Contacts of the strand formed by residues 7002 - 7009 (chain C) 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 ALA7002 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6968C LYS* 3.4 4.5 - - - +
6969C ILE* 2.8 39.8 + - + +
6990C ALA* 4.4 4.5 - - + -
6991C PHE 3.3 19.5 - - - +
6992C VAL* 4.0 6.1 - - + +
7000C SER 3.6 0.6 + - - -
7001C GLU* 1.3 73.2 - - - +
7003C PHE* 1.3 65.0 + - - +
7004C LEU 4.0 0.4 - - - -
7026C TYR* 3.2 36.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE7003 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6844C LYS* 4.1 26.9 - - + -
6845C TYR* 5.4 6.7 - + - -
6848C LEU* 3.9 46.9 - - + -
6926C ILE* 5.5 2.7 - - + -
6927C SER 4.1 8.3 - - - -
6928C ASP* 4.2 9.4 - - + -
6966C ALA* 4.4 9.0 - - + -
6967C ILE 3.5 3.1 - - - +
6968C LYS* 3.6 36.3 - - + -
6990C ALA* 3.5 1.7 - - - -
6991C PHE* 2.7 41.1 + + - +
6993C THR* 4.2 12.6 - - + -
7001C GLU* 4.1 18.2 - - - -
7002C ALA* 1.3 75.8 - - - +
7004C LEU* 1.3 62.2 - - - +
7005C ILE* 3.3 12.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU7004 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6965C VAL* 3.8 3.3 - - - +
6966C ALA* 3.4 2.3 + - - -
6967C ILE* 2.8 46.2 + - + +
6969C ILE* 3.6 43.1 - - + -
6975C ASN 5.6 0.4 - - - +
6978C LEU* 3.9 21.1 - - + -
6979C TYR* 3.6 40.6 - - + +
6982C MET* 4.2 15.7 - - + -
6988C TRP* 4.2 6.5 - - + -
6989C THR 3.5 3.4 - - - +
6990C ALA* 3.9 21.8 - - + -
7002C ALA 4.0 0.8 - - - -
7003C PHE* 1.3 68.4 - - - +
7005C ILE* 1.3 60.5 + - - +
7006C GLY 4.0 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE7005 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6848C LEU* 4.0 9.9 - - + -
6851C TYR* 3.7 21.8 - - + -
6852C LEU* 3.9 17.5 - - + -
6855C LEU* 3.8 23.8 - - + -
6857C LEU* 6.1 0.4 - - + -
6964C SER* 5.9 2.0 - - - -
6965C VAL 3.2 9.4 - - - +
6966C ALA* 4.1 14.6 - - + -
6982C MET* 3.8 2.8 - - - +
6987C TRP* 5.3 1.1 - - + -
6988C TRP* 3.0 9.4 - - - +
6989C THR* 2.8 42.3 + - + +
6991C PHE* 3.7 28.3 - - + -
7003C PHE* 3.6 9.4 - - + +
7004C LEU* 1.3 74.3 - - - +
7006C GLY* 1.3 66.6 + - - +
7007C CYS* 4.7 3.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY7006 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6964C SER* 3.2 7.3 - - - -
6965C VAL* 2.9 37.9 + - - +
6982C MET* 3.8 8.2 - - - -
6985C PHE* 3.2 32.4 - - - -
6987C TRP 3.8 2.5 - - - -
6988C TRP* 4.4 0.4 - - - -
7005C ILE* 1.3 73.9 - - - +
7007C CYS* 1.3 58.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS7007 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6855C LEU* 4.0 17.7 - - + -
6856C THR* 3.7 30.3 - - - -
6857C LEU* 4.2 4.0 - - - -
6964C SER* 3.4 9.6 - - - -
6985C PHE* 3.6 0.8 - - - -
6986C ALA* 3.2 14.0 + - - +
6987C TRP* 2.8 41.2 + - + +
7005C ILE* 4.0 2.8 - - + -
7006C GLY* 1.3 71.5 - - - -
7008C ASN* 1.3 92.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN7008 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6856C THR* 2.8 42.7 + - - -
6858C ALA 4.2 3.0 - - - +
6962C GLY 3.1 19.1 + - - +
6963C GLY 3.3 6.0 + - - -
6964C SER* 3.1 14.8 + - - -
6985C PHE* 3.7 1.5 - - - -
6986C ALA* 2.9 31.7 + - + +
7007C CYS* 1.3 76.1 - - - +
7009C TYR* 1.3 65.6 + - - +
7010C LEU* 3.6 4.8 + - - +
7073C LEU 3.2 24.6 + - - +
7074C SER 3.5 9.9 - - - +
7076C GLY* 3.6 10.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR7009 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6955C ILE* 3.6 27.7 + - + -
6956C GLN* 3.6 11.0 - - + +
6959C LEU* 3.6 42.0 - - + -
6960C ALA 3.7 9.6 - - - +
6961C LEU* 3.4 17.5 - - + +
6962C GLY* 2.8 26.4 + - - +
6963C GLY 2.7 18.1 + - - +
6981C LEU* 5.9 0.4 - - + -
6984C HIS* 3.6 28.2 + - + -
6985C PHE* 3.5 23.1 - + + -
7008C ASN* 1.3 71.0 - - - +
7010C LEU* 1.3 61.4 + - - +
7011C GLY* 3.4 26.3 - - - -
7073C LEU* 4.4 1.0 - - - +
7103C NA 2.6 26.5 - - - -
----------------------------------------------------------
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