Contacts of the helix formed by residues 252 - 262 (chain B) in PDB entry 4I93
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 252 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A ILE* 3.6 32.8 - - + +
312A PRO* 4.2 16.4 - - + +
314A GLN* 3.7 23.8 - - + +
317A LEU* 3.9 13.9 - - + -
218B PHE* 3.7 5.1 - - + -
250B HIS 3.8 7.2 - - - +
251B ILE* 1.4 86.4 - - + +
253B PRO* 1.3 74.3 - - + +
254B SER* 3.3 1.8 - - - +
255B HIS* 3.0 21.5 + - + +
256B ALA 3.1 9.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 253 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B ALA 3.5 21.1 - - - +
218B PHE* 4.0 8.7 - - + -
236B TYR* 3.6 23.3 - - + +
240B THR* 3.8 26.7 - - + -
243B LEU* 4.1 18.8 - - + -
251B ILE 3.4 6.7 - - - +
252B PRO* 1.3 83.5 - - + +
254B SER* 1.3 51.9 + - - +
256B ALA* 3.2 1.0 + - - +
257B LEU* 2.7 45.4 + - + +
293B LEU* 4.4 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 254 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A ILE* 5.7 1.0 - - - +
312A PRO* 3.2 35.4 - - - +
252B PRO* 3.3 0.9 - - - +
253B PRO* 1.3 77.4 - - - +
255B HIS* 1.3 58.7 + - - +
257B LEU* 3.8 10.3 - - - +
258B ASP* 3.0 36.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 255 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A ASP* 6.0 1.6 - - - -
312A PRO* 3.9 19.5 + - + +
315A LYS* 3.5 29.6 + - - -
251B ILE* 4.2 20.6 - - + -
252B PRO* 3.0 16.8 + - + +
254B SER* 1.3 78.9 + - - +
256B ALA* 1.3 66.7 + - - +
258B ASP* 3.2 14.2 + - + +
259B LEU* 3.1 44.5 + - + +
267B MSE 5.8 2.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 256 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B LEU* 3.6 40.8 - - + -
251B ILE* 4.0 22.2 - - + -
252B PRO 3.1 10.4 + - - +
253B PRO 3.6 2.2 - - - +
255B HIS* 1.3 77.6 - - - +
257B LEU* 1.3 58.1 + - + +
259B LEU* 3.2 7.1 + - - +
260B ILE* 2.9 32.5 + - + +
268B LEU* 4.0 8.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 257 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B TYR* 5.5 2.7 - - - +
253B PRO* 2.7 31.3 + - + +
254B SER* 3.8 8.7 - - - +
256B ALA* 1.3 74.3 - - - +
258B ASP* 1.3 56.5 + - - +
260B ILE* 3.3 18.1 + - + +
261B ARG* 2.8 30.7 + - - +
290B SER* 4.7 12.3 - - - +
293B LEU* 4.1 43.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 258 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B SER* 3.0 23.6 + - - +
255B HIS* 3.2 16.3 + - + +
257B LEU* 1.3 75.3 - - - +
259B LEU* 1.3 65.2 + - + +
261B ARG* 3.3 14.4 + - - +
262B ASP* 3.2 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 259 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B ILE* 4.6 4.5 - - + -
255B HIS* 3.1 46.5 + - + +
256B ALA* 3.2 8.0 + - - +
258B ASP* 1.3 74.5 - - + +
260B ILE* 1.3 61.9 + - - +
262B ASP* 3.3 9.5 + - - +
264B ASN* 2.9 50.2 + - + +
267B MSE 3.9 28.0 - - + +
268B LEU* 4.0 37.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 260 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B LEU* 4.3 15.9 - - + -
256B ALA 2.9 24.8 + - - +
257B LEU* 3.7 17.5 - - + +
259B LEU* 1.3 71.7 - - - +
261B ARG* 1.3 60.1 + - - +
263B ARG* 2.8 25.4 + - - +
264B ASN 4.9 0.9 - - - +
268B LEU* 3.8 25.4 - - + -
286B ILE* 3.8 28.3 - - + +
290B SER* 3.8 24.7 - - - +
293B LEU* 5.6 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 261 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B LEU 2.8 17.6 + - - +
258B ASP* 3.3 15.2 + - - +
260B ILE* 1.3 78.1 - - - +
262B ASP* 1.3 68.3 + - - +
263B ARG* 3.2 1.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 262 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B ASP* 3.2 18.2 + - - +
259B LEU* 3.7 10.3 - - - +
260B ILE 3.1 0.8 - - - -
261B ARG* 1.3 89.2 + - - +
263B ARG* 1.3 66.2 + - - +
264B ASN* 3.0 16.2 + - + +
----------------------------------------------------------
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