Contacts of the strand formed by residues 191 - 197 (chain D) in PDB entry 1MPX
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 191 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154D ILE* 4.1 17.4 - - + +
168D VAL* 3.4 12.8 - - - +
169D GLY 4.1 0.7 - - - -
170D MSE 3.7 40.6 - - + +
180D VAL* 5.6 0.4 - - + +
183D ALA* 4.4 10.3 - - + -
184D LEU* 4.4 16.4 - - + -
187D PRO* 3.8 24.2 - - + -
188D HIS 3.0 17.2 + - - +
189D PRO 4.1 2.4 - - - +
190D ALA* 1.3 74.2 - - - +
192D LYS* 1.3 62.6 + - - +
193D VAL 3.5 24.0 - - - +
194D ALA* 4.9 2.7 - - + -
297D VAL* 3.7 19.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 192 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166D GLY 5.1 1.3 - - - -
167D LYS* 4.1 30.1 - - + +
168D VAL 2.9 4.9 + - - -
189D PRO* 2.8 26.5 + - - +
190D ALA* 3.3 17.3 - - - +
191D LEU* 1.3 73.7 - - - +
193D VAL* 1.3 61.1 + - - +
297D VAL* 3.9 4.0 - - - -
298D PRO* 3.2 23.6 - - - +
375D TYR* 3.4 35.5 - - + +
376D LEU* 3.9 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 193 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168D VAL 3.9 0.2 + - - -
169D GLY* 3.3 4.0 - - - -
170D MSE 3.1 22.2 + - - -
191D LEU* 3.5 6.8 - - - +
192D LYS* 1.3 79.4 - - - +
194D ALA* 1.3 63.9 + - - +
297D VAL* 3.6 4.9 - - - +
298D PRO 3.5 9.2 - - - +
371D PHE* 3.3 41.1 - - + +
372D PHE* 3.6 21.8 - - + -
375D TYR* 4.1 13.9 - - + -
376D LEU* 3.6 36.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 194 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170D MSE 3.4 9.4 - - + -
180D VAL* 3.7 21.1 - - + -
184D LEU* 3.9 28.0 - - + -
191D LEU* 4.9 2.7 - - + -
193D VAL* 1.3 76.3 - - - +
195D VAL* 1.3 66.3 + - - +
196D PRO* 3.8 1.8 - - - -
297D VAL* 4.2 2.2 - - + -
298D PRO 3.0 7.1 + - - +
299D THR* 3.3 8.8 - - - +
300D MSE 2.9 23.9 + - - +
371D PHE* 4.4 1.2 - - - -
372D PHE* 5.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 195 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170D MSE 2.9 9.9 + - - +
171D ILE* 3.5 32.2 - - + +
172D GLY 3.6 1.6 + - - -
180D VAL* 4.3 2.0 - - - -
194D ALA* 1.3 81.1 - - - +
196D PRO* 1.3 61.7 - - - +
197D GLU* 3.3 28.1 + - + +
300D MSE 3.5 32.1 - - + +
302D LEU* 4.8 4.3 - - + -
363D PHE* 4.9 2.5 - - + -
368D LEU* 3.7 15.7 - - + -
371D PHE* 4.2 5.2 - - + -
372D PHE* 3.5 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 196 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172D GLY 4.1 2.9 - - - +
177D GLY* 3.9 9.9 - - - +
180D VAL* 3.8 16.8 - - + -
181D VAL* 3.7 24.5 - - + -
184D LEU* 4.2 2.7 - - + -
194D ALA 3.8 0.4 - - - -
195D VAL* 1.3 86.6 - - - +
197D GLU* 1.3 60.1 + - - +
199D PRO* 3.8 7.7 - - + +
299D THR* 3.7 20.4 - - + -
300D MSE 3.2 15.3 - - - +
301D TRP* 3.7 26.2 - - + +
302D LEU 3.1 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 197 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171D ILE* 3.6 26.8 - - - +
172D GLY* 2.9 22.2 + - - +
173D SER* 3.1 9.7 - - - +
174D SER 3.0 18.0 + - - -
177D GLY* 4.0 0.4 - - - -
195D VAL* 3.6 24.5 - - + +
196D PRO* 1.3 70.1 - - - +
198D SER* 1.3 72.2 + - - +
199D PRO* 2.9 3.8 - - - +
302D LEU* 3.5 18.8 - - + -
343D VAL* 3.9 18.2 - - + +
344D ASN* 3.2 29.0 + - - +
363D PHE* 4.2 13.9 - - - -
364D ARG* 6.1 0.2 - - - +
368D LEU* 4.8 1.0 - - - +
----------------------------------------------------------
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