Contacts of the helix formed by residues 250 - 262 (chain A) in PDB entry 4N6N
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 THR 250 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A LYS 3.5 4.7 + - - +
249A GLU* 1.3 82.2 - - - +
251A LEU* 1.3 64.8 + - - +
252A HIS* 3.7 7.4 + - - +
253A LYS* 3.0 27.4 + - - +
254A GLN 3.0 18.0 + - - -
276A SER 3.6 11.4 - - - -
277A THR* 3.5 20.4 - - - +
278A MET 3.4 4.9 - - - -
279A LYS* 4.1 13.9 - - + +
280A VAL* 3.6 3.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A PHE* 6.2 0.7 - - + -
183A VAL* 4.1 15.0 - - + -
185A TYR* 3.5 29.9 + - + +
205A TYR* 4.5 9.8 - - + -
207A THR* 5.8 0.2 - - - +
250A THR* 1.3 72.1 - - - +
252A HIS* 1.3 52.9 + - - +
254A GLN* 3.3 2.9 + - - +
255A TYR* 2.8 36.3 + - - +
275A ILE* 3.6 21.5 - - + +
276A SER* 3.6 14.6 - - - +
278A MET 3.0 15.9 + - - +
279A LYS 4.5 0.2 - - - +
280A VAL* 3.9 29.1 - - + +
283A PHE* 3.7 34.3 - - + -
284A GLN* 4.9 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A TYR* 5.0 0.2 - - - -
250A THR* 3.7 7.6 + - - +
251A LEU* 1.3 76.0 - - - +
253A LYS* 1.3 65.2 + - - +
255A TYR* 3.3 5.4 + - - +
256A HIS* 3.0 65.9 + + + -
269A GLN* 5.0 9.9 - - - -
276A SER* 2.8 37.3 + - - +
277A THR* 4.8 2.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A GLU* 3.7 26.7 + - - -
249A GLU* 3.8 20.2 - - + +
250A THR* 3.0 23.7 + - - +
252A HIS* 1.3 79.1 + - - +
254A GLN* 1.3 64.7 + - - +
256A HIS* 3.3 6.2 + - - +
257A LEU* 3.0 45.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A TYR* 2.6 31.0 + - + +
237A TRP* 3.4 16.0 + - + -
240A ASP* 2.9 24.2 + - - +
241A SER* 2.9 24.0 + - - +
249A GLU* 3.6 20.5 + - - +
250A THR 3.0 11.7 + - - +
251A LEU* 3.6 7.6 - - - +
253A LYS* 1.3 74.9 - - - +
255A TYR* 1.3 65.0 + - - +
257A LEU* 3.3 3.4 + - - +
258A VAL* 2.9 39.1 + - + +
280A VAL* 4.2 9.4 - - + +
284A GLN* 3.0 17.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A TYR* 5.4 0.4 + - - -
205A TYR* 3.9 11.7 - - - +
207A THR* 3.8 22.9 - - + -
251A LEU 2.8 20.7 + - - +
252A HIS* 3.5 4.7 - + - +
254A GLN* 1.3 74.6 - - - +
256A HIS* 1.3 87.7 + + - +
258A VAL* 3.3 4.5 + - - +
259A LYS* 2.8 42.0 + - + +
267A VAL* 2.8 40.3 + - + -
268A MET* 3.5 18.7 - - - +
269A GLN* 3.5 42.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A HIS* 3.0 60.5 + + + +
253A LYS* 4.0 4.9 - - - +
255A TYR* 1.3 99.3 - + - +
257A LEU* 1.3 60.6 + - - +
259A LYS* 3.7 24.1 + - - +
260A SER* 2.8 36.0 + - - +
269A GLN* 4.5 4.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A ASP* 3.3 18.4 - - + +
244A GLU* 3.2 28.3 - - - +
249A GLU* 3.8 8.5 - - - +
253A LYS* 3.0 36.5 + - + +
254A GLN* 3.7 3.6 - - - +
256A HIS* 1.3 73.6 - - + +
258A VAL* 1.3 61.9 + - + +
260A SER* 3.2 5.4 + - - -
261A HIS* 2.8 61.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A TYR* 3.7 42.4 - - + +
236A ASN* 3.9 11.9 - - + +
237A TRP* 3.5 36.3 - - + +
240A ASP* 5.2 1.6 - - + -
254A GLN* 2.9 27.3 + - + +
255A TYR* 3.7 5.6 - - - +
257A LEU* 1.3 76.7 - - + +
259A LYS* 1.3 58.2 + - - +
261A HIS* 4.7 0.4 - - - -
262A THR* 2.7 44.9 + - - +
267A VAL* 4.2 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A TYR* 2.8 44.6 + - + +
256A HIS* 3.7 28.3 + - - +
258A VAL* 1.3 74.8 - - - +
260A SER* 1.3 62.2 + - - +
262A THR 3.3 17.8 - - - +
265A SER 5.2 0.2 - - - +
266A HIS* 5.9 1.1 - - - -
267A VAL* 3.9 33.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A HIS* 2.8 24.3 + - - +
257A LEU* 3.6 8.0 - - - +
259A LYS* 1.3 78.6 - - - +
261A HIS* 1.3 69.6 + - - +
262A THR 3.6 0.3 + - - -
263A GLN* 3.3 17.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 261 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A TRP* 5.2 5.7 - - - -
236A ASN* 3.4 32.7 + - - +
240A ASP* 5.7 3.7 - - + +
257A LEU* 2.8 53.3 + - + +
258A VAL* 4.2 1.1 - - - +
260A SER* 1.3 81.2 - - - +
262A THR* 1.3 59.0 + - - +
263A GLN* 3.3 20.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 262 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A TRP* 4.2 13.9 - - + -
233A TYR* 3.8 10.2 - - + +
236A ASN* 2.9 16.2 + - - +
258A VAL* 2.7 31.6 + - - +
259A LYS 3.3 12.1 - - - +
260A SER 3.4 0.4 - - - -
261A HIS* 1.3 74.1 - - - +
263A GLN* 1.3 59.6 + - - +
264A THR* 4.1 11.7 - - - +
265A SER* 3.2 38.4 - - - +
267A VAL* 3.7 15.4 - - + +
----------------------------------------------------------
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