Contacts of the strand formed by residues 210 - 215 (chain C) in PDB entry 1SMR
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 CYS 210 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193C THR* 3.5 1.8 - - - +
194C MET* 2.7 42.1 + - + +
206C CYS* 2.1 54.7 - - + -
208C GLU* 3.8 10.3 - - - -
209C GLY* 1.3 75.3 - - - -
211C GLU* 1.3 62.5 + - - +
299C TRP* 3.9 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 211 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C SER* 2.6 29.6 + - - +
186C LYS* 5.1 0.2 - - - +
191C GLN* 2.9 32.4 + - - +
192C ILE 3.7 1.7 - - - +
193C THR* 2.9 27.1 + - - +
210C CYS* 1.3 73.2 - - - +
212C VAL* 1.3 63.5 - - - +
297C PRO 4.6 8.2 + - - +
298C VAL* 3.7 11.5 - - + -
299C TRP* 2.9 27.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 212 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191C GLN* 3.3 2.7 - - - +
192C ILE* 3.0 59.5 + - + +
194C MET* 4.1 25.6 - - + -
211C GLU* 1.3 78.6 - - - +
213C VAL* 1.3 66.8 + - - +
214C VAL* 5.4 0.2 - - + -
262C LEU* 4.3 5.6 - - + -
298C VAL* 4.7 0.2 - - - -
299C TRP* 3.3 27.8 - - + +
300C VAL 3.9 0.2 - - - +
301C LEU* 3.5 37.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 213 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C THR 4.9 1.1 - - - +
34C GLY* 4.6 7.4 - - - -
128C GLN* 5.9 0.7 - - - +
189C SER* 4.2 10.3 - - - +
190C TRP* 3.3 17.9 - - + +
191C GLN* 4.0 15.5 - - - +
212C VAL* 1.3 76.4 - - - +
214C VAL* 1.3 66.9 + - - +
215C ASP* 3.3 9.0 + - + +
295C THR* 6.2 1.8 - - + -
298C VAL* 3.8 27.8 - - + -
299C TRP 3.1 7.6 + - - +
300C VAL* 3.5 6.7 - - + +
301C LEU 3.2 21.7 + - - -
6D LPL 3.8 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 214 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C THR* 2.7 23.0 + - - -
190C TRP* 2.8 18.6 + - - +
192C ILE* 4.2 17.5 - - + -
212C VAL* 4.9 0.7 - - + +
213C VAL* 1.3 70.2 - - - +
215C ASP* 1.3 51.4 + - - +
216C THR 4.0 0.2 - - - -
301C LEU* 3.8 23.8 - - + +
305C PHE* 5.4 0.9 - - + -
306C ILE* 4.6 11.0 - - + -
311C THR* 4.2 12.8 - - + +
313C PHE* 3.7 26.0 - - + -
320C ILE* 3.8 22.7 - - + -
322C PHE* 4.2 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 215 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C ASP* 3.0 21.8 - - - +
33C THR* 3.5 2.5 - - - -
34C GLY* 3.2 14.9 + - - +
213C VAL* 3.3 9.8 + - + +
214C VAL* 1.3 69.7 - - - +
216C THR* 1.3 60.0 + - - +
217C GLY 3.0 4.7 + - - -
218C SER* 3.3 21.0 + - - -
300C VAL* 3.6 21.3 - - + +
301C LEU 3.2 7.7 + - - -
302C GLY* 3.3 19.1 - - - -
306C ILE* 4.3 1.8 - - - -
6D LPL 2.7 38.7 + - + +
----------------------------------------------------------
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