Contacts of the helix formed by residues 85 - 96 (chain u) in PDB entry 6QY3
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 HIS 85 (chain u).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62u ASN* 4.0 23.9 + - - +
64u LEU* 5.1 13.0 - - + -
83u ALA 3.8 0.4 + - - -
84u ARG* 1.3 79.2 - - - +
86u ASP* 1.3 64.6 + - - +
87u SER* 3.2 13.7 + - - +
88u SER* 3.5 19.1 + - - +
89u LEU* 4.0 3.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 86 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85u HIS* 1.3 72.7 - - - +
87u SER* 1.3 59.5 + - - +
88u SER 3.3 0.2 - - - -
89u LEU* 3.0 13.7 + - + +
90u GLN* 2.9 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 87 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85u HIS* 3.2 8.1 - - - +
86u ASP* 1.3 78.6 - - - +
88u SER* 1.3 57.6 + - - +
90u GLN* 2.8 25.4 + - - +
91u ILE* 2.9 15.2 + - - +
194u VAL 5.8 1.3 - - - -
195u CYS 4.5 4.5 - - - -
196u GLY* 4.2 27.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 88 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84u ARG* 5.0 10.3 - - - -
85u HIS* 3.5 13.2 + - - +
86u ASP 3.3 0.4 - - - -
87u SER* 1.3 78.7 - - - +
89u LEU* 1.3 61.4 + - - +
91u ILE* 3.6 17.6 + - - +
92u ALA* 4.2 4.2 + - - +
211v GLN* 6.0 7.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 89 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85u HIS 4.0 2.3 + - - +
86u ASP* 3.0 17.8 + - + +
88u SER* 1.3 77.9 - - - +
90u GLN* 1.3 60.9 + - - +
91u ILE 3.3 0.2 - - - -
92u ALA* 3.7 16.5 + - - +
93u ARG* 4.4 1.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 90 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86u ASP 2.9 11.9 + - - +
87u SER* 2.8 15.7 + - - +
89u LEU* 1.3 75.0 - - - +
91u ILE* 1.3 61.7 + - - +
92u ALA 3.2 2.2 - - - -
93u ARG* 3.3 18.0 + - + +
94u GLN* 3.5 8.7 + - - +
195u CYS 5.1 8.3 - - - +
196u GLY 6.3 0.7 - - - -
197u CYS* 6.0 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 91 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87u SER 2.9 9.7 + - - +
88u SER* 3.8 13.9 - - - +
89u LEU 3.3 0.8 - - - -
90u GLN* 1.3 75.7 - - - +
92u ALA* 1.3 59.3 + - - +
94u GLN* 3.0 12.4 + - + +
95u ILE* 2.9 25.6 + - - +
196u GLY 4.5 13.5 - - - +
197u CYS* 5.3 5.4 - - - +
198u MET* 5.4 5.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 92 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88u SER 4.2 4.0 + - - +
89u LEU* 3.7 13.6 + - - +
90u GLN 3.2 0.4 - - - -
91u ILE* 1.3 78.5 - - - +
93u ARG* 1.3 56.0 + - - +
95u ILE* 3.2 11.2 + - - +
96u ALA* 3.0 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 93 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89u LEU 4.4 1.6 + - - +
90u GLN* 3.3 14.4 + - - +
91u ILE 3.2 0.6 - - - -
92u ALA* 1.3 75.4 - - - +
94u GLN* 1.3 62.6 + - - +
96u ALA* 3.0 22.0 + - - +
97u TRP* 3.1 12.3 + - - +
277u LEU 5.6 1.7 - - - +
278u ASN* 4.6 24.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 94 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90u GLN 3.5 4.4 + - - +
91u ILE* 3.0 17.5 + - + +
93u ARG* 1.3 78.5 - - - +
95u ILE* 1.3 61.2 + - - +
96u ALA 3.4 0.3 + - - -
97u TRP* 3.4 19.9 + - - +
197u CYS* 4.4 22.4 - - + -
198u MET* 5.2 4.7 - - + +
201u ILE* 5.5 9.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 95 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91u ILE 2.9 11.2 + - - +
92u ALA* 3.2 13.2 + - - +
94u GLN* 1.3 76.5 - - - +
96u ALA* 1.3 56.8 + - - +
97u TRP 3.4 2.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 96 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92u ALA 3.0 14.5 + - - +
93u ARG* 3.0 12.2 + - - +
95u ILE* 1.3 77.1 - - - +
97u TRP* 1.3 63.9 + - - +
98u LYS* 3.2 4.5 + - - +
----------------------------------------------------------
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