Contacts of the helix formed by residues 684 - 692 (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 PRO 684 (chain U).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683U VAL* 1.3 74.4 - - - +
685U ASP* 1.3 60.2 + - - +
686U TRP* 3.0 7.9 - - + +
687U LEU* 2.8 33.2 + - + +
688U HIS* 3.1 10.6 + - - -
1086U SER* 3.6 16.5 - - - +
1088U LEU* 4.5 21.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 685 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683U VAL 3.3 4.0 + - - -
684U PRO* 1.3 71.4 - - - +
686U TRP* 1.3 59.6 + - - +
687U LEU 3.1 1.0 + - - -
688U HIS* 3.9 15.6 + - - +
689U ASP* 4.8 3.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 686 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684U PRO* 3.0 6.3 - - + +
685U ASP* 1.3 77.7 - - - +
687U LEU* 1.3 57.9 + - - +
689U ASP 5.4 0.4 - - - -
690U ILE* 5.0 4.5 + - - +
699U SER* 5.0 9.2 - - - +
700U ALA* 3.6 29.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 687 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683U VAL* 5.0 6.1 - - + -
684U PRO* 2.8 24.2 + - + +
686U TRP* 1.3 79.0 - - - +
688U HIS* 1.3 65.4 + - - +
689U ASP 3.3 2.5 - - - -
690U ILE* 3.1 9.3 + - - +
691U ILE* 2.9 26.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 688 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683U VAL* 5.3 9.9 - - + +
684U PRO 3.1 12.0 + - - +
685U ASP* 3.9 11.3 + - - +
686U TRP 3.8 0.4 - - - -
687U LEU* 1.3 77.2 - - - +
689U ASP* 1.3 62.6 + - - +
691U ILE* 3.4 7.1 + - - +
692U LEU* 3.1 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 689 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685U ASP 4.8 2.4 + - - -
686U TRP 5.4 0.9 - - - -
687U LEU 3.3 0.2 - - - -
688U HIS* 1.3 79.3 - - - +
690U ILE* 1.3 57.1 + - - +
692U LEU* 3.3 6.4 + - - +
693U GLY 3.0 19.1 + - - -
694U TYR* 2.8 29.1 + - - +
695U GLY* 5.0 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 690 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686U TRP 5.0 4.4 + - - +
687U LEU* 3.1 13.6 + - - +
689U ASP* 1.3 75.4 - - - +
691U ILE* 1.3 63.6 + - - +
693U GLY* 2.8 21.6 + - - +
694U TYR 3.9 4.2 + - - -
696U ASP 5.4 8.3 - - - +
697U PRO* 5.5 10.8 - - + +
1126U VAL* 5.7 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 691 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457U LEU 5.2 1.4 - - - +
459U PHE* 5.8 0.3 - - - +
687U LEU* 2.9 19.3 + - + +
688U HIS* 3.6 7.9 - - - +
690U ILE* 1.3 78.1 - - - +
692U LEU* 1.3 58.5 + - - +
693U GLY* 3.3 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 692 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457U LEU 4.3 0.7 - - - -
458U GLN* 3.2 5.0 - - - +
459U PHE* 3.0 49.9 + - + +
460U LEU 5.3 4.0 - - - +
461U THR* 5.6 5.8 - - - -
462U LEU 5.9 0.4 - - - +
465U TYR* 6.0 2.5 - - - -
688U HIS 3.1 16.5 + - - +
689U ASP* 3.8 5.8 - - - +
690U ILE 3.2 0.2 - - - -
691U ILE* 1.3 76.3 - - - +
693U GLY* 1.3 59.0 + - - +
694U TYR* 3.4 5.7 + - + +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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