Contacts of the helix formed by residues 255 - 270 (chain B) in PDB entry 2VUU
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 PRO 255 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B ILE* 1.3 98.6 - - + +
256B VAL* 1.3 67.8 + - + +
257B GLY 3.2 4.2 + - - +
258B TYR* 4.0 21.3 - - + +
259B ARG* 3.2 15.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 256 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B ILE 3.9 2.0 + - - -
255B PRO* 1.3 72.7 - - + +
257B GLY* 1.3 57.9 + - - +
259B ARG* 3.1 22.3 - - + +
260B GLU* 2.7 58.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 257 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B PRO* 5.0 1.9 - - - +
127B MET* 3.8 12.1 - - - +
255B PRO* 3.2 3.6 + - - +
256B VAL* 1.3 80.7 - - - +
258B TYR* 1.3 60.4 + - - +
259B ARG 3.1 1.8 - - - -
260B GLU* 3.4 16.0 + - - +
261B GLN* 3.0 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 258 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B MET* 3.7 18.8 - - + +
163B PRO* 4.1 32.4 + - + +
164B LEU* 4.9 6.7 - - + +
165B PHE* 5.2 5.5 - - - -
254B ILE* 4.6 13.9 - - + -
255B PRO* 3.3 26.2 + - + +
257B GLY* 1.3 75.7 - - - +
259B ARG* 1.3 57.7 + - - +
261B GLN* 3.3 15.9 - - + +
262B LEU* 2.8 65.5 + - + +
265B ILE* 5.7 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 259 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B ILE* 4.6 16.8 - - + +
252B VAL 4.8 3.2 + - - -
253B ASN* 4.9 0.8 - - - +
254B ILE* 3.7 32.8 + - + +
255B PRO 3.2 11.4 + - - +
256B VAL* 3.1 27.9 + - + +
257B GLY 3.1 0.8 - - - -
258B TYR* 1.3 76.6 - - - +
260B GLU* 1.3 56.1 + - + +
262B LEU* 3.1 13.7 + - - +
263B GLU* 2.9 50.3 + - + +
250D ILE 4.4 6.3 + - - -
251D LYS* 3.5 34.0 + - - +
252D VAL* 3.4 20.7 + - - +
253D ASN* 2.7 31.3 + - - +
259D ARG* 5.7 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 260 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B PRO* 4.1 11.6 - - + +
256B VAL* 2.7 38.3 - - + +
257B GLY* 3.4 13.2 + - - +
259B ARG* 1.3 71.8 - - + +
261B GLN* 1.3 65.7 + - - +
263B GLU* 3.4 19.5 + - - +
264B ALA* 3.1 23.0 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
125B VAL* 3.0 35.4 - - - +
126B PRO* 3.2 18.5 - - + +
127B MET* 3.2 33.2 + - + +
128B TRP* 3.7 20.6 - - - +
257B GLY 3.0 14.8 + - - +
258B TYR* 3.3 23.6 - - + +
260B GLU* 1.3 78.0 - - - +
262B LEU* 1.3 60.0 + - - +
264B ALA* 3.4 4.9 + - - +
265B ILE* 2.9 44.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 262 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B PRO* 4.0 12.1 - - + -
164B LEU* 3.9 27.8 - - + -
248B VAL* 3.9 28.9 - - + +
250B ILE* 4.4 11.0 - - + -
254B ILE* 3.8 21.3 - - + -
258B TYR* 2.8 59.9 + - + +
259B ARG* 3.1 6.0 + - - +
261B GLN* 1.3 72.1 - - - +
263B GLU* 1.3 61.0 + - + +
265B ILE* 3.0 10.2 + - + +
266B GLU* 2.9 35.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 263 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B LYS* 5.7 6.1 - - - +
250B ILE* 6.2 1.8 - - + -
259B ARG* 2.9 44.1 + - + +
260B GLU* 3.6 20.6 - - - +
