Contacts of the strand formed by residues 6907 - 6910 (chain A) in PDB entry 6W75
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 SER6907 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6893A LEU 3.5 2.6 + - - -
6894A VAL* 3.4 12.4 - - - -
6895A ASP* 3.0 24.3 + - - +
6905A ALA* 3.5 3.0 - - - +
6906A ASP* 1.3 81.1 + - - +
6908A THR* 1.3 66.0 + - - +
6909A LEU* 5.7 0.9 - - - -
7088A ILE* 5.3 0.4 - - - -
7092C VAL* 4.3 17.5 - - - +
7093C LEU 4.6 2.1 + - - -
7094C VAL* 3.5 36.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR6908 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6895A ASP* 2.7 17.0 + - - +
6901A PHE* 3.4 45.1 - - + +
6903A SER* 3.4 16.7 + - - -
6905A ALA* 4.1 3.1 + - - +
6907A SER* 1.3 75.8 - - - +
6909A LEU* 1.3 68.7 + - - +
6910A ILE* 3.8 15.2 + - + +
4346B LYS* 4.8 5.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU6909 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6866A ILE* 5.6 0.2 - - + -
6894A VAL* 4.5 6.7 - - + -
6895A ASP 3.0 10.8 + - - +
6896A SER* 3.0 39.5 + - - +
6897A ASP 3.2 3.3 + - - -
6907A SER* 5.7 0.4 - - - -
6908A THR* 1.3 80.6 - - - +
6910A ILE* 1.3 63.5 + - - +
6916A VAL* 3.9 17.9 - - + -
7088A ILE* 3.4 43.1 - - + -
7089A SER* 4.0 11.7 - - - +
7090A SER* 4.2 25.4 - - - +
7092C VAL* 4.5 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE6910 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6897A ASP 3.3 1.6 - - - +
6898A LEU 3.8 10.5 - - - +
6899A ASN 3.6 5.4 - - - +
6900A ASP* 3.7 42.6 - - + +
6901A PHE* 3.5 38.6 - - + -
6908A THR* 3.8 16.6 + - + +
6909A LEU* 1.3 73.0 - - - +
6911A GLY* 1.3 60.9 + - - +
6916A VAL* 6.5 0.7 - - - -
7090A SER* 3.2 18.0 + - - -
7091A ASP 5.3 0.7 - - - +
----------------------------------------------------------
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