Contacts of the helix formed by residues 210 - 216 (chain C) in PDB entry 1SIW
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 PRO 210 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B LEU* 4.2 20.0 - - + +
88B ILE* 4.4 13.9 - - + -
197B PRO* 3.6 41.1 - - + +
198B SER* 5.1 1.1 - - - -
220B TRP* 3.9 15.5 - - + +
208C SER 2.7 10.9 - - - +
209C VAL* 1.3 85.1 - - + +
211C VAL* 1.3 63.2 + - - +
212C GLU* 3.4 5.2 - - + +
213C TYR* 3.4 16.4 + - + +
806C HEM 4.3 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 211 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B LEU* 5.7 0.7 - - - -
209C VAL* 2.8 40.1 + - + +
210C PRO* 1.3 71.7 - - - +
212C GLU* 1.3 70.9 + - + +
213C TYR 3.1 1.4 + - - -
214C LEU* 3.3 26.4 + - + +
215C THR* 4.6 1.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 212 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A TYR* 2.8 34.5 + - - +
13A LYS* 5.6 0.7 + - - -
197B PRO 4.1 6.2 - - - +
198B SER* 3.5 26.9 - - - +
199B GLY* 4.4 1.0 - - - -
210C PRO* 5.0 3.4 - - + -
211C VAL* 1.3 84.7 - - + +
213C TYR* 1.3 65.4 + - - +
215C THR* 3.2 18.2 + - - +
216C ARG* 3.2 37.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 213 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B PRO* 5.1 1.4 - - - +
80B ASN 5.3 0.5 - - - -
81B ARG* 3.2 48.8 + - + +
84B LEU* 3.4 29.9 - - + +
85B LEU* 3.2 26.7 - - + -
194B ALA 2.6 30.5 + - - -
195B THR* 4.6 2.9 - - - +
196B CYS 3.9 8.5 - - - -
197B PRO* 3.4 24.0 - - + +
210C PRO 3.4 11.8 + - - +
211C VAL 3.1 1.2 + - - -
212C GLU* 1.3 82.0 - - - +
214C LEU* 1.3 63.0 + - - +
215C THR 3.1 1.4 + - - -
216C ARG* 3.2 36.5 + - + +
218C TYR* 4.0 11.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 214 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B ARG* 3.2 21.9 + - + +
82B ALA* 4.0 28.5 - - + +
85B LEU* 3.3 32.5 - - + -
211C VAL* 3.3 16.5 + - + +
212C GLU 3.2 0.8 - - - -
213C TYR* 1.3 77.4 - - - +
215C THR* 1.3 66.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 215 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B ARG* 4.7 1.6 - - - +
211C VAL 5.5 1.6 - - - +
212C GLU* 3.2 11.7 + - - -
213C TYR 3.1 0.6 - - - -
214C LEU* 1.3 86.1 - - + +
216C ARG* 1.3 63.9 + - - +
217C LYS* 3.8 6.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 216 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B ARG* 2.9 28.1 + - - -
193B VAL 2.8 24.6 + - - -
194B ALA* 3.7 12.3 + - - +
196B CYS 2.8 27.3 + - - -
197B PRO 4.5 0.6 + - - -
199B GLY* 3.4 16.1 - - - +
212C GLU* 3.2 38.6 + - - +
213C TYR* 3.2 25.1 + - + +
215C THR* 1.3 78.2 - - - +
217C LYS* 1.3 75.8 + - - +
218C TYR* 3.0 21.9 + - - +
220C LEU* 3.9 27.8 - - + +
----------------------------------------------------------
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