262B LEU* 1.3 74.8 - - + +
264B ALA* 1.3 60.2 + - - +
266B GLU* 3.3 30.1 + - - +
267B VAL* 2.9 23.0 + - - +
251D LYS* 5.6 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 264 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B PRO* 4.7 9.6 - - + -
124B ALA 4.2 4.7 - - - +
125B VAL* 4.1 11.7 - - + -
126B PRO* 3.7 21.8 - - + -
260B GLU 3.1 12.7 + - - +
261B GLN 3.5 9.4 - - - +
262B LEU 3.2 0.2 - - - -
263B GLU* 1.3 74.2 - - - +
265B ILE* 1.3 61.6 + - - +
267B VAL* 3.3 8.9 + - - +
268B VAL* 3.0 33.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 265 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B VAL* 4.1 10.1 - - + -
128B TRP* 5.1 9.2 - - + -
164B LEU* 3.9 28.3 - - + -
180B PRO* 5.0 3.7 - - + +
181B PHE* 4.3 20.9 - - + -
248B VAL* 5.5 2.9 - - + -
258B TYR* 5.7 0.7 - - + -
261B GLN* 2.9 46.2 - - + +
262B LEU* 3.0 11.8 + - + +
264B ALA* 1.3 73.8 - - - +
266B GLU* 1.3 66.0 + - - +
268B VAL* 4.6 1.3 - - - -
269B PHE* 2.9 50.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 266 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B PRO* 4.3 11.2 - - + -
246B PRO 4.2 9.8 - - - +
247B LYS* 3.0 35.6 + - - +
248B VAL* 2.9 45.4 + - + +
250B ILE* 5.2 1.9 - - - +
262B LEU* 2.9 20.6 + - - +
263B GLU* 3.3 23.7 + - - +
264B ALA 3.2 0.2 - - - -
265B ILE* 1.3 76.3 - - - +
267B VAL* 1.3 57.5 + - + +
270B GLY* 2.9 10.4 + - - -
271B GLU* 2.9 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 267 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B PRO* 3.9 18.2 - - + -
263B GLU 2.9 19.3 - - - +
264B ALA* 3.6 11.4 - - - +
265B ILE 3.2 0.2 - - - -
266B GLU* 1.3 75.6 - - + +
268B VAL* 1.3 58.1 + - - +
271B GLU* 3.1 25.5 - - - +
272B HIS* 2.9 57.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 268 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B HIS* 3.9 17.7 - - + +
122B TRP* 4.3 5.8 - - + -
123B PRO* 3.7 37.5 - - + +
125B VAL* 4.1 10.8 - - + -
264B ALA 3.0 19.9 + - - +
265B ILE* 4.6 0.4 - - - -
267B VAL* 1.3 77.5 - - - +
269B PHE* 1.3 79.1 + - + +
272B HIS* 3.6 6.1 - - - -
273B LYS 3.4 4.7 + - - -
274B ALA* 2.7 52.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 269 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B HIS* 4.6 0.4 - - - -
125B VAL* 5.1 1.3 - - + -
128B TRP* 4.1 19.5 - + - -
180B PRO* 3.7 8.0 - - + +
181B PHE* 3.4 39.7 - + + +
182B ASP* 4.5 5.9 + - - +
187B LEU* 4.2 9.6 - - + -
265B ILE* 2.9 32.7 + - + +
268B VAL* 1.3 98.1 - - + +
270B GLY* 1.3 62.7 + - - +
273B LYS* 3.2 21.2 - - - +
274B ALA 3.7 12.8 - - - +
275B PRO 4.3 0.4 - - - -
276B TYR* 3.4 61.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 270 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B PRO* 3.3 27.1 + - - +
244B GLN* 5.1 6.2 + - - -
246B PRO* 5.3 4.5 - - - -
265B ILE 3.6 1.6 + - - -
266B GLU 2.9 14.9 + - - -
269B PHE* 1.3 82.5 - - - +
271B GLU* 1.3 58.1 + - - -
272B HIS 3.6 0.2 - - - -
273B LYS* 3.8 17.8 - - - +
----------------------------------------------------------
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