Contacts of the helix formed by residues 360 - 376 (chain B) in PDB entry 5IWG
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 THR 360 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B ASN 5.3 2.2 - - - +
358B GLN* 3.3 10.3 + - - +
359B ASN* 1.3 75.4 - - - +
361B PRO* 1.4 74.1 - - + +
362B GLU* 3.7 13.3 + - - +
363B TYR* 3.0 27.4 + - + +
364B MET* 3.1 21.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 361 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B ASN 4.3 2.5 - - - +
360B THR* 1.4 84.9 - - + +
362B GLU* 1.3 69.9 + - - +
364B MET* 3.4 7.0 + - + +
365B GLU* 3.1 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 362 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B THR* 3.2 16.8 - - - +
361B PRO* 1.3 86.2 - - - +
363B TYR* 1.3 61.0 + - - +
365B GLU* 3.9 4.6 - - - +
366B LYS* 2.9 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 363 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B PHE* 4.8 0.7 - + - -
232B PRO* 2.6 39.0 + - - +
233B MET* 4.0 0.7 + - - -
234B ARG* 3.7 40.8 + - + -
358B GLN 5.5 1.6 - - - +
359B ASN* 3.6 23.8 - - + -
360B THR* 3.0 26.3 + - - +
362B GLU* 1.3 76.1 - - - +
364B MET* 1.3 78.9 + - - +
366B LYS* 3.8 4.2 - - - +
367B ILE* 3.1 52.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 364 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B PHE* 3.6 25.1 - - + -
233B MET* 4.3 1.1 - - + -
237B ILE* 3.6 19.5 - - + -
241B SER* 4.0 14.4 - - - +
245B ILE* 3.5 45.0 - - + +
359B ASN* 3.6 33.0 - - + +
360B THR 3.1 21.9 + - - +
361B PRO* 3.7 6.7 - - + +
362B GLU 3.3 0.2 - - - -
363B TYR* 1.3 88.6 - - - +
365B GLU* 1.3 57.5 + - - +
368B LYS* 3.0 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 365 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B PRO 3.1 17.9 + - - +
362B GLU* 4.3 4.3 - - - +
364B MET* 1.3 73.4 - - - +
366B LYS* 1.3 60.2 + - - +
368B LYS* 2.8 45.2 + - - +
369B GLN* 2.9 52.9 + - - +
372B PHE* 5.5 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 366 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B GLU 2.9 19.7 + - - +
363B TYR* 3.8 4.9 - - - +
365B GLU* 1.3 74.9 - - - +
367B ILE* 1.3 69.1 + - + +
369B GLN* 3.4 12.0 + - + +
370B ARG* 3.1 62.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 367 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B LEU* 3.7 37.0 - - + -
231B PHE* 3.8 36.6 - - + -
232B PRO* 4.2 11.2 - - + -
363B TYR* 3.1 50.9 + - + +
366B LYS* 1.3 76.9 - - + +
368B LYS* 1.3 65.7 + - - +
370B ARG* 3.2 10.9 + - - +
371B LEU* 3.0 23.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 368 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B PHE* 3.9 11.3 - - + -
244B GLN* 3.3 23.8 + - - +
245B ILE* 3.7 23.9 - - + +
248B PRO* 4.2 9.9 - - + +
249B ILE* 3.9 15.7 - - + -
364B MET 3.0 16.1 + - - +
365B GLU* 2.8 40.6 + - - +
366B LYS 3.4 0.2 - - - -
367B ILE* 1.3 76.5 - - - +
369B GLN* 1.3 57.5 + - + +
371B LEU* 3.3 3.5 + - - +
372B PHE* 2.9 65.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 369 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B GLU* 2.9 44.7 + - + +
366B LYS* 3.8 12.3 + - + +
368B LYS* 1.3 73.2 - - + +
370B ARG* 1.3 61.3 + - + +
372B PHE* 3.3 16.0 + - + +
373B GLU* 3.0 41.2 + - - +
376B ARG* 4.7 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 370 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B LEU* 3.7 33.6 - - + +
366B LYS* 3.1 51.4 + - + +
367B ILE* 3.2 9.9 + - - +
369B GLN* 1.3 77.0 - - + +
371B LEU* 1.3 60.3 + - - +
373B GLU* 3.4 21.0 + - - +
374B ASN* 3.3 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 371 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B LEU* 3.4 27.8 - - + +
219B ILE* 6.3 0.2 - - + -
229B VAL* 4.1 27.4 - - + -
230B ASN 3.5 19.1 - - - +
231B PHE* 3.4 37.0 - - + -
249B ILE* 3.9 17.9 - - + -
367B ILE* 3.0 16.6 + - + +
368B LYS 3.7 6.1 - - - +
370B ARG* 1.3 72.6 - - - +
372B PHE* 1.3 61.3 + - - +
374B ASN* 3.2 17.2 + - + +
375B LEU* 2.9 34.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 372 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B PRO* 3.7 31.2 - - + -
249B ILE* 3.7 20.9 - - + -
252B LYS* 4.0 25.2 - - + -
365B GLU* 5.5 1.1 - - - -
368B LYS* 2.9 48.9 + - + -
369B GLN* 3.3 15.9 + - + +
371B LEU* 1.3 74.6 - - - +
373B GLU* 1.3 57.7 + - - +
375B LEU* 3.3 7.1 + - + +
376B ARG* 3.0 58.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 373 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B GLN* 3.0 27.9 + - - +
370B ARG* 3.5 21.1 - - - +
371B LEU 3.3 0.2 - - - -
372B PHE* 1.3 77.0 - - - +
374B ASN* 1.3 63.1 + - - +
376B ARG* 3.7 24.2 + - - +
377B MET* 3.6 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 374 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B LEU* 4.5 5.9 + - - +
219B ILE* 3.6 30.2 - - + +
226B TYR* 3.6 34.4 - - + +
229B VAL* 6.3 3.4 - - + -
370B ARG* 3.3 15.2 + - - +
371B LEU* 3.2 23.4 + - + +
373B GLU* 1.3 79.4 - - - +
375B LEU* 1.3 63.0 + - + +
377B MET* 3.2 21.7 + - - +
378B LEU 4.2 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 375 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B MET* 4.3 15.9 - - + -
226B TYR 5.1 2.0 - - - +
229B VAL* 4.2 21.1 - - + -
249B ILE* 4.3 10.3 - - + +
252B LYS* 3.8 31.9 - - + +
253B VAL* 3.8 37.0 - - + -
256B MET* 3.5 20.5 - - + +
371B LEU* 2.9 27.7 + - + +
372B PHE* 3.3 9.2 + - + +
374B ASN* 1.3 75.5 - - + +
376B ARG* 1.3 61.0 + - - +
378B LEU* 3.3 24.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 376 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B LYS* 4.2 22.6 - - - +
256B MET* 4.5 9.2 - - + +
369B GLN 4.7 0.4 + - - -
372B PHE* 3.0 39.5 + - - +
373B GLU* 3.6 43.9 - - - +
374B ASN 3.3 0.4 - - - -
375B LEU* 1.3 75.9 - - - +
377B MET* 1.3 61.5 + - - +
378B LEU 3.3 7.9 + - - +
----------------------------------------------------------
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