Contacts of the strand formed by residues 172 - 178 (chain D) in PDB entry 6S6A
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 ASN 172 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138D GLY 3.6 7.4 + - - +
139D ALA* 3.3 11.9 - - + -
140D LEU 3.0 25.7 + - - -
170D ASP 3.1 14.3 + - - +
171D MET* 1.3 76.3 - - - +
173D PHE* 1.3 59.3 + - - +
174D GLU* 4.0 15.7 - - - +
235D LYS* 3.1 33.3 + - - +
236D LEU* 4.3 6.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 173 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140D LEU* 3.6 20.2 - - + -
161D VAL* 3.5 39.0 - - + -
164D ALA* 4.0 1.8 - - + -
165D TYR* 4.2 22.4 - + - -
169D PRO 4.5 3.1 - - - -
171D MET* 2.8 52.9 - - + -
172D ASN* 1.3 75.0 - - - +
174D GLU* 1.3 60.9 + - - +
175D VAL 4.3 0.2 - - - -
211D LEU* 3.4 29.8 - - + -
212D HIS 3.8 10.0 + - - +
213D LEU* 3.8 23.4 - - + -
214D SER* 3.2 29.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 174 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D ALA* 4.5 3.2 - - + +
140D LEU 3.1 14.3 + - - +
141D ILE* 3.0 20.7 - - + +
142D TYR 2.8 29.6 + - - -
172D ASN* 4.0 18.1 + - - +
173D PHE* 1.3 81.3 - - - +
175D VAL* 1.3 58.8 + - - +
176D PHE* 3.9 2.0 - - + -
214D SER* 3.2 20.9 + - - -
216D TYR* 3.2 26.8 + - + -
232D VAL* 3.8 46.6 - - + +
235D LYS* 4.7 8.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 175 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142D TYR* 3.3 9.2 - - + +
144D ILE* 3.5 33.0 - - + -
157D LEU* 4.4 18.4 - - + -
174D GLU* 1.3 72.6 - - - +
176D PHE* 1.3 66.0 - - - +
177D ILE* 3.7 5.4 + - + -
195D ILE* 4.8 1.6 - - + -
213D LEU* 3.7 33.4 - - + -
214D SER 2.8 15.0 + - - +
215D PHE* 3.4 26.0 - - + +
216D TYR* 3.1 25.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 176 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D LEU* 4.9 1.6 - - + -
77D ILE* 5.3 3.1 - - + -
141D ILE* 3.6 38.1 - - + -
142D TYR 2.9 12.0 + - - +
143D VAL* 3.7 12.5 - - + -
144D ILE* 3.1 26.9 + - - +
174D GLU* 4.5 2.0 - - + -
175D VAL* 1.3 75.2 - - - +
177D ILE* 1.3 60.8 + - - +
178D HIS* 3.4 7.7 + - + +
216D TYR* 3.5 34.5 - + + -
218D THR* 3.4 25.8 - - + +
225D ILE* 4.3 7.0 - - + -
228D ALA* 3.9 13.0 - - + -
229D PHE* 3.8 31.9 - + - -
232D VAL* 3.9 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 177 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144D ILE* 3.9 7.2 - - + -
146D ALA* 4.1 18.4 - - + -
175D VAL* 4.5 5.4 - - + +
176D PHE* 1.3 67.6 - - - +
178D HIS* 1.3 53.0 + - - +
180D VAL* 3.3 6.1 - - + +
188D LYS* 6.4 0.4 - - - -
191D THR* 4.7 9.9 - - + -
192D GLN* 4.7 15.3 - - + +
195D ILE* 4.2 32.3 - - + -
215D PHE* 3.9 39.5 - - + -
216D TYR 2.8 14.2 + - - +
217D LEU* 3.3 29.5 - - + -
218D THR* 2.9 27.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 178 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D SER 4.2 10.5 - - - +
73D GLY* 4.5 0.2 - - - -
77D ILE* 3.4 39.2 - - + +
143D VAL* 4.1 9.4 - - + -
144D ILE 3.1 16.4 + - - +
146D ALA* 3.1 23.7 + - - +
176D PHE* 3.9 8.2 - - + +
177D ILE* 1.3 72.0 - - - +
179D LYS* 1.3 87.5 - - + +
218D THR* 2.9 37.5 + - - +
219D SER* 3.8 6.3 - - - -
220D ILE* 3.7 7.8 - - + +
225D ILE* 4.5 2.7 - - + -
401D GDP 2.8 43.0 + - - -
----------------------------------------------------------
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