Contacts of the strand formed by residues 264 - 270 (chain A) in PDB entry 3N2Q
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 ASN 264 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A TYR 3.6 8.2 - - - +
230A PRO* 5.5 2.8 - - - +
262A PRO* 4.1 13.6 + - - +
263A VAL* 1.3 77.3 - - - +
265A ALA* 1.3 62.6 + - - +
279A MSE 3.2 6.4 - - - +
280A ASN* 2.9 52.1 + - + +
281A ILE* 4.6 2.6 - - - +
282A VAL* 5.3 7.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A SER* 3.5 0.9 + - - -
229A TYR* 2.9 50.1 + - + +
245A ILE* 5.2 0.7 - - + -
263A VAL* 6.1 0.2 - - + -
264A ASN* 1.3 79.0 - - - +
266A LYS* 1.3 72.7 + - - +
267A VAL* 4.4 0.9 - - + -
277A LEU* 3.7 15.0 - - + -
278A ASN 3.1 12.6 - - - +
279A MSE 3.7 17.9 - - + -
280A ASN* 5.8 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 266 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A SER* 4.9 7.0 - - - +
227A TYR 3.3 7.6 - - - +
228A SER* 3.2 28.2 + - - +
265A ALA* 1.3 77.2 - - - +
267A VAL* 1.3 61.5 + - - +
268A SER 4.1 0.4 - - - -
276A THR 3.9 1.6 - - - +
277A LEU* 3.6 2.3 - - - +
278A ASN* 3.0 44.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 267 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A SER* 4.0 1.8 - - - -
227A TYR* 2.9 42.4 + - - +
229A TYR* 4.4 9.0 - - + -
234A PHE* 4.0 26.0 - - + -
245A ILE* 4.1 5.4 - - + -
265A ALA* 4.4 6.3 - - + -
266A LYS* 1.3 76.4 - - - +
268A SER* 1.3 60.9 + - - +
269A TYR* 3.6 20.5 - - + +
274A MSE 3.9 34.5 - - + -
276A THR 3.5 4.7 - - - +
277A LEU* 3.8 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 268 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A GLU* 3.1 24.1 + - - -
225A LYS 3.5 7.2 - - - -
226A SER* 3.5 15.7 + - - -
266A LYS 4.1 1.0 - - - -
267A VAL* 1.3 72.0 - - - +
269A TYR* 1.3 69.0 + - - +
274A MSE 3.9 1.4 - - - +
275A ASP* 2.9 24.1 + - - -
276A THR* 2.8 45.3 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
224A GLU* 3.6 6.1 - - - +
225A LYS* 3.1 31.6 + - + +
227A TYR* 3.8 19.1 - + + -
234A PHE* 3.2 25.2 - + - -
238A HIS* 3.2 43.5 - + + +
241A ASP* 2.8 29.7 + - - +
267A VAL* 3.6 24.2 - - + -
268A SER* 1.3 81.1 - - - +
270A LYS* 1.3 68.2 + - - +
272A ASP* 3.3 29.8 - - - +
273A GLN 3.3 13.5 - - - +
274A MSE 3.6 13.4 - - - +
275A ASP* 4.2 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 270 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A GLY* 5.9 5.6 - - - -
86A ASN* 4.1 31.8 + - + +
90A GLN* 5.2 0.4 - - - +
202A THR* 4.5 13.1 + - - -
203A TYR* 5.0 9.1 + - - +
222A ILE* 3.9 25.4 - - - +
223A ASP 4.2 11.9 - - - +
224A GLU* 3.4 29.9 + - + -
269A TYR* 1.3 78.8 - - - +
271A LYS* 1.3 73.7 + - - +
272A ASP 3.2 1.2 + - - -
273A GLN* 3.3 16.6 + - - +
275A ASP* 3.6 33.5 + - - +
----------------------------------------------------------
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