Contacts of the helix formed by residues 786 - 800 (chain q) 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 PRO 786 (chain q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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785q PRO* 1.3 77.5 - - - +
787q TYR* 1.3 67.1 + - - +
788q GLU* 4.4 7.6 - - + +
789q THR* 3.1 21.9 + - - +
790q LEU* 3.5 7.4 + - - +
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Residues in contact with TYR 787 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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777q MET* 6.0 5.8 - - + -
785q PRO 3.5 3.5 + - - -
786q PRO* 1.3 72.3 - - - +
788q GLU* 1.3 59.0 + - - +
790q LEU* 3.0 10.6 + - - +
791q LEU* 2.9 28.0 + - - +
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Residues in contact with GLU 788 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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786q PRO* 3.1 5.5 - - + +
787q TYR* 1.3 76.5 - - - +
789q THR* 1.3 65.5 + - - +
791q LEU* 3.2 8.1 + - - +
792q LEU* 2.9 24.1 + - - +
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Residues in contact with THR 789 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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759q THR 4.9 11.9 - - - -
760q SER* 6.2 0.7 - - - -
761q LEU* 4.2 11.6 + - - +
785q PRO* 5.3 6.3 - - - -
786q PRO* 3.1 20.2 + - - +
788q GLU* 1.3 78.0 - - - +
790q LEU* 1.3 63.0 + - - +
792q LEU* 3.4 6.3 + - - +
793q ALA* 3.1 21.7 + - - +
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Residues in contact with LEU 790 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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761q LEU* 4.6 6.7 - - + +
765q VAL* 5.6 1.1 - - - +
776q LEU* 5.4 13.9 - - + +
777q MET* 6.1 2.7 - - - +
785q PRO* 5.9 3.5 - - + +
786q PRO 3.5 6.2 + - - +
787q TYR* 3.0 13.1 + - - +
789q THR* 1.3 76.0 - - - +
791q LEU* 1.3 65.8 + - - +
793q ALA* 3.0 9.2 + - - +
794q LEU* 3.0 21.7 + - - +
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Residues in contact with LEU 791 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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787q TYR 2.9 13.0 + - - +
788q GLU* 3.2 11.4 + - - +
790q LEU* 1.3 74.9 - - - +
792q LEU* 1.3 64.7 + - - +
794q LEU* 3.0 9.2 + - - +
795q GLU* 3.0 22.3 + - - +
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Residues in contact with LEU 792 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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788q GLU 2.9 16.3 + - - +
789q THR* 3.6 7.0 - - - +
791q LEU* 1.3 76.8 - - - +
793q ALA* 1.3 58.9 + - - +
795q GLU* 3.2 8.5 + - - +
796q GLN* 2.9 28.8 + - - +
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Residues in contact with ALA 793 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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761q LEU* 3.7 14.8 - - + +
762q GLY* 3.7 33.4 - - - +
765q VAL* 4.3 9.4 - - + -
789q THR 3.1 12.2 + - - +
790q LEU* 3.0 10.2 + - - +
792q LEU* 1.3 77.1 - - - +
794q LEU* 1.3 62.7 + - - +
796q GLN* 3.2 8.5 + - - +
797q LEU* 2.9 23.8 + - - +
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Residues in contact with LEU 794 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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765q VAL* 5.1 6.9 - - + +
790q LEU 3.0 11.2 + - - +
791q LEU* 3.0 9.6 + - - +
793q ALA* 1.3 75.8 - - - +
795q GLU* 1.3 64.1 + - - +
797q LEU* 3.2 8.8 + - - +
798q TYR* 2.9 22.6 + - - +
803q LEU* 5.0 2.7 - - - +
807q GLY* 6.4 2.2 - - - -
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Residues in contact with GLU 795 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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791q LEU 3.0 12.2 + - - +
792q LEU* 3.5 10.8 - - - +
794q LEU* 1.3 77.2 - - - +
796q GLN* 1.3 62.6 + - - +
798q TYR* 3.0 10.5 + - - +
799q ALA* 3.0 21.8 + - - +
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Residues in contact with GLN 796 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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762q GLY* 6.0 3.1 - - - -
792q LEU 2.9 13.4 + - - +
793q ALA* 3.2 11.0 + - - +
795q GLU* 1.3 76.5 - - - +
797q LEU* 1.3 55.7 + - - +
799q ALA* 3.2 8.4 + - - +
800q LEU* 2.9 28.4 + - - +
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Residues in contact with LEU 797 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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762q GLY* 5.8 4.5 - - - +
765q VAL* 5.9 4.5 - - + -
766q LEU* 6.2 5.2 - - + +
793q ALA 2.9 13.1 + - - +
794q LEU* 3.6 10.8 - - - +
796q GLN* 1.3 77.3 - - - +
798q TYR* 1.3 56.4 + - - +
800q LEU* 3.3 8.3 - - - +
801q GLY 2.9 6.1 + - - -
802q ALA* 2.9 42.2 + - + -
803q LEU* 3.3 13.4 + - + -
823q PRO* 6.4 2.5 - - + -
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Residues in contact with TYR 798 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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794q LEU 2.9 13.5 + - - +
795q GLU* 3.2 13.2 - - - +
797q LEU* 1.3 74.3 - - - +
799q ALA* 1.3 60.9 + - - +
801q GLY* 2.8 21.7 + - - -
803q LEU* 3.4 19.1 - - + +
804q ASN 4.7 10.3 - - - +
805q HIS* 5.4 4.0 - - - +
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Residues in contact with ALA 799 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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795q GLU 3.0 11.1 + - - +
796q GLN* 3.6 10.5 - - - +
798q TYR* 1.3 76.3 - - - +
800q LEU* 1.3 61.5 + - - +
801q GLY* 3.0 1.6 + - - -
1013q ALA* 5.7 4.3 - - - +
1015q HIS* 5.8 7.2 - - + +
1016q TYR* 5.1 17.0 - - + +
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Residues in contact with LEU 800 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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796q GLN 2.9 14.2 + - - +
797q LEU* 3.3 16.6 - - - +
799q ALA* 1.3 76.8 - - - +
801q GLY* 1.3 57.4 - - - +
802q ALA* 3.2 9.7 + - + +
812q SER* 5.6 2.4 - - - -
823q PRO* 5.7 9.2 - - + +
824q MET* 6.5 0.4 - - - -
827q LYS* 5.1 15.6 - - + +
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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