Contacts of the helix formed by residues 1002 - 1013 (chain A) 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 ASP1002 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
824A PRO* 6.3 0.2 - - - -
825A ILE 3.2 19.4 + - - +
826A PRO* 4.4 2.2 - - + +
827A PHE* 4.2 24.0 - - + +
1001A VAL* 1.3 76.6 - - - +
1003A HIS* 1.3 60.7 + - - +
1004A ASN* 3.3 6.4 + - + +
1005A ILE* 3.4 8.5 + - + +
1006A ALA* 2.9 22.3 + - - +
448u THR* 4.9 8.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1003 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
998A ARG* 4.6 13.2 - - + -
1001A VAL 3.7 2.3 + - - -
1002A ASP* 1.3 71.7 - - - +
1004A ASN* 1.3 58.5 + - - +
1006A ALA* 3.7 8.7 - - - +
1007A ASP* 2.9 32.6 + - - +
448u THR* 4.9 12.2 - - - -
449u GLU 5.4 8.1 - - - +
450u ASP* 6.3 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1004 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
885A LEU 3.8 15.7 - - - +
886A LEU* 4.6 10.8 - - - +
1002A ASP* 3.3 5.0 - - + +
1003A HIS* 1.3 78.1 - - - +
1005A ILE* 1.3 57.6 + - - +
1007A ASP* 4.5 3.5 + - - +
1008A TYR* 3.9 9.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1005 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
885A LEU* 4.9 8.5 - - + +
1001A VAL* 6.0 1.3 - - + -
1002A ASP* 3.4 9.6 + - + +
1004A ASN* 1.3 76.5 - - + +
1006A ALA* 1.3 61.8 + - - +
1007A ASP 3.3 1.1 - - - -
1008A TYR* 3.4 10.8 - - + +
1009A MET* 2.9 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1006 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
994A ASN* 4.9 8.5 - - - +
997A LEU* 3.9 25.1 - - + +
998A ARG* 4.1 12.6 - - + -
1001A VAL* 4.9 4.2 - - + +
1002A ASP 2.9 18.3 + - - +
1003A HIS* 3.2 10.1 + - - +
1005A ILE* 1.3 76.0 - - - +
1007A ASP* 1.3 56.9 + - - +
1009A MET* 3.3 6.6 + - - +
1010A THR* 2.9 30.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1007 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
889A ARG* 5.6 2.7 - - + -
994A ASN* 5.8 2.9 - - - -
1003A HIS 2.9 17.2 + - - +
1004A ASN* 4.6 3.8 - - - +
1006A ALA* 1.3 73.4 - - - +
1008A TYR* 1.3 59.5 + - - +
1010A THR* 3.6 5.0 - - - +
1011A ALA* 2.9 33.4 + - - +
79L PRO* 6.1 4.3 - - + +
80L THR* 4.4 9.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1008 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
884A HIS 5.7 0.7 - - - +
885A LEU* 4.5 14.4 - - + +
888A GLN 5.3 8.3 - - - +
889A ARG* 5.4 5.4 - - - -
1004A ASN 3.9 7.3 + - - +
1005A ILE* 3.3 22.9 + - + +
1006A ALA 3.2 0.6 - - - -
1007A ASP* 1.3 78.3 - - - +
1009A MET* 1.3 57.8 + - - +
1011A ALA* 3.3 4.8 + - - +
1012A LYS* 3.0 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1009 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1005A ILE 2.9 16.3 + - - +
1006A ALA* 3.3 6.9 + - - +
1008A TYR* 1.3 76.3 - - - +
1010A THR* 1.3 61.1 + - - +
1011A ALA 3.5 0.5 + - - -
1012A LYS* 3.5 12.8 + - - +
1013A ASN* 3.6 13.3 + - - +
1036A PHE* 5.7 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1010 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
990A LEU* 4.3 21.8 - - - +
993A LEU* 5.4 2.9 - - - -
994A ASN* 4.0 27.8 - - - -
1006A ALA 2.9 17.6 + - - -
1007A ASP* 3.6 3.4 - - - -
1009A MET* 1.3 76.1 - - - +
1011A ALA* 1.3 57.3 + - - +
1013A ASN* 4.3 12.1 + - - +
1014A ASN* 5.3 1.6 + - - +
80L THR* 3.4 17.4 - - - -
81L GLN* 4.8 1.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1011 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
889A ARG* 3.6 42.3 - - + +
891A PHE* 5.4 4.3 + - - +
1007A ASP 2.9 18.2 + - - +
1008A TYR 3.9 3.4 - - - +
1010A THR* 1.3 79.5 - - - +
1012A LYS* 1.3 61.3 + - - +
1013A ASN 3.2 2.0 + - - -
1014A ASN* 3.7 16.4 + - - +
80L THR* 4.1 12.6 - - - -
81L GLN* 5.0 5.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1012 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
891A PHE* 5.6 7.4 - - - -
1008A TYR 3.0 16.1 + - - +
1009A MET* 3.5 7.5 + - - +
1011A ALA* 1.3 75.8 - - - +
1013A ASN* 1.3 57.9 + - - +
1014A ASN 3.1 14.1 + - - +
1015A VAL* 4.7 3.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1013 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
990A LEU* 5.8 6.7 - - + -
1009A MET 3.6 13.4 + - - +
1010A THR* 4.6 10.5 - - - +
1011A ALA 3.2 2.0 - - - -
1012A LYS* 1.3 77.2 - - - +
1014A ASN* 1.3 57.5 + - - +
1026A ASN* 4.7 2.3 - - - +
1029A GLY 4.2 9.2 - - - +
1030A ILE* 4.2 18.7 - - + -
1031A ILE* 4.2 23.8 + - - +
----------------------------------------------------------
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