Contacts of the strand formed by residues 271 - 276 (chain P) in PDB entry 3Q2K
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 ILE 271 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137P THR* 4.3 23.5 - - + +
140P LEU* 4.9 17.3 - - + -
141P VAL* 5.3 0.2 - - + -
261P VAL* 5.2 0.2 - - + -
262P ARG 3.9 2.5 - - - +
263P VAL* 4.4 13.9 - - + +
269P ASN 4.1 1.8 + - - -
270P ARG* 1.3 71.0 - - - +
272P ASP* 1.3 63.9 + - - +
273P GLU 4.0 10.3 - - - +
274P TRP* 3.1 54.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 272 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262P ARG* 2.5 38.3 + - + +
264P GLY* 4.0 12.3 - - - -
270P ARG* 2.4 63.9 + - - +
271P ILE* 1.3 72.8 - - - +
273P GLU* 1.3 70.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 273 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248O LEU* 3.7 31.9 - - + +
260P THR* 3.5 15.9 - - + +
261P VAL* 2.9 11.4 - - - +
262P ARG* 2.8 50.7 + - + +
271P ILE* 3.7 2.5 - - - +
272P ASP* 1.3 85.0 - - - +
274P TRP* 1.3 64.6 + - - +
275P LYS* 3.0 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 274 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140P LEU* 3.8 31.6 - - + -
141P VAL* 4.4 8.5 - - + -
144P ALA* 4.3 9.6 - - + -
149P ARG* 3.8 19.5 - - - +
260P THR 3.6 2.0 - - - -
261P VAL* 3.7 28.7 - - + -
271P ILE* 3.1 46.0 - - + -
273P GLU* 1.3 76.6 + - - +
275P LYS* 1.3 61.9 + - - +
276P PHE* 3.2 31.2 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 275 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244O TYR* 4.1 18.4 + - + +
245O PRO* 4.0 25.9 - - + +
246O GLN* 5.3 8.7 + - - +
247O ASN 5.4 0.6 + - - -
248O LEU* 3.6 22.8 - - - +
259P GLY* 3.4 3.5 - - - -
260P THR* 2.9 43.0 + - + +
273P GLU* 3.0 29.0 + - - +
274P TRP* 1.3 75.3 - - - +
276P PHE* 1.3 64.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 276 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244O TYR* 3.7 10.8 + - - -
144P ALA* 3.9 18.4 - - + -
149P ARG* 3.3 69.1 - - + +
150P PHE* 3.9 21.5 - + - -
258P LYS 3.3 6.1 - - - -
259P GLY* 3.8 7.0 - - - -
261P VAL* 3.5 24.0 - - + -
274P TRP* 3.2 41.8 + + - -
275P LYS* 1.3 76.2 - - - +
277P ALA* 1.3 59.2 + - - +
278P GLU* 3.0 12.8 + - + +
279P PRO* 4.4 5.8 - - - +
----------------------------------------------------------
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