Contacts of the strand formed by residues 192 - 196 (chain D) in PDB entry 6AHU
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 ILE 192 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185D THR* 3.8 27.1 - - + -
186D VAL 3.7 3.8 - - - +
187D GLU* 4.6 16.2 - - + -
188D THR 5.8 0.7 - - - +
190D GLY 5.3 1.3 - - - -
191D PHE* 1.3 83.1 - - - +
193D SER* 1.3 61.4 + - - +
194D TYR* 4.3 17.7 + - + +
242J ILE 4.0 0.9 - - - +
243J SER* 3.4 1.3 - - - -
244J THR* 2.8 44.1 + - - +
246J LYS* 3.7 42.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 193 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126D ILE* 6.1 0.9 - - - -
130D LEU* 3.7 22.7 - - - +
184D PHE 3.8 0.5 - - - +
186D VAL* 3.0 45.7 + - - +
188D THR* 4.7 3.4 + - - -
191D PHE* 4.3 1.9 - - - -
192D ILE* 1.3 75.2 - - - +
194D TYR* 1.3 62.3 + - - +
195D ILE* 3.9 4.0 + - - +
241J ILE* 4.0 15.5 - - - +
242J ILE 3.6 4.5 - - - -
243J SER* 3.9 17.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 194 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143D THR* 3.7 20.7 + - + -
183D VAL* 3.7 17.7 - - + -
184D PHE 3.4 1.8 - - - -
185D THR* 3.2 32.6 - - + +
192D ILE* 4.7 13.6 - - + +
193D SER* 1.3 73.4 - - - +
195D ILE* 1.3 60.2 + - - +
196D TYR* 4.0 16.3 - + + -
240J GLY 4.0 0.7 - - - +
241J ILE* 3.3 28.9 - - - +
242J ILE* 2.9 28.0 + - + +
244J THR* 4.2 21.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 195 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130D LEU* 5.5 4.5 - - + +
135D LEU* 3.9 28.7 - - + -
183D VAL* 3.5 2.5 - - - -
184D PHE* 2.8 46.3 + - + +
186D VAL* 3.8 26.5 - - + -
193D SER* 4.5 9.0 - - - +
194D TYR* 1.3 76.8 - - - +
196D TYR* 1.3 62.0 + - - +
197D GLY* 3.2 4.2 + - - +
200D PHE* 3.7 32.5 - - + -
240J GLY 4.2 2.7 - - - -
241J ILE* 3.8 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 196 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144D LYS* 5.9 3.7 + - + -
182D CYS 3.7 2.9 - - - +
183D VAL* 3.6 28.3 - - + -
194D TYR* 4.7 12.0 - + + +
195D ILE* 1.3 68.8 - - - +
197D GLY* 1.3 58.9 + - - +
198D SER* 3.1 11.0 + - - +
199D LYS* 3.6 6.9 + - + +
200D PHE* 3.2 20.0 - - + -
218D ILE* 3.6 48.2 - - + -
220D LEU* 4.4 9.9 - - + -
230J LEU* 6.0 1.6 - - - +
233J GLU* 4.9 3.8 + - - -
234J THR* 6.0 4.5 - - + -
239J PHE 5.1 2.0 - - - -
240J GLY* 3.3 31.1 + - - +
242J ILE* 3.5 40.4 - - + +
----------------------------------------------------------
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