Contacts of the helix formed by residues 264 - 269 (chain B) in PDB entry 4IL6
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 264 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ARG* 4.9 3.4 - - + -
167B TRP* 3.5 42.6 - - + +
169B SER* 5.6 5.2 - - - -
260B SER 4.0 3.3 - - - +
261B ALA 4.1 12.8 - - - +
262B THR 3.5 7.6 - - - +
263B THR* 1.4 90.8 - - - +
265B ILE* 1.3 60.1 + - - +
266B GLU* 3.3 2.0 - - - +
267B LEU* 3.1 17.8 + - + -
268B PHE* 3.0 35.5 + - + -
448B ARG* 3.5 1.1 + - - -
62H TRP* 4.6 6.5 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
56B TRP* 3.3 7.6 + - - -
171B PRO 5.3 1.1 - - - +
172B TYR* 3.9 2.7 - - - +
173B GLY* 3.8 23.1 - - - +
264B PRO* 1.3 73.1 - - - +
266B GLU* 1.3 59.1 + - - +
269B GLY* 2.8 48.1 + - - +
270B PRO* 3.9 2.5 - - + +
274B GLN* 3.7 22.4 - - - +
280B PHE* 3.6 25.4 - - + -
312B TYR* 3.6 30.9 + - + +
448B ARG* 3.7 7.6 - - - +
62H TRP* 3.9 23.9 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
54B PRO* 4.6 4.6 - - - +
55B MET* 4.1 7.8 - - - +
56B TRP* 3.3 19.2 + - - +
167B TRP* 3.8 21.8 + - + +
169B SER* 2.7 29.3 + - - -
173B GLY* 3.3 28.4 - - - +
174B LEU 3.6 1.6 - - - +
176B GLY* 2.9 30.5 + - - +
264B PRO* 3.3 1.6 - - - +
265B ILE* 1.3 77.9 - - - +
267B LEU* 1.3 63.7 + - - +
308B LYS* 2.9 26.7 + - - +
312B TYR* 3.3 7.0 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
55B MET* 3.7 26.5 - - + +
56B TRP* 3.7 7.5 - - - +
64B PRO* 3.4 45.6 - - + +
67B ALA* 3.8 20.4 - - + -
68B ARG* 3.7 22.9 - - + +
167B TRP* 3.8 40.4 - - + -
264B PRO* 3.1 21.9 + - + +
266B GLU* 1.3 87.4 - - - +
268B PHE* 1.3 66.5 + - + +
269B GLY 3.7 0.4 - - - -
447B PRO* 4.8 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 268 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B TRP* 3.6 8.0 - - - +
61B PHE* 4.9 0.7 - + - -
64B PRO* 3.7 26.2 - - + -
65B PHE* 3.5 45.8 - + - -
68B ARG* 4.9 3.6 - - - -
256B MET* 3.7 25.8 - - + -
262B THR 4.1 5.8 - - - -
263B THR* 3.9 19.1 - - - -
264B PRO* 3.0 27.2 + - + -
267B LEU* 1.3 86.4 - - + +
269B GLY* 1.3 59.3 + - - +
446B SER* 3.4 12.8 + - - -
447B PRO* 4.2 14.8 - - + +
448B ARG* 3.4 41.6 + - + +
451B PHE* 5.5 1.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 269 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B TRP* 3.5 18.3 - - - -
265B ILE* 2.8 20.4 + - - -
268B PHE* 1.3 78.0 - - - +
270B PRO* 1.3 70.0 - - - +
446B SER* 4.8 2.2 - - - -
448B ARG* 2.7 38.6 + - - -
----------------------------------------------------------
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