Contacts of the helix formed by residues 277 - 288 (chain A) in PDB entry 2IUK
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 PHE 277 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU 3.2 28.0 - - - -
25A PHE* 3.6 33.9 - + + -
28A ILE* 3.7 9.9 - - + -
268A ASN* 6.1 0.4 - - - -
269A PHE 4.9 2.0 - - - -
270A GLY* 4.4 4.9 - - - -
271A HIS* 3.3 42.4 - + + -
273A LYS 3.3 23.8 - - - -
274A SER* 3.4 10.7 + - - +
275A SER 4.7 0.9 - - - +
276A ASP* 1.3 73.2 - - - +
278A LEU* 1.3 61.6 + - - +
279A THR* 3.1 12.4 + - + +
280A TYR* 3.3 40.2 + + + +
281A GLY* 3.4 8.8 + - - -
336A ALA* 4.6 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 278 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A HIS* 5.5 0.2 - - - -
275A SER 3.7 20.0 - - - +
276A ASP* 3.1 12.5 + - - +
277A PHE* 1.3 72.7 - - - +
279A THR* 1.3 59.2 + - - +
281A GLY* 3.7 3.1 - - - +
282A ILE* 3.2 32.5 + - - +
339A GLU* 6.0 1.1 - - - +
340A ILE* 6.3 2.0 - - + -
779A ILE* 3.6 21.0 - - + +
782A ARG* 3.4 35.0 - - + +
783A HIS 6.0 0.4 - - - -
784A ALA* 4.7 13.7 - - + +
787A GLU* 6.0 0.9 - - - +
851A GLU* 5.9 2.2 - - - +
863A SER 5.5 1.8 - - - +
864A ILE* 3.6 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 279 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A ASN* 5.6 2.7 - - - +
271A HIS* 6.5 0.4 - - + -
277A PHE* 4.6 8.3 - - + -
278A LEU* 1.3 78.4 - - - +
280A TYR* 1.3 81.9 + - + +
281A GLY 3.2 0.4 - - - -
282A ILE* 3.4 7.7 + - - +
283A LYS* 2.8 38.5 + - - +
560A ASP* 5.8 2.7 - - - -
563A ASN* 4.8 22.0 + - - +
564A ILE* 4.9 8.9 - - - +
567A LEU* 3.3 29.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 280 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A PHE* 3.6 46.7 - + + +
26A ASN* 4.3 15.7 + - - -
268A ASN* 6.3 1.1 - - - -
277A PHE* 3.3 37.2 + + + +
279A THR* 1.3 96.0 - - + +
281A GLY* 1.3 57.0 + - - +
283A LYS* 3.2 31.6 - - + +
284A SER* 3.1 27.7 + - - -
336A ALA* 4.0 6.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 281 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A PHE 3.4 7.5 + - - -
278A LEU* 3.6 6.5 + - - -
279A THR 3.2 0.6 - - - -
280A TYR* 1.3 76.8 - - - +
282A ILE* 1.3 59.8 + - - +
284A SER* 3.8 3.1 + - - -
285A LEU* 3.1 18.9 + - - +
336A ALA* 3.9 24.4 - - - +
337A LEU* 4.1 5.7 - - - +
779A ILE* 3.3 23.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 282 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A LEU 3.2 17.4 + - - +
279A THR* 3.7 8.1 - - - +
281A GLY* 1.3 75.2 - - - +
283A LYS* 1.3 65.5 + - - +
285A LEU* 2.9 17.2 + - - +
286A SER* 3.2 13.7 + - - -
564A ILE* 5.1 4.9 - - + -
567A LEU* 3.5 29.8 - - + -
571A SER* 5.0 3.4 - - - -
572A LEU* 3.7 25.1 - - + -
578A ILE* 4.9 3.4 - - + -
776A VAL* 4.5 8.5 - - + -
779A ILE* 3.6 19.5 - - + -
780A LEU* 3.5 31.6 - - + -
864A ILE* 4.3 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 283 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A THR* 2.8 28.4 + - - +
280A TYR* 3.2 51.0 - - + +
281A GLY 3.5 0.2 - - - -
282A ILE* 1.3 75.9 - - - +
284A SER* 1.3 58.5 + - - +
286A SER* 3.3 8.1 + - - -
287A HIS* 3.2 26.1 + - - +
567A LEU* 3.3 28.0 - - + -
570A GLN* 4.0 12.8 - - - +
571A SER* 4.2 7.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 284 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A TYR 3.1 19.9 + - - -
281A GLY 3.8 0.4 - - - -
283A LYS* 1.3 76.0 - - - +
285A LEU* 1.3 64.5 + - - +
287A HIS* 3.9 2.5 - - - -
288A ASP* 3.0 40.1 + - - +
289A VAL* 3.4 3.8 + - - +
334A LEU* 3.8 6.2 - - - +
335A PRO* 5.8 1.1 - - - +
336A ALA* 5.3 2.7 - - - -
337A LEU* 3.0 27.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 285 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A GLY 3.1 11.4 + - - +
282A ILE* 2.9 13.6 + - - +
284A SER* 1.3 79.9 - - - +
286A SER* 1.3 62.6 + - - +
287A HIS 3.1 0.5 + - - -
289A VAL* 3.4 15.4 + - + -
290A ILE* 3.0 52.0 + - + -
337A LEU* 3.9 20.6 - - + -
340A ILE* 5.0 0.4 - - + -
341A PHE* 4.7 1.6 - - + -
578A ILE* 4.0 2.5 - - + -
772A ILE 4.3 2.2 - - - +
775A SER* 3.7 34.1 - - - +
776A VAL* 3.5 28.0 - - + +
779A ILE* 4.1 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 286 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A ILE 3.2 5.4 + - - -
283A LYS 3.3 10.0 + - - -
285A LEU* 1.3 78.5 - - - +
287A HIS* 1.3 58.4 + - - +
290A ILE* 3.8 14.4 - - - +
291A PRO* 3.4 17.2 - - - +
571A SER* 4.0 23.3 + - - -
578A ILE* 3.9 22.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 287 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A LYS 3.2 19.4 + - - +
284A SER* 4.4 2.0 - - - -
285A LEU 3.1 0.8 - - - -
286A SER* 1.3 80.6 + - - +
288A ASP* 1.3 75.5 + - - +
291A PRO* 3.1 16.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 288 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A SER* 3.0 30.7 + - - +
287A HIS* 1.3 93.1 - - - +
289A VAL* 1.3 63.6 + - - +
291A PRO* 3.4 9.5 - - - +
292A LEU* 3.2 27.8 - - + +
330A GLN 5.2 0.5 - - - +
334A LEU* 3.8 28.8 - - + +
----------------------------------------------------------
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