Contacts of the strand formed by residues 157 - 162 (chain D) in PDB entry 6QCG
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 ALA 157 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155D GLY* 4.9 0.2 - - - -
156D ASP* 1.3 83.1 + - + +
158D VAL* 1.3 59.7 + - - +
159D VAL* 5.4 1.2 - - - +
170D SER 4.1 0.2 - - - +
171D ALA* 3.8 21.3 - - - +
172D SER 4.7 2.6 + - - +
206D THR* 3.9 20.4 - - + -
207D PHE 3.2 15.9 - - - +
208D ALA* 4.5 1.6 - - - -
209D LEU* 4.2 4.0 - - - +
254D LYS* 4.4 13.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 158 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147D ILE* 5.9 0.2 - - + -
148D CYS* 5.8 0.7 - - - -
151D LEU* 3.7 20.4 - - + -
157D ALA* 1.3 73.0 - - - +
159D VAL* 1.3 66.9 + - - +
160D ILE* 4.0 9.3 + - + -
169D PHE* 3.8 24.0 - - + -
170D SER 3.3 12.3 - - - +
171D ALA* 4.9 0.2 - - - -
205D LEU 3.9 0.7 - - - +
206D THR* 3.4 2.4 - - - +
207D PHE* 3.0 37.7 + - + +
209D LEU* 3.7 22.3 - - + +
212D LEU* 3.5 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 159 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157D ALA 5.4 1.6 - - - +
158D VAL* 1.3 73.9 - - - +
160D ILE* 1.3 59.9 + - - +
161D SER* 3.7 8.6 + - - +
168D LYS 3.2 6.8 - - - +
169D PHE* 3.5 0.3 - - - -
170D SER* 2.7 46.6 + - - +
171D ALA* 6.0 0.4 - - - -
204D GLN* 3.8 30.7 - - + +
205D LEU 3.2 10.5 - - - +
206D THR* 3.6 24.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 160 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144D PHE* 5.3 2.2 - - + -
158D VAL* 4.2 14.1 - - + -
159D VAL* 1.3 69.5 - - - +
161D SER* 1.3 60.4 - - - +
167D VAL* 4.0 16.2 - - + -
168D LYS 3.6 3.4 - - - -
169D PHE* 3.8 38.8 - - + +
203D VAL 3.9 2.4 - - - +
204D GLN* 3.4 3.1 - - - -
205D LEU 2.8 31.4 + - - +
207D PHE* 3.9 27.8 - - + -
212D LEU* 4.9 4.9 - - + -
227D LEU* 4.8 9.2 - - + -
229D MET* 3.8 30.3 - - + +
235D LEU* 4.3 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 161 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159D VAL* 3.9 7.8 + - - +
160D ILE* 1.3 71.8 - - - +
162D CYS* 1.3 60.5 + - - +
167D VAL* 3.4 5.2 - - - +
168D LYS* 2.7 62.5 + - - +
170D SER* 5.0 1.9 + - - -
203D VAL 3.6 5.4 - - - -
204D GLN* 3.0 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 162 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135D CYS* 3.0 35.1 - - + -
137D VAL* 3.8 20.2 - - - -
160D ILE 5.3 1.3 - - - +
161D SER* 1.3 73.0 - - - +
163D ALA* 1.3 58.5 + - - +
166D GLY 4.0 1.8 - - - -
167D VAL* 4.2 13.2 - - + -
197D ILE* 3.8 22.9 - - - -
199D MET* 3.5 2.2 - - - +
202D PRO* 3.4 27.9 - - - +
203D VAL 3.0 16.2 + - - +
229D MET* 4.6 8.3 - - + -
----------------------------------------------------------
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