Contacts of the strand formed by residues 187 - 193 (chain D) in PDB entry 1M7X
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 LEU 187 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154D GLY* 3.6 16.0 - - - -
155D GLN* 3.7 43.1 + - + +
156D PHE* 3.9 9.5 - - - -
159D TRP* 4.7 9.9 - - + -
185D GLY 4.1 4.0 - - - +
186D GLN* 1.3 75.8 - - - +
188D TYR* 1.3 65.4 + - - +
211D GLN* 5.8 6.5 - - + -
217D ALA* 4.8 12.1 - - + +
218D SER 3.3 6.5 - - - +
219D LEU* 3.9 34.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 188 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127D ALA* 3.9 16.2 + - + +
140D PHE* 3.7 18.8 - + + -
152D VAL* 4.2 12.1 - - + -
153D VAL 3.0 15.0 - - - +
154D GLY* 4.2 1.1 - - - -
156D PHE* 4.8 4.5 - - + -
159D TRP* 4.3 2.3 - - - -
187D LEU* 1.3 77.7 - - - +
189D LYS* 1.3 82.6 + - - +
190D TYR* 3.7 29.4 - + - -
204D ASP* 2.7 29.2 + - + +
206D TYR 4.9 0.3 + - - -
207D ALA* 4.6 4.5 - - - -
208D PHE 5.6 0.2 + - - -
217D ALA* 3.8 0.4 - - - +
218D SER* 2.8 58.1 + - - +
219D LEU 4.0 7.1 + - - -
220D ILE* 3.7 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 189 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152D VAL* 3.5 5.7 - - - +
153D VAL* 2.8 41.7 + - + -
159D TRP* 3.6 17.7 - - + -
188D TYR* 1.3 91.1 - - - +
190D TYR* 1.3 66.1 + - - +
201D LEU* 4.0 43.8 + - + +
202D LYS 3.7 9.2 - - - +
203D SER* 3.8 15.9 + - - +
216D THR* 3.4 26.5 + - - -
217D ALA* 3.7 17.7 - - + -
218D SER* 4.6 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 190 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126D GLY 4.0 2.8 + - - -
140D PHE* 3.9 9.8 - - + +
141D SER 3.5 18.0 + - - -
142D VAL* 3.8 26.0 - - + -
150D VAL* 4.3 9.9 - - + -
151D SER 3.1 7.9 - - - +
152D VAL* 4.4 4.5 - - + -
166D MET* 3.4 42.0 - - + -
188D TYR* 3.7 16.3 - + - -
189D LYS* 1.3 75.2 - - - +
191D GLU* 1.3 60.7 + - - +
192D MET* 3.9 3.5 + - + -
200D ARG 3.8 0.5 - - - +
201D LEU* 3.6 2.4 - - - -
202D LYS* 2.7 51.1 + - + +
203D SER 4.6 0.9 - - - -
204D ASP* 3.1 58.4 + - + -
205D PRO* 5.2 0.4 - - + -
351D PHE* 5.5 0.4 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 191 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149D ARG* 2.6 31.5 + - - +
150D VAL* 3.2 4.0 - - - +
151D SER* 2.8 33.3 + - - +
153D VAL* 3.9 22.9 - - + +
159D TRP* 4.1 7.4 - - - +
161D GLY* 4.1 9.6 + - - -
189D LYS 4.0 1.4 + - - -
190D TYR* 1.3 75.1 - - - +
192D MET* 1.3 62.8 + - - +
199D LEU* 3.2 32.7 - - + +
200D ARG 3.4 8.1 - - - +
201D LEU* 3.9 20.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 192 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142D VAL* 6.2 0.4 - - + -
144D ALA* 4.4 8.1 - - + -
147D ALA* 3.9 10.3 - - + -
149D ARG* 3.6 16.6 - - - +
150D VAL* 3.9 12.6 - - + -
190D TYR* 3.9 3.1 + - + +
191D GLU* 1.3 76.0 - - - +
193D ILE* 1.3 72.9 + - - +
194D ASP* 4.3 5.4 - - - +
198D ASN 3.3 1.2 - - - +
199D LEU* 3.3 8.0 - - - +
200D ARG* 2.9 45.9 + - + +
202D LYS* 3.4 29.2 - - + -
351D PHE* 4.1 15.3 - - + -
352D ASP* 3.2 44.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 193 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147D ALA* 3.7 4.9 - - - +
148D ARG* 3.0 41.4 + - + +
149D ARG* 3.4 41.8 + - + +
192D MET* 1.3 89.6 - - - +
194D ASP* 1.3 68.4 + - - +
197D GLY* 3.2 35.4 - - - +
198D ASN 2.9 10.3 - - - +
199D LEU* 4.0 13.9 - - + +
----------------------------------------------------------
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