Contacts of the strand formed by residues 6985 - 6993 (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 PHE6985 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6955A ILE* 4.1 10.8 - - + -
6959A LEU* 3.7 22.9 - - + -
6963A GLY 3.8 3.4 - - - -
6965A VAL* 3.9 18.2 - - + -
6981A LEU* 3.3 22.0 - - + -
6982A MET* 3.3 28.7 + - + +
6983A GLY 3.3 0.8 - - - -
6984A HIS* 1.3 79.5 - - - +
6986A ALA* 1.3 66.6 + - - +
6987A TRP* 3.1 18.9 + - - +
7006A GLY* 3.2 32.5 - - - -
7007A CYS 3.6 2.5 - - - +
7008A ASN 3.4 4.5 - - - -
7009A TYR* 3.5 40.2 - + + -
7010A LEU* 3.9 4.3 - - - -
7014A ARG* 3.1 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA6986 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6985A PHE* 1.3 71.9 - - - +
6987A TRP* 1.3 63.8 + - + +
7007A CYS 3.3 8.0 + - - +
7008A ASN* 2.9 15.2 + - + +
7010A LEU* 3.8 11.1 - - + +
7014A ARG* 3.5 17.9 + - - +
7074A SER* 3.5 44.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP6987 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6808A ALA* 5.6 1.8 - - + -
6809A MET 5.9 0.7 - - - -
6811A ASN* 3.8 18.2 + - - +
6814A LYS* 3.7 16.5 - - - +
6851A TYR* 3.3 23.6 - - - -
6855A LEU* 3.7 30.5 - - + -
6985A PHE* 3.1 7.2 - - - +
6986A ALA* 1.3 82.9 - - + +
6988A TRP* 1.3 88.4 + - - +
6989A THR* 3.5 24.9 - - + -
7005A ILE* 5.0 2.0 - - + -
7007A CYS* 2.8 44.5 + - + +
7014A ARG* 5.3 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP6988 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6809A MET* 3.5 20.4 - - + -
6814A LYS* 2.6 48.2 + - + +
6979A TYR* 4.2 8.3 - + - -
6982A MET* 3.5 50.5 - - + +
6987A TRP* 1.3 90.3 - - - +
6989A THR* 1.3 94.9 + - - +
6990A ALA* 4.2 0.7 - - + -
7004A LEU* 4.0 16.8 - - + -
7005A ILE 3.0 14.8 - - - +
7006A GLY* 4.2 1.1 - - - -
7014A ARG* 4.6 3.1 - - - -
7017A ILE* 3.7 7.2 - - + +
7022A MET* 3.5 43.3 - - + -
7111A FMT 3.1 32.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR6989 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6808A ALA* 3.6 7.5 - - + +
6809A MET* 3.4 30.8 + - - +
6814A LYS* 4.6 3.4 - - - +
6851A TYR* 3.6 21.5 - - + +
6987A TRP* 3.5 31.3 - - + -
6988A TRP* 1.3 91.3 - - - +
6990A ALA* 1.3 67.7 + - - +
6991A PHE 4.4 0.9 - - - +
7004A LEU* 3.5 3.6 - - - -
7005A ILE* 2.8 40.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA6990 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6808A ALA* 3.5 1.4 - - - -
6809A MET* 2.8 44.5 + - + +
6979A TYR* 5.8 0.4 - - + -
6988A TRP* 4.2 1.4 - - - -
6989A THR* 1.3 77.0 + - - +
6991A PHE* 1.3 59.3 + - - +
7002A ALA* 4.4 3.6 - - + -
7003A PHE 3.4 4.7 - - - -
7004A LEU* 3.9 17.9 - - + -
7026A TYR* 3.7 33.2 - - + -
7029A TRP* 3.7 5.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE6991 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6805A PRO* 3.9 4.7 - - + -
6806A GLY* 3.5 44.0 - - - -
6807A VAL 3.6 15.0 - - - -
6808A ALA* 4.0 1.8 - - - +
6847A GLN 3.9 9.0 - - - -
6848A LEU* 4.0 19.7 - - + -
6851A TYR* 3.3 52.3 - + + -
6989A THR* 4.0 2.0 - - + -
6990A ALA* 1.3 73.7 - - - +
6992A VAL* 1.3 61.7 + - - +
6993A THR* 3.9 24.6 + - + -
7002A ALA* 3.3 3.6 - - - -
7003A PHE* 2.7 41.4 + + + +
7005A ILE* 3.7 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL6992 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6806A GLY* 3.1 4.7 - - - -
6807A VAL 2.8 38.1 + - - +
6991A PHE* 1.3 76.7 - - - +
6993A THR* 1.3 72.4 + - - +
6994A ASN* 4.6 0.3 - - - +
6996A ASN 4.9 1.8 - - - +
6997A ALA* 3.9 18.2 - - + -
7001A GLU 3.8 13.2 - - - +
7002A ALA* 4.1 5.2 - - + +
7029A TRP* 3.8 22.2 - - + -
7030A ARG* 3.5 34.3 - - - +
7035A ILE* 3.8 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR6993 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6805A PRO 3.8 5.2 - - - -
6844A LYS* 3.6 35.9 - - + +
6847A GLN* 3.5 15.5 - - + -
6848A LEU* 4.2 2.0 - - - +
6991A PHE* 3.9 18.9 + - + -
6992A VAL* 1.3 79.2 - - - +
6994A ASN* 1.3 65.0 + - - +
6995A VAL* 3.7 5.9 - - - +
6996A ASN* 3.4 24.1 + - - +
6997A ALA* 3.2 16.3 + - - -
7001A GLU* 4.4 3.4 + - - +
7003A PHE* 4.4 13.9 - - + -
----------------------------------------------------------
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