Contacts of the strand formed by residues 708 - 713 (chain E) in PDB entry 6C3P
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 LEU 708 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
707E GLN* 1.3 70.5 - - - +
709E THR* 1.3 63.0 + - - +
710E MET* 4.9 3.4 - - + -
868E MET* 4.4 11.7 - - + -
872E ILE* 3.5 25.8 - - + -
876E LEU* 3.6 31.2 - - + +
883E VAL* 3.5 29.4 - - + +
885E LEU* 3.8 25.8 - - + -
895E HIS 3.8 18.6 - - - +
896E ALA* 3.8 5.1 - - - -
897E ASP* 2.7 47.0 + - - +
898E TRP 3.2 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 709 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703E ILE* 4.0 20.2 - - + -
707E GLN 3.7 1.9 + - - -
708E LEU* 1.3 76.1 - - - +
710E MET* 1.3 68.7 + - - +
711E ILE* 4.5 0.2 - - + -
883E VAL 3.6 3.4 + - - -
884E VAL* 3.6 36.6 - - + -
885E LEU* 3.3 22.3 + - - +
898E TRP* 2.8 38.5 + - - -
900E ILE* 3.1 21.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 710 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
708E LEU* 4.9 5.8 - - + -
709E THR* 1.3 81.6 + - - +
711E ILE* 1.3 63.2 + - - +
712E VAL* 4.2 7.2 - - + -
856E PHE* 6.3 0.9 - - + -
868E MET* 3.9 16.2 - - + -
885E LEU* 3.5 26.9 - - + +
887E THR* 4.2 12.6 - - + -
892E TYR* 3.2 37.2 - - + +
893E LEU* 3.6 31.9 - - + -
896E ALA* 3.6 24.2 - - + +
898E TRP 3.0 5.4 + - - +
899E ILE* 3.4 4.0 - - + +
900E ILE 2.7 31.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 711 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703E ILE* 6.4 0.4 - - + -
709E THR* 4.5 0.2 - - + -
710E MET* 1.3 81.0 - - - +
712E VAL* 1.3 68.9 + - - +
719E LYS* 3.9 24.5 - - + +
722E LEU* 6.0 1.3 - - + -
723E LEU* 4.4 13.7 - - + -
884E VAL* 3.7 24.5 - - + -
885E LEU 3.2 18.1 + - - +
886E VAL* 3.2 34.3 - - + +
887E THR 3.8 1.4 + - - -
900E ILE* 3.2 32.5 - - + +
902E MET* 3.6 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 712 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710E MET* 4.8 3.1 - - + -
711E ILE* 1.3 81.3 - - - +
713E GLY* 1.3 61.2 + - - +
719E LYS* 3.6 11.0 - - - +
887E THR* 3.6 25.8 - - + +
890E LEU* 3.6 33.0 - - + -
893E LEU* 4.5 7.2 - - + -
899E ILE* 4.8 9.9 - - + -
900E ILE 3.1 10.2 + - - +
901E ALA* 4.6 10.5 - - + -
902E MET* 3.3 27.5 + - - +
926E HIS* 4.7 14.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 713 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712E VAL* 1.3 82.3 - - - +
714E GLN* 1.3 71.0 + - - +
717E CYS* 3.9 3.4 - - - -
719E LYS* 3.0 11.8 + - - +
902E MET 3.2 15.0 - - - -
903E LYS* 5.6 0.2 - - - -
1512E ASP* 3.4 14.4 - - - +
----------------------------------------------------------
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