) in PDB entry 6FF7
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 781 (chain u).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1221 GLU* 5.3 12.8 - - + -
779u SER* 3.5 6.6 - - - +
780u PRO* 1.3 81.7 - - - +
782u GLU* 1.3 62.9 + - - +
783u GLU* 3.4 5.6 - - + +
784u MET* 3.8 14.5 + - + +
785u LYS* 3.4 19.4 + - - +
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Residues in contact with GLU 782 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91 LEU* 6.1 5.6 - - + -
780u PRO 3.7 2.5 + - - +
781u ASP* 1.3 72.0 - - - +
783u GLU* 1.3 59.9 + - - +
785u LYS* 3.3 9.0 + - - +
786u LYS* 2.9 26.9 + - - +
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Residues in contact with GLU 783 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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781u ASP* 3.4 3.7 - - + +
782u GLU* 1.3 79.4 - - - +
784u MET* 1.3 57.4 + - - +
786u LYS* 3.2 9.3 + - - +
787u ILE* 2.9 26.4 + - - +
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Residues in contact with MET 784 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744u ALA* 4.5 17.9 - - + -
776u GLU 6.1 0.4 - - - -
779u SER* 4.7 17.0 - - - -
781u ASP* 3.8 16.2 + - + +
782u GLU 3.4 0.4 - - - -
783u GLU* 1.3 75.6 - - - +
785u LYS* 1.3 60.4 + - - +
787u ILE* 3.7 7.9 - - - +
788u VAL* 2.9 31.4 + - - +
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Residues in contact with LYS 785 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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779u SER* 5.5 5.6 - - - +
781u ASP 3.4 13.0 + - - +
782u GLU* 3.3 13.2 + - - +
783u GLU 3.2 0.4 - - - -
784u MET* 1.3 78.1 - - - +
786u LYS* 1.3 56.9 - - - +
788u VAL* 3.9 3.3 - - - +
789u LEU* 2.9 31.9 + - - +
818u PHE* 6.5 1.1 - - + -
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Residues in contact with LYS 786 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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782u GLU 2.9 13.3 + - - +
783u GLU* 3.2 12.1 + - - +
785u LYS* 1.3 74.6 - - - +
787u ILE* 1.3 57.4 + - - +
789u LEU* 3.3 7.0 + - - +
790u LYS* 3.0 28.6 + - - +
828u ARG 5.4 8.1 - - - +
829u ASN* 5.6 10.1 - - + +
832u GLN* 5.3 7.3 - - + +
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Residues in contact with ILE 787 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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744u ALA* 4.5 22.9 - - + +
747u LEU* 6.3 0.9 - - + -
748u LYS* 5.0 12.9 - - + +
783u GLU 2.9 15.9 + - - +
784u MET* 3.7 8.3 - - - +
785u LYS 3.3 0.2 - - - -
786u LYS* 1.3 76.8 - - - +
788u VAL* 1.3 56.8 + - - +
790u LYS* 3.2 7.8 + - - +
791u VAL* 2.9 26.7 + - - +
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Residues in contact with VAL 788 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
773u LEU* 5.7 13.2 - - + +
776u GLU* 5.4 13.2 - - + +
784u MET 2.9 17.2 + - - +
785u LYS* 4.3 3.4 - - - +
787u ILE* 1.3 76.2 - - - +
789u LEU* 1.3 57.3 + - - +
791u VAL* 3.6 9.2 - - + +
792u VAL* 2.9 30.7 + - - +
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Residues in contact with LEU 789 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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785u LYS 2.9 20.7 + - - +
786u LYS* 3.6 8.7 - - - +
788u VAL* 1.3 78.7 - - - +
790u LYS* 1.3 58.5 + - - +
792u VAL* 4.0 4.0 + - - +
793u LYS 3.8 4.3 + - - -
832u GLN* 4.6 19.3 - - + +
833u LEU* 5.5 3.4 - - - +
836u THR* 3.4 27.7 - - - -
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Residues in contact with LYS 790 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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786u LYS 3.0 13.8 + - - +
787u ILE* 3.2 9.2 + - - +
789u LEU* 1.3 74.4 - - - +
791u VAL* 1.3 63.9 + - - +
793u LYS* 3.4 14.3 + - - +
794u GLN* 3.5 14.0 + - - +
832u GLN* 5.6 5.5 - - + +
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Residues in contact with VAL 791 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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747u LEU* 4.9 18.8 - - + +
748u LYS* 5.9 1.8 - - - -
751u GLY* 5.2 11.5 - - - -
773u LEU* 6.5 0.7 - - + -
787u ILE 2.9 17.4 + - - +
788u VAL* 3.2 11.0 + - + +
790u LYS* 1.3 76.0 - - - +
792u VAL* 1.3 59.6 + - - +
793u LYS 3.3 0.2 + - - -
794u GLN* 3.5 1.9 + - - +
795u CYS* 2.9 38.0 + - + +
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Residues in contact with VAL 792 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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788u VAL 2.9 16.1 + - - +
789u LEU* 4.3 7.2 - - - +
790u LYS 3.4 0.4 - - - -
791u VAL* 1.3 75.4 - - - +
793u LYS* 1.3 63.5 + - - +
795u CYS* 4.2 3.1 - - - -
796u CYS* 3.5 23.4 + - - +
836u THR* 5.3 4.7 - - - -
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Residues in contact with LYS 793 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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789u LEU 3.8 4.5 + - - +
790u LYS* 3.4 11.6 + - - +
791u VAL 3.2 0.8 - - - -
792u VAL* 1.3 81.0 - - - +
794u GLN* 1.3 61.0 + - + +
795u CYS 3.5 0.2 + - - -
796u CYS 3.5 17.0 - - - +
797u GLY* 4.3 1.4 + - - -
835u ASP 4.5 5.8 - - - +
836u THR* 4.0 31.1 - - - +
839u GLU* 4.2 16.9 - - + +
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Residues in contact with GLN 794 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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751u GLY 3.9 21.8 - - - +
754u ILE* 5.7 1.7 - - - +
755u PRO* 5.0 19.8 - - + +
790u LYS 3.5 8.6 + - - +
791u VAL* 3.5 3.3 + - - +
793u LYS* 1.3 79.3 - - - +
795u CYS* 1.3 60.2 + - - +
796u CYS 3.4 0.6 + - - -
797u GLY* 4.5 4.7 + - - -
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Residues in contact with CYS 795 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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751u GLY* 5.7 7.2 - - - -
754u ILE* 6.1 5.4 - - + -
766u THR* 4.5 20.6 - - - -
791u VAL* 2.9 23.1 + - + +
792u VAL* 4.6 2.9 - - - +
794u GLN* 1.3 77.2 - - - +
796u CYS* 1.3 58.2 + - - +
797u GLY 3.8 1.3 + - - -
801u VAL* 5.3 5.5 + - - +
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Residues in contact with CYS 796 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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792u VAL 3.5 15.9 + - - +
793u LYS 3.5 11.1 - - - +
794u GLN 3.4 0.4 - - - -
795u CYS* 1.3 79.3 - - - +
797u GLY* 1.3 56.5 + - - +
801u VAL* 4.9 17.3 - - + +
839u GLU* 4.3 17.5 - - - +
840u LEU* 6.2 2.9 - - - -
843u LYS* 4.3 14.7 - - + +
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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
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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