Contacts of the strand formed by residues 6525 - 6529 (chain F) in PDB entry 2H7C
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 GLY6525 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6446F MET 4.8 0.9 + - - -
6518F PRO* 3.8 23.0 - - - +
6519F GLU 3.9 11.3 + - - +
6520F TYR* 3.3 25.3 - - - +
6521F ASN* 4.6 0.8 + - - -
6523F LYS* 3.4 4.2 - - - +
6524F GLU* 1.3 79.0 - - - +
6526F TYR* 1.3 58.8 + - - -
6536F ALA 3.3 11.4 - - - -
6537F GLN* 4.2 8.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR6526 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6446F MET* 3.3 27.6 - - + +
6448F GLU* 4.1 17.0 + - + -
6517F TRP* 4.4 2.7 - - - +
6518F PRO* 3.8 7.4 - - - +
6520F TYR* 4.8 1.3 - - + -
6524F GLU 3.9 6.3 - - - +
6525F GLY* 1.3 74.3 - - - +
6527F LEU* 1.3 69.8 + - - +
6528F GLN* 3.3 35.1 + - + -
6535F ALA* 3.4 4.0 - - - +
6536F ALA* 2.9 43.0 + - + +
6537F GLN 3.6 20.7 + - - -
6538F LYS 5.2 0.2 - - - -
6539F LEU* 3.5 60.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU6527 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6446F MET 3.0 7.9 + - - +
6447F TYR* 3.1 4.5 - - - +
6448F GLU 2.9 26.0 + - - -
6499F PHE* 3.5 24.9 - - + -
6515F PRO* 5.1 2.7 - - + -
6516F HIS 3.6 21.8 - - - +
6517F TRP* 3.4 50.4 - - + +
6526F TYR* 1.3 76.7 - - - +
6528F GLN* 1.3 60.8 + - - +
6529F ILE* 3.5 12.0 + - + -
6533F THR* 3.7 20.0 - - + -
6534F GLN* 3.6 25.4 - - - -
6535F ALA* 3.8 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN6528 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6352F LYS* 5.6 3.6 - - - +
6448F GLU* 3.5 16.1 + - + +
6450F GLN* 6.1 0.9 - - - +
6526F TYR* 3.3 34.5 + - + -
6527F LEU* 1.3 69.6 - - - +
6529F ILE* 1.3 62.0 + - - +
6532F ASN 4.0 2.6 - - - +
6533F THR* 3.1 8.7 - - - +
6534F GLN* 2.9 60.1 + - + +
6535F ALA 4.7 0.2 - - - +
6536F ALA* 3.7 17.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE6529 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6447F TYR* 3.7 31.2 - - + -
6448F GLU 2.9 9.3 + - - +
6449F PHE* 3.5 30.5 - - + -
6450F GLN* 2.9 29.9 + - - +
6492F LEU* 3.9 5.6 - - + -
6495F MET* 3.8 19.3 - - + -
6496F VAL* 4.1 6.3 - - + -
6499F PHE* 5.1 3.6 - - + -
6500F TRP* 4.2 22.2 - - + -
6517F TRP* 4.2 7.4 - - + -
6527F LEU* 3.9 24.7 - - + +
6528F GLN* 1.3 74.1 - - - +
6530F GLY* 1.3 60.3 + - - +
6533F THR* 3.8 5.2 - - + -
----------------------------------------------------------
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