Contacts of the helix formed by residues 265 - 274 (chain A) in PDB entry 3TMP
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 ASP 265 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A GLU* 1.3 73.5 - - - +
266A PHE* 1.3 68.3 + - - +
267A THR* 3.5 10.9 + - - -
268A THR* 2.9 39.0 + - - +
269A TYR* 3.0 19.9 + - - +
263E THR 4.2 9.0 - - - +
47F GLY* 3.9 19.2 - - - +
48F LYS* 5.6 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 266 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A LEU* 3.4 33.0 - - + -
252A MET* 4.0 9.2 - - - -
255A ALA* 3.6 20.4 - - + -
258A PHE* 4.0 18.4 - - + -
259A SER* 3.7 40.4 - - - -
262A VAL* 4.0 24.0 - - + -
264A GLU 3.3 5.1 + - - +
265A ASP* 1.3 76.9 + - - +
267A THR* 1.3 63.4 + - - +
269A TYR* 3.2 10.4 + + - +
270A ILE* 3.0 50.1 + - + +
46F ALA* 4.0 14.5 + - + +
47F GLY* 5.8 1.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 267 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A MET* 4.0 27.2 - - + +
265A ASP* 3.3 9.4 + - - -
266A PHE* 1.3 76.8 - - - +
268A THR* 1.3 57.2 + - - +
270A ILE* 3.3 1.7 + - + +
271A ASN* 2.9 52.6 + - - +
45F PHE 4.3 0.7 + - - -
46F ALA* 3.3 17.6 + - - +
48F LYS* 4.0 34.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 268 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A GLU* 3.9 13.7 - - + +
265A ASP* 2.9 32.4 + - - +
266A PHE 3.2 0.2 - - - -
267A THR* 1.3 77.5 - - - +
269A TYR* 1.3 61.9 + - - +
271A ASN* 3.5 10.5 + - + +
272A ARG* 3.3 30.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 269 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A ASN* 3.8 10.5 - - + -
177A SEP 3.6 14.0 + - - -
262A VAL* 3.7 28.5 - - + -
264A GLU* 3.4 28.2 + - + +
265A ASP 3.0 13.1 + - - +
266A PHE* 3.4 11.9 - + - +
268A THR* 1.3 76.5 - - - +
270A ILE* 1.3 78.6 + - + +
272A ARG* 3.3 10.8 - - - +
273A LYS* 3.0 58.4 + - + +
281A ASN* 5.1 0.3 - - - +
283A ILE* 3.5 29.7 - - + +
284A GLU* 2.3 39.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 270 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A MET* 3.8 26.9 - - + +
251A LEU* 3.7 42.2 - - + -
252A MET* 3.8 22.4 - - + -
266A PHE* 3.0 38.7 + - + +
267A THR* 3.3 3.1 + - + +
269A TYR* 1.3 88.2 - - + +
271A ASN* 1.3 58.2 + - - +
273A LYS* 3.6 2.9 - - - -
274A ARG* 2.8 45.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 271 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A THR* 2.9 40.9 + - - +
268A THR* 3.5 10.0 - - - +
270A ILE* 1.3 78.4 - - - +
272A ARG* 1.3 62.3 + - + +
274A ARG* 3.6 22.1 + - - +
275A LYS* 4.0 16.2 + - - +
48F LYS* 6.1 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 272 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A TYR* 3.4 35.3 - - + +
177A SEP 2.7 41.4 + - - -
181A TYR* 3.3 11.3 + - - -
264A GLU* 2.8 45.3 + - - -
268A THR* 3.3 17.5 - - + +
269A TYR* 3.3 15.0 - - - +
271A ASN* 1.3 79.9 - - - +
273A LYS* 1.3 63.1 + - - +
275A LYS* 2.9 37.5 + - - +
278A CYS* 3.4 27.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 273 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A SEP 2.7 38.9 + - - -
226A PHE* 5.9 0.2 - - + -
244A ARG* 2.8 31.2 + - - +
248A MET* 3.6 27.4 - - + +
269A TYR* 3.0 47.3 + - + +
270A ILE* 3.2 4.0 + - - +
272A ARG* 1.3 80.5 - - + +
274A ARG* 1.3 58.2 + - - +
275A LYS 3.1 0.4 - - - -
278A CYS* 3.5 17.7 - - - +
279A HIS 2.8 24.3 + - - +
280A GLY* 5.3 0.4 - - - -
281A ASN* 3.8 1.6 - - - +
284A GLU* 2.9 31.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 274 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A ARG* 3.3 13.7 - - - +
245A LYS* 3.8 17.8 + - - +
248A MET* 3.7 30.6 + - + +
249A ASP* 2.9 39.6 + - - +
252A MET* 4.1 13.7 - - - +
270A ILE* 2.8 25.3 + - - +
271A ASN* 3.6 15.9 + - - +
272A ARG 3.1 0.2 - - - -
273A LYS* 1.3 75.4 - - - +
275A LYS* 1.3 62.0 + - - +
276A ASN* 3.6 5.2 + - - +
60F ASN* 3.5 18.6 - - - +
----------------------------------------------------------
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