Contacts of the helix formed by residues 193 - 202 (chain A) in PDB entry 3W31
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 SER 193 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A HIS* 4.7 2.2 + - - -
191A HIS 4.0 3.0 + - - -
192A VAL* 1.3 73.2 - - - +
194A ASP* 1.3 57.3 + - - +
195A GLN* 3.0 33.4 + - - +
196A GLU* 3.2 17.1 + - - +
197A PHE* 2.7 32.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A LEU* 5.7 5.9 - - - +
76A TYR* 5.9 0.2 - - - +
192A VAL 4.5 4.0 - - - +
193A SER* 1.3 71.9 + - - +
195A GLN* 1.3 61.7 + - + +
197A PHE* 3.2 14.7 + - + +
198A ASP* 2.8 38.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A SER* 3.2 12.3 + - - +
194A ASP* 1.3 77.6 - - + +
196A GLU* 1.3 55.4 + - - +
198A ASP* 2.8 9.3 + - - +
199A HIS* 2.6 38.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A TYR* 2.7 34.5 + - - -
94A PHE* 4.3 7.0 - - - -
97A ARG* 2.5 40.3 + - - -
98A HIS* 3.3 30.5 - - + +
192A VAL* 3.8 11.7 - - + -
193A SER* 3.2 21.9 + - - +
195A GLN* 1.3 78.6 - - - +
197A PHE* 1.3 60.5 + - - +
199A HIS* 3.3 6.9 + - - +
200A TYR* 3.1 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LEU* 4.2 11.9 - - + -
70A CYS* 3.6 21.1 - - + -
71A MET* 3.2 34.2 - - + +
74A LEU* 3.3 31.0 - - + -
76A TYR* 3.8 14.4 + - - +
135A VAL* 3.9 17.3 - - + -
192A VAL* 2.9 50.9 - - + -
193A SER 2.7 20.2 + - - -
194A ASP* 3.2 16.9 + - + +
195A GLN 3.0 0.6 - - - -
196A GLU* 1.3 78.7 - - - +
198A ASP* 1.3 60.4 + - - +
200A TYR 3.7 0.3 + - - -
201A ALA* 3.4 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A TYR* 2.6 29.1 + - - -
194A ASP* 2.8 25.1 + - - +
195A GLN* 2.8 11.0 + - - +
197A PHE* 1.3 74.5 - - - +
199A HIS* 1.3 64.4 + - - +
200A TYR 3.2 0.4 - - - -
201A ALA* 3.2 6.8 + - - +
202A ASN* 3.2 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A TYR* 3.0 34.8 - + - -
97A ARG* 4.6 15.1 + - - -
195A GLN 2.6 19.9 + - - +
196A GLU* 3.5 11.9 - - - +
198A ASP* 1.3 74.4 - - - +
200A TYR* 1.3 59.8 + - - +
202A ASN* 3.4 12.7 + - - +
203A SER* 3.3 22.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LEU* 4.0 17.5 - - + -
68A HIS* 3.0 29.9 + + - -
71A MET* 3.9 20.2 - - + -
82A PRO* 3.9 13.5 - - - +
90A TYR* 3.2 62.8 + + + +
91A MET* 5.6 1.5 - - - -
196A GLU 3.1 11.1 + - - +
197A PHE 4.1 3.8 - - - +
198A ASP 3.2 0.4 - - - -
199A HIS* 1.3 73.2 - - - +
201A ALA* 1.3 51.6 + - - +
202A ASN 3.1 4.7 - - - -
203A SER* 2.9 15.4 + - - -
205A SER* 4.0 7.7 + - - -
206A TRP* 2.7 76.1 - + + +
209A LYS* 4.4 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A MET* 5.1 0.9 - - - -
76A TYR* 3.7 28.3 - - + -
197A PHE 3.4 15.0 + - - +
198A ASP* 3.2 8.1 + - - +
200A TYR* 1.3 79.3 - - - +
202A ASN* 1.3 56.1 + - - +
203A SER 3.4 1.3 - - - -
206A TRP* 3.4 26.0 + - + +
207A LYS* 3.2 16.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A ASP 3.2 15.3 + - - +
199A HIS* 3.4 13.8 + - - +
200A TYR 3.1 0.4 - - - -
201A ALA* 1.3 79.4 - - - +
203A SER* 1.3 57.9 + - - +
204A SER 4.2 0.2 + - - -
207A LYS* 3.4 25.0 + - - +
----------------------------------------------------------
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