Contacts of the helix formed by residues 256 - 270 (chain B) in PDB entry 2V62
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 256 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B ASN* 2.9 17.2 + - + +
254B LEU 3.1 0.8 - - - -
255B LYS* 1.3 79.4 - - - +
257B PRO* 1.3 65.4 - - - +
258B VAL* 3.3 11.6 + - - +
259B ALA* 3.1 37.9 + - + +
260B VAL* 3.1 11.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 257 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B HIS* 3.5 35.0 - - + +
214B ILE* 3.9 27.1 - - + -
222B HIS* 3.4 10.2 + - - -
254B LEU 4.6 1.1 - - - +
255B LYS 3.6 7.6 - - - +
256B ASP* 1.3 87.4 - - - +
258B VAL* 1.3 58.3 + - + +
260B VAL* 3.3 7.0 + - + -
261B GLN* 3.0 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 258 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B HIS* 4.0 23.3 - - + +
256B ASP* 3.2 8.5 + - - +
257B PRO* 1.3 78.5 - - + +
259B ALA* 1.3 58.1 + - - +
261B GLN* 3.3 10.6 + - - +
262B THR* 3.0 37.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 259 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B ASN* 4.1 21.5 - - + +
256B ASP* 3.1 35.5 + - + +
258B VAL* 1.3 74.6 - - - +
260B VAL* 1.3 64.6 + - - +
262B THR* 3.2 8.9 + - - -
263B ALA* 3.0 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 260 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B ILE* 3.5 34.1 - - + +
222B HIS* 3.7 3.4 - - + +
250B TRP* 3.6 20.4 - - + -
253B ASN* 3.4 32.8 - - + +
254B LEU* 4.0 8.1 - - + -
256B ASP 3.1 6.0 + - - +
257B PRO 3.6 7.4 - - - +
258B VAL 3.3 0.2 - - - -
259B ALA* 1.3 75.1 - - - +
261B GLN* 1.3 58.1 + - - +
263B ALA* 3.2 2.8 + - - +
264B LYS* 2.9 57.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 261 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B HIS* 3.4 20.4 + - - -
219B LEU* 3.4 12.9 - - + +
222B HIS* 3.7 36.2 - - + +
223B LYS* 3.8 24.9 - - - +
257B PRO 3.0 12.7 + - - +
258B VAL* 3.3 17.1 + - - +
260B VAL* 1.3 77.2 - - - +
262B THR* 1.3 62.2 + - + +
264B LYS 3.3 1.2 + - - -
265B THR* 2.8 35.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 262 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B VAL* 3.0 23.7 + - + +
259B ALA* 3.2 16.5 + - - -
261B GLN* 1.3 80.2 - - + +
263B ALA* 1.3 56.1 + - - +
265B THR* 3.3 7.7 + - - -
266B ASN* 2.9 41.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 263 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B PRO* 5.4 3.7 - - + +
250B TRP* 3.8 32.9 - - + +
253B ASN* 5.1 4.0 - - - +
259B ALA 3.0 19.2 + - - +
260B VAL 3.2 4.5 + - - +
262B THR* 1.3 76.7 + - - +
264B LYS* 1.3 56.5 + - - +
266B ASN* 3.5 9.6 + - - +
267B LEU* 3.0 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 264 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B ILE 2.9 25.9 + - - -
215B GLU 3.6 15.4 + - - -
217B THR 2.8 33.0 + - - +
219B LEU* 3.7 12.3 - - + -
222B HIS* 3.0 24.2 + - + +
238B TYR* 3.5 22.9 - - + +
250B TRP* 3.8 30.5 - - + +
260B VAL* 2.9 27.2 + - - +
263B ALA* 1.3 72.2 - - - +
265B THR* 1.3 66.7 + - - +
267B LEU* 3.2 2.8 + - - +
268B LEU* 3.0 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 265 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B LEU* 3.5 23.6 - - + +
261B GLN* 2.8 28.0 + - - +
262B THR* 3.5 8.8 - - - -
264B LYS* 1.3 76.7 - - - +
266B ASN* 1.3 60.2 + - - +
268B LEU* 3.3 2.1 + - - +
269B ASP* 2.9 51.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 266 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B THR* 2.9 30.0 + - - +
263B ALA* 3.7 8.3 - - - +
265B THR* 1.3 78.4 - - - +
267B LEU* 1.3 64.6 + - - +
269B ASP* 3.4 7.3 + - - +
270B GLU* 3.0 43.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 267 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B TYR* 4.1 16.2 - - + -
241B LEU* 4.3 12.8 - - + -
249B PRO* 4.1 25.1 - - + -
250B TRP* 4.0 23.6 - - + -
263B ALA 3.0 14.7 + - - +
264B LYS 3.2 6.9 + - - +
266B ASN* 1.3 75.6 - - - +
268B LEU* 1.3 65.6 + - + +
270B GLU* 3.3 5.6 + - - -
271B LEU* 3.4 5.4 + - - +
274B SER* 2.7 50.8 + - - +
275B VAL* 4.0 22.0 - - + -
278B TRP* 6.0 0.2 - - + -
292B LEU* 4.3 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 268 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B LEU* 3.6 27.1 - - + -
234B GLU* 4.3 12.3 - - + +
238B TYR* 3.7 20.9 - - + +
264B LYS 3.0 16.6 + - - +
265B THR* 3.9 3.6 - - - +
267B LEU* 1.3 81.2 - - + +
269B ASP* 1.3 66.6 + - - +
270B GLU 3.3 0.3 + - - -
271B LEU* 3.4 37.1 + - + +
292B LEU* 4.1 26.5 - - + +
295B ALA* 6.5 0.2 - - + -
296B HIS* 3.4 43.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 269 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B THR* 2.9 36.2 + - - +
266B ASN* 3.9 9.2 - - - +
268B LEU* 1.3 79.9 - - - +
270B GLU* 1.3 61.1 + - + +
271B LEU 3.4 4.1 + - - +
296B HIS* 4.0 15.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 270 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B ASN* 3.0 30.6 + - - +
267B LEU* 3.3 0.4 + - - -
268B LEU 3.2 0.4 - - - -
269B ASP* 1.3 80.0 - - + +
271B LEU* 1.3 63.2 + - - +
273B GLN* 3.3 6.9 + - - +
274B SER* 3.0 36.4 + - - +
----------------------------------------------------------
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