Contacts of the helix formed by residues 248 - 263 (chain B) in PDB entry 1V1A
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 GLY 248 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ASN* 4.2 1.7 - - - +
246B PRO 3.5 1.0 + - - -
247B VAL* 1.3 76.7 - - - +
249B ALA* 1.3 63.6 + - - +
250B GLY 3.3 2.2 - - - -
251B ASP* 3.3 22.2 + - - +
252B ALA* 3.1 18.2 + - - +
281B VAL* 3.1 11.2 - - - +
287B ASP 3.2 16.7 - - - +
288B HIS* 6.0 0.2 - - - +
1302B KDG 3.8 11.4 + - - -
1303B ADP 4.6 2.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 249 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B PRO 3.3 18.8 + - - +
247B VAL 3.2 0.8 - - - -
248B GLY* 1.3 77.8 - - - +
250B GLY* 1.3 56.9 + - - +
252B ALA* 3.3 4.3 + - - +
253B PHE* 2.9 26.9 + - - +
278B GLY* 3.5 22.4 - - - +
281B VAL* 3.2 15.7 - - + +
282B ALA* 4.2 5.6 - - + -
1303B ADP 3.7 27.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 250 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B ASN* 6.0 1.1 - - - -
219B LYS* 3.4 23.4 + - - -
248B GLY 3.3 0.4 - - - -
249B ALA* 1.3 74.7 - - - +
251B ASP* 1.3 59.5 + - - +
253B PHE* 3.1 9.1 - - - +
254B ALA* 2.9 23.9 + - - +
1303B ADP 2.8 37.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 251 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ALA* 3.5 25.4 - - - +
38B ASN* 2.9 22.3 + - + -
39B VAL* 3.9 11.4 - - + +
130B HIS* 5.9 0.9 + - - -
163B ASP* 3.9 1.0 - - - +
165B ASN* 3.4 26.3 + - - +
248B GLY* 3.3 7.1 + - - +
250B GLY* 1.3 73.3 - - - +
252B ALA* 1.3 56.1 + - - +
254B ALA* 3.2 8.3 + - - +
255B ALA* 2.7 36.5 + - - +
1302B KDG 2.8 36.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 252 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ASN* 5.6 0.6 - - - +
42B ALA* 4.8 8.5 - - + -
248B GLY 3.1 4.2 + - - +
249B ALA 3.5 7.6 - - - +
251B ASP* 1.3 79.2 - - - +
253B PHE* 1.3 53.8 + - - +
255B ALA* 4.1 6.1 - - - -
256B GLY 2.7 28.9 + - - -
277B LEU* 3.1 33.9 - - + +
281B VAL* 3.2 34.3 - - + -
291B ALA* 6.0 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 253 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B PHE* 4.4 8.7 - + - -
217B VAL* 3.3 27.4 - - + -
219B LYS* 3.3 22.7 - - + -
225B ALA* 3.1 25.6 - - + -
249B ALA 2.9 13.8 + - - +
250B GLY 3.1 10.8 - - - +
252B ALA* 1.3 77.2 - - - +
254B ALA* 1.3 61.8 - - - +
256B GLY 3.3 0.7 + - - -
257B TYR* 3.0 19.2 + - + +
271B LEU* 4.3 4.7 - - + -
274B ALA* 3.1 43.5 - - + +
275B ASN* 3.1 26.9 - - - -
278B GLY* 4.2 0.9 - - - +
1303B ADP 3.2 33.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 254 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B VAL* 5.2 1.6 - - + -
130B HIS* 4.5 12.8 - - + +
163B ASP* 4.5 7.9 - - - +
191B PHE* 3.6 38.5 - - + -
250B GLY 2.9 12.8 + - - +
251B ASP* 3.5 11.4 - - - +
253B PHE* 1.3 74.0 - - - +
255B ALA* 1.3 64.5 + - - +
257B TYR* 3.2 2.9 + - - +
258B LEU* 3.0 32.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 255 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B VAL* 4.1 14.3 - - + +
42B ALA* 3.6 30.1 - - + -
43B LEU* 3.4 27.4 - - + +
46B LEU* 4.5 0.2 - - - +
251B ASP 2.7 21.2 + - - +
252B ALA 3.6 4.3 - - - +
254B ALA* 1.3 73.2 - - - +
256B GLY* 1.3 63.7 + - - +
258B LEU* 4.3 1.1 - - - -
259B ALA* 3.1 21.8 + - - +
