Contacts of the strand formed by residues 215 - 219 (chain D) in PDB entry 3C6M
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 MET 215 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192D LYS 3.2 3.5 + - - +
193D ASP* 3.3 15.2 - - - +
194D VAL 2.8 27.2 + - - +
213D PRO 3.5 0.4 - - - -
214D LYS* 1.3 87.0 - - + +
216D VAL* 1.3 62.6 + - - +
217D THR* 4.0 11.6 + - - +
246D GLY 5.5 1.1 - - - +
247D ASP 4.8 3.6 - - - +
248D CYS* 3.4 22.0 - - - +
249D TYR 3.6 16.6 - - - +
250D GLN* 3.4 43.5 - - + +
268D ARG* 4.6 7.6 - - - +
270D PHE* 5.7 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 216 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194D VAL* 3.5 14.8 - - + -
196D ILE* 3.5 34.1 - - + -
205D LEU* 3.7 14.8 - - + +
208D ILE* 3.3 31.9 - - + -
209D VAL* 5.0 3.4 - - + -
213D PRO* 3.5 21.8 - - + -
215D MET* 1.3 77.4 - - - +
217D THR* 1.3 64.5 + - - +
248D CYS 2.8 11.3 + - - +
249D TYR* 3.1 10.5 - - + +
250D GLN* 2.9 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 217 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194D VAL 2.9 13.2 + - - -
195D LEU* 3.3 16.9 - - + +
196D ILE 2.7 31.0 + - - -
215D MET* 4.0 5.0 - - - +
216D VAL* 1.3 78.0 - - - +
218D MET* 1.3 55.8 + - - +
219D VAL* 4.6 2.2 - - + -
250D GLN* 3.1 38.8 + - + +
252D LEU* 4.3 11.2 - - + -
263D TYR* 3.4 25.4 - - - +
268D ARG* 3.9 9.6 + - - +
270D PHE* 4.3 6.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 218 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196D ILE* 3.5 19.1 - - + -
198D GLY 3.3 16.8 - - - +
199D GLY* 3.3 36.1 - - - +
200D GLY 4.0 0.7 - - - +
202D GLY* 5.0 0.2 - - - -
204D ILE* 6.4 0.2 - - - -
205D LEU* 3.9 40.4 - - + +
216D VAL 4.1 0.6 - - - -
217D THR* 1.3 73.5 - - - +
219D VAL* 1.3 57.4 + - - +
220D GLU* 3.9 4.0 - - + -
226D ILE* 3.7 28.0 - - + -
241D LEU* 4.8 2.9 - - + -
250D GLN 2.7 12.8 + - - +
251D VAL* 3.3 18.4 - - + +
252D LEU* 2.5 35.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 219 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195D LEU* 3.9 24.7 - - + -
196D ILE 3.0 10.8 + - - +
197D LEU* 4.3 1.9 - - + -
198D GLY 3.0 23.9 + - - -
217D THR* 4.6 2.5 - - + -
218D MET* 1.3 75.2 - - - +
220D GLU* 1.3 59.8 + - - +
252D LEU* 3.4 16.2 - - + +
254D GLU* 3.2 24.9 - - + +
256D CYS* 3.7 26.0 - - + +
259D VAL* 3.8 31.6 - - + -
401D MTA 3.4 7.6 - - - -
----------------------------------------------------------
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