Contacts of the strand formed by residues 270 - 277 (chain R) in PDB entry 2X1X
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 LYS 270 (chain R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262R TYR* 3.7 32.1 - - + +
264R SER* 2.7 48.7 + - - -
265R SER* 5.0 0.2 - - - +
266R LYS 3.5 10.5 + - - -
267R HIS* 4.0 34.0 + - + +
268R GLN* 3.5 30.5 + - - +
269R HIS* 1.3 73.4 - - - +
271R LYS* 1.3 66.9 + - - +
292R LEU* 5.4 5.6 - - + -
293R THR 3.5 5.6 - - - +
294R ILE* 4.2 21.0 - - + +
301R ASP* 4.6 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 271 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269R HIS 5.0 1.8 - - - +
270R LYS* 1.3 79.5 - - - +
272R LEU* 1.3 63.6 + - - +
273R VAL* 4.7 15.3 - - + -
291R THR 3.3 5.2 - - - +
292R LEU* 3.5 6.4 - - - +
293R THR* 3.0 55.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 272 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258R PHE* 5.6 5.4 - - + +
259R ASN* 6.3 0.2 - - - -
260R TRP* 3.4 43.1 - - + +
262R TYR* 6.2 1.3 - - + -
271R LYS* 1.3 75.4 - - - +
273R VAL* 1.3 65.9 + - - +
274R ASN* 4.1 11.3 + - - +
290R SER* 3.5 13.7 - - - +
291R THR 3.5 16.8 - - - +
292R LEU* 4.0 15.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 273 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271R LYS* 4.7 14.1 - - + -
272R LEU* 1.3 80.7 - - - +
274R ASN* 1.3 72.6 + - - +
275R ARG* 4.9 14.3 - - + +
289R LEU 3.7 1.4 - - - +
290R SER* 3.5 1.7 - - - -
291R THR* 3.0 41.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 274 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147E ALA* 6.0 1.6 - - - -
148E THR* 4.0 23.3 + - + +
149E ASN* 5.9 0.4 + - - -
258R PHE* 4.0 23.5 + - + +
272R LEU* 4.1 12.5 - - - +
273R VAL* 1.3 79.6 - - - +
275R ARG* 1.3 64.0 + - - +
289R LEU 3.3 4.3 - - - +
290R SER* 2.7 28.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 275 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C NAG 5.0 3.9 + - - -
2C NAG 3.1 34.6 - - - +
148E THR* 3.6 15.0 - - - +
273R VAL* 4.9 14.1 - - + +
274R ASN* 1.3 76.6 - - - +
276R ASP* 1.3 65.7 + - - +
277R LEU* 3.4 27.1 - - - +
288R PHE* 3.8 2.1 - - - -
289R LEU* 2.7 51.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 276 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142E LYS* 6.1 1.7 - - - -
147E ALA 3.9 19.6 - - - +
148E THR* 4.4 3.9 - - - -
275R ARG* 1.3 82.3 + - - +
277R LEU* 1.3 67.3 + - - +
278R LYS* 4.3 21.8 + - - +
286R LYS* 5.3 6.4 + - - +
287R LYS 4.2 3.2 - - - +
288R PHE* 3.2 33.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 277 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C NAG 5.1 3.1 - - - +
247R THR* 4.9 5.6 - - + +
275R ARG* 3.4 39.5 - - - +
276R ASP* 1.3 77.2 - - - +
278R LYS* 1.3 63.8 + - - +
279R THR 3.4 5.7 + - - -
287R LYS* 3.0 57.7 + - + +
288R PHE 4.9 0.4 - - - -
289R LEU* 3.9 37.2 - - + +
----------------------------------------------------------
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