277B LEU* 4.0 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 256 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B LEU* 4.7 0.9 - - - -
252B ALA 2.7 17.6 + - - -
253B PHE 3.7 2.2 - - - -
254B ALA 3.2 0.2 - - - -
255B ALA* 1.3 75.7 - - - +
257B TYR* 1.3 59.3 + - - +
259B ALA* 3.6 0.5 + - - +
260B GLY* 3.2 15.4 + - - -
273B LEU* 3.3 21.5 - - - +
274B ALA* 3.9 14.8 - - - -
277B LEU* 3.3 21.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 257 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B LEU* 4.0 11.4 - - + -
191B PHE* 3.7 30.5 - + + -
215B GLU* 2.6 34.4 + - - +
217B VAL* 3.7 21.4 - - + +
227B ALA* 3.7 7.1 - - - +
253B PHE 3.0 11.1 + - - +
254B ALA 3.2 8.0 + - - +
256B GLY* 1.3 76.3 - - - +
258B LEU* 1.3 54.9 + - - +
260B GLY* 2.6 24.4 + - - -
261B ALA* 3.0 12.8 + - + +
267B VAL* 3.6 20.3 - - - +
270B ARG* 3.1 56.7 - - + +
271B LEU* 3.9 17.3 - - + -
274B ALA* 3.8 6.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 258 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B VAL* 4.8 7.9 - - + -
39B VAL* 4.3 13.0 - - + -
43B LEU* 4.3 13.0 - - + -
128B PHE* 3.8 16.8 - - + -
130B HIS* 4.2 24.0 - - + +
161B SER* 3.2 36.3 - - - +
189B LEU* 3.7 15.9 - - + -
191B PHE* 4.1 1.6 - - + -
254B ALA 3.0 21.1 - - - +
255B ALA* 3.8 4.9 - - - +
257B TYR* 1.3 75.9 - - - +
259B ALA* 1.3 58.0 + - - +
261B ALA* 3.3 5.6 + - - +
262B VAL* 2.8 39.6 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
43B LEU* 4.5 3.3 - - + +
46B LEU* 3.6 31.2 - - + -
48B VAL* 4.2 14.4 - - + -
255B ALA 3.1 11.9 + - - +
256B GLY 3.8 3.8 - - - +
258B LEU* 1.3 76.8 - - - +
260B GLY* 1.3 62.9 + - - +
262B VAL* 4.3 6.1 - - - -
263B TRP* 3.0 49.4 + - + -
273B LEU* 4.2 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 260 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B GLY 3.2 4.4 + - - -
257B TYR 2.6 16.4 + - - -
259B ALA* 1.3 75.3 - - - +
261B ALA* 1.3 54.0 + - - +
264B GLY 3.2 3.1 + - - -
265B LEU* 2.8 56.5 + - - +
270B ARG* 3.3 14.6 - - - -
273B LEU* 3.7 5.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 261 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B PHE* 4.1 24.9 - - + -
159B ARG* 5.0 4.0 - - - +
189B LEU* 6.1 0.7 - - + -
257B TYR* 3.0 11.7 + - + +
258B LEU* 3.8 7.4 - - + +
260B GLY* 1.3 71.5 - - - +
262B VAL* 1.3 57.7 + - - +
264B GLY* 2.4 31.9 + - - -
265B LEU 4.3 1.3 - - - +
270B ARG* 3.3 30.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 262 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B GLU* 3.7 33.0 - - + +
4B VAL* 4.0 26.9 - - + -
48B VAL* 4.6 5.8 - - + -
127B ARG* 4.4 19.7 - - + +
128B PHE* 4.0 19.5 - - + -
258B LEU 2.8 25.4 + - - +
259B ALA* 3.9 6.1 - - - +
261B ALA* 1.3 71.4 - - - +
263B TRP* 1.3 68.8 + - + +
264B GLY* 3.2 3.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 263 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B GLU* 5.4 3.2 + - - -
46B LEU* 3.3 37.2 - - + -
47B GLY 5.1 4.4 + - - -
48B VAL* 4.0 21.5 - - + +
259B ALA* 3.0 32.2 + - + +
260B GLY 3.7 2.9 - - - +
261B ALA 3.0 0.4 - - - -
262B VAL* 1.3 86.1 - - + +
264B GLY* 1.3 64.9 + - - +
265B LEU* 3.5 18.8 + - + +
273B LEU* 3.6 25.6 - - + -
294B ARG* 4.2 13.7 - - - -
297B LEU* 3.8 26.0 - - + -
----------------------------------------------------------
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