Contacts of the helix formed by residues 265 - 281 (chain B) in PDB entry 4HNI
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 ASP 265 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B PHE* 3.9 17.4 - - + -
263B LYS 3.6 2.7 + - - +
264B PRO* 1.3 69.1 - - - +
266B TYR* 1.3 63.2 + - - +
267B SER* 3.4 11.8 + - - -
268B TYR* 3.1 33.1 + - + +
269B LEU* 3.3 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 266 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B ILE* 4.2 18.5 - - + +
117B GLU* 3.1 63.7 - - + +
120B HIS* 2.5 37.1 + + + +
192B ARG* 3.9 3.2 - - - -
196B LEU* 3.8 28.0 - - + -
263B LYS* 5.0 11.2 - - + -
264B PRO* 3.2 33.8 + - + +
265B ASP* 1.3 68.9 + - - +
267B SER* 1.3 55.8 + - - +
269B LEU* 2.9 8.2 + - - +
270B ARG* 2.7 43.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 267 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A TYR* 5.6 7.8 - - - -
117B GLU* 5.4 1.2 + - - -
265B ASP* 3.3 9.1 + - - -
266B TYR* 1.3 77.3 - - - +
268B TYR* 1.3 53.7 + - - +
270B ARG* 2.9 21.2 + - - +
271B GLN* 2.6 40.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 268 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B THR* 3.9 18.6 - - + +
254B PHE* 4.0 27.8 - + - -
265B ASP* 3.1 30.5 + - + +
266B TYR 3.2 0.2 - - - -
267B SER* 1.3 78.9 - - - +