Contacts of the helix formed by residues 197 - 203 (chain M) in PDB entry 3TDD
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 TRP 197 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182 TYR* 3.4 58.1 + - + +
192 ARG* 6.1 1.8 - - - -
292 ARG* 3.3 66.0 - - + -
302 VAL* 4.6 5.6 - - + -
1712 GLY* 3.4 24.7 - - - -
1722 VAL* 3.7 15.7 - - + -
163M TYR* 5.9 4.7 - + - -
164M TYR* 4.1 13.1 - + - -
195M MET* 3.5 46.2 + - + +
196M LYS* 1.3 71.9 - - - +
198M ASP* 1.3 57.9 + - - +
199M PHE* 3.2 7.3 - - - -
200M ALA* 2.7 39.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 198 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182 TYR* 3.5 18.1 - - + +
197M TRP* 1.3 78.2 - - - +
199M PHE* 1.3 64.0 + - - +
200M ALA 3.0 1.6 + - - -
201M LYS* 2.7 60.9 + - - +
144V GLN* 3.9 14.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 199 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292 ARG* 3.7 18.2 - - - -
302 VAL* 3.5 30.1 - - + -
196M LYS* 3.3 32.8 - - + -
197M TRP* 3.0 7.7 + - - -
198M ASP* 1.3 77.1 + - - +
200M ALA* 1.3 62.2 + - - +
201M LYS 3.1 1.5 + - - -
202M ASP* 3.2 19.9 + - - +
203M ILE* 3.8 10.4 + - + +
123V TYR* 3.7 37.2 - + + -
124V TYR* 3.6 30.3 - + - -
142V TRP* 4.0 22.4 - + + -
144V GLN* 3.9 20.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 200 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182 ILE* 3.8 13.9 - - + -
302 VAL* 3.9 27.8 - - + -
1722 VAL* 4.0 14.6 - - + -
1742 ARG* 2.8 40.6 + - - +
197M TRP* 2.7 19.5 + - + +
199M PHE* 1.3 80.2 - - - +
201M LYS* 1.3 55.2 + - - +
203M ILE* 3.4 6.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 201 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182 ILE* 3.5 38.0 - - + +
1742 ARG* 4.4 2.4 + - - +
198M ASP* 2.7 44.8 + - - +
199M PHE 3.1 1.0 - - - -
200M ALA* 1.3 75.3 - - - +
202M ASP* 1.3 86.1 + - - +
203M ILE 3.1 12.9 + - - +
204M LYS* 4.5 6.2 + - - +
144V GLN* 4.9 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 202 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199M PHE* 3.2 7.7 + - - +
201M LYS* 1.3 106.9 + - - +
203M ILE* 1.3 59.1 + - - +
204M LYS* 3.0 28.9 + - - +
123V TYR* 2.9 24.2 + - - +
144V GLN* 3.0 24.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 203 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302 VAL* 3.4 42.4 - - + +
322 ASP* 4.6 2.3 - - + +
1742 ARG* 3.5 16.9 + - - +
1862 ARG* 5.5 0.5 + - - -
199M PHE* 3.9 17.0 - - + +
200M ALA 3.4 17.0 + - - +
201M LYS 3.1 3.9 - - - +
202M ASP* 1.3 80.9 - - - +
204M LYS* 1.3 65.8 + - - +
205M GLY 4.9 2.0 - - - +
121V VAL* 4.0 34.3 - - + +
122V GLY* 3.8 22.2 - - - -
123V TYR* 4.2 20.4 - - + -
----------------------------------------------------------
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