Contacts of the helix formed by residues 259 - 267 (chain B) in PDB entry 4ZG9
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 259 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B TYR* 3.5 30.7 - - + +
218B ALA* 3.1 12.6 - - + +
219B THR* 3.8 3.3 - - + -
252B HIS* 3.9 16.4 - - + -
257B GLY 4.5 0.4 - - - -
258B GLN* 1.3 86.4 - - - +
260B LEU* 1.3 65.7 + - - +
261B TRP* 3.6 48.2 - - + +
262B ILE* 3.0 22.8 + - + +
263B THR* 3.0 11.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 260 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B LEU* 4.8 1.3 - - + -
168B ILE* 4.0 15.5 - - + -
218B ALA* 2.7 20.4 + - - +
259B PRO* 1.3 71.4 - - - +
261B TRP* 1.3 57.8 + - - +
262B ILE 3.2 0.2 + - - -
263B THR* 3.2 2.8 + - - -
264B ALA* 2.9 29.8 + - - +
274B PHE* 4.2 17.3 - - + -
303B VAL* 4.6 8.1 - - + -
510B TYR* 3.9 10.7 - - + -
513B MET* 3.7 48.5 - - + +
514B CYS* 3.8 30.3 - - - +
517B LEU* 4.6 6.3 - - + -
519B LEU* 4.4 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 261 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B TYR* 4.2 15.0 - + - -
218B ALA* 3.8 19.3 - - + -
250B PHE* 4.5 8.3 - + - -
252B HIS* 4.6 7.0 + - + +
259B PRO* 3.6 28.4 - - + +
260B LEU* 1.3 78.6 - - - +
262B ILE* 1.3 79.7 + - + +
264B ALA* 4.1 2.0 - - - -
265B THR* 2.9 27.4 + - - -
271B ALA* 3.6 20.3 - - + +
272B GLY 4.8 1.3 - - - +
274B PHE* 3.3 64.4 - + + -
275B PHE* 3.8 30.5 - + - -
303B VAL* 5.6 0.9 - - - -
909B 4O2 4.2 8.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 262 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B HIS* 3.3 48.2 - - + +
258B GLN* 3.6 25.1 - - + +
259B PRO* 3.0 13.9 + - + +
261B TRP* 1.3 96.5 - - + +
263B THR* 1.3 67.2 + - - +
265B THR* 2.9 12.4 + - + -
266B LYS* 2.9 40.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 263 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B GLN* 2.6 25.1 + - - +
259B PRO 3.0 10.8 + - - -
260B LEU* 3.6 9.6 - - - -
262B ILE* 1.3 77.2 - - - +
264B ALA* 1.3 66.4 + - - +
266B LYS* 3.3 5.1 + - - -
267B GLN* 3.3 46.5 - - - +
510B TYR* 2.5 30.0 + - - +
514B CYS* 4.1 13.7 - - - -
519B LEU* 4.3 5.8 - - + -
520B LYS 3.6 9.9 - - - +
522B ALA 4.6 0.7 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
260B LEU 2.9 16.9 + - - +
261B TRP* 4.1 5.6 - - - +
263B THR* 1.3 74.8 - - - +
265B THR* 1.3 54.7 + - - +
267B GLN* 2.7 26.3 + - - +
269B VAL* 3.1 36.9 + - + +
271B ALA* 4.5 9.4 - - + -
303B VAL* 4.7 8.5 - - + -
517B LEU* 5.0 0.4 - - + -
519B LEU* 3.5 26.3 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
261B TRP 2.9 15.3 + - - -
262B ILE* 2.9 19.0 + - + +
264B ALA* 1.3 75.3 - - - +
266B LYS* 1.3 64.0 + - + +
267B GLN 3.1 1.2 + - - -
268B GLY* 3.3 11.4 + - - -
269B VAL 3.1 9.2 + - - -
270B LYS* 5.1 1.1 - - - +
271B ALA* 4.1 13.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 266 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B GLN* 3.9 19.3 - - - +
262B ILE* 2.9 37.9 + - + +
263B THR* 3.9 6.5 - - - +
264B ALA 3.1 0.4 + - - -
265B THR* 1.3 74.6 - - + +
267B GLN* 1.3 62.9 + - + +
268B GLY 3.4 1.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 267 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B GLN* 5.3 0.4 + - - -
263B THR* 3.3 30.3 + - - +
264B ALA 2.7 4.9 + - - +
266B LYS* 1.3 84.4 - - + +
268B GLY* 1.3 59.0 + - - +
269B VAL* 3.2 11.6 + - - +
518B GLY 4.5 1.9 - - - +
519B LEU* 3.5 17.1 - - + +
520B LYS* 2.8 55.2 + - - +
----------------------------------------------------------
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