Contacts of the strand formed by residues 194 - 198 (chain D) in PDB entry 2VM8
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 194 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162D ASN* 2.9 32.2 + - - +
163D SER* 4.0 5.6 - - - -
164D PHE 3.1 25.8 + - - +
188D ILE* 3.6 6.2 - - - +
193D ALA* 1.3 77.4 - - - +
195D ALA* 1.3 62.4 + - - +
196D GLN* 4.2 8.7 - - + -
249D PRO* 4.1 7.9 - - + +
250D LEU 5.0 0.9 - - - +
251D TYR* 3.7 34.1 - - + -
275D TYR* 6.2 3.6 - - + -
391D VAL* 3.6 27.1 - - + +
392D PHE* 4.1 12.3 - - + -
475D PRO* 4.1 14.8 - - + -
478D VAL* 5.1 12.3 - - + -
479D TYR* 5.5 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 195 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164D PHE 3.8 2.9 - - - -
185D LEU* 3.9 23.1 - - + -
188D ILE* 3.7 16.7 - - + +
194D ILE* 1.3 72.8 - - - +
196D GLN* 1.3 55.5 + - - +
248D CYS* 3.8 18.2 - - - -
249D PRO 3.1 19.2 + - - +
250D LEU* 3.3 10.1 - - + +
251D TYR 2.8 30.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 196 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107D HIS* 3.5 17.1 + - - -
138D HIS* 3.0 48.4 + - + +
163D SER* 4.3 1.5 - - - -
164D PHE 3.0 19.4 + - - +
165D LEU* 3.3 18.0 - - + +
166D VAL* 2.9 28.8 + - - +
194D ILE* 4.2 9.4 - - + +
195D ALA* 1.3 74.5 - - - +
197D VAL* 1.3 62.3 + - - +
251D TYR* 3.3 34.6 - - + +
253D THR* 3.5 22.0 - - + +
277D GLU* 4.7 1.6 + - - -
392D PHE* 5.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 197 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165D LEU* 4.4 3.1 - - - -
166D VAL* 3.3 30.5 - - + +
168D MET* 4.2 24.7 - - + -
181D ILE* 5.2 5.2 - - + -
185D LEU* 6.2 0.9 - - + -
196D GLN* 1.3 73.2 - - - +
198D HIS* 1.3 61.3 + - - +
199D ALA* 3.7 7.0 + - + -
239D ALA* 4.2 9.6 - - + -
250D LEU* 3.4 24.9 - - + -
251D TYR 3.0 16.8 + - - +
252D ILE* 3.5 16.7 - - + +
253D THR* 3.0 30.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 198 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D ARG* 5.9 2.2 + - - +
165D LEU* 4.4 4.7 - - + +
166D VAL 3.0 8.2 + - - +
167D TYR* 3.4 31.4 - + + -
168D MET 2.9 25.3 + - - -
169D ALA* 3.8 14.9 + - + +
170D PHE* 3.5 24.0 - + - -
197D VAL* 1.3 71.9 - - - +
199D ALA* 1.3 60.0 + - - +
200D GLU* 2.7 31.0 + - + -
253D THR* 4.0 9.6 + - - +
254D LYS* 4.7 10.3 + - - +
304D SER* 3.4 31.6 + - - -
305D PRO* 3.9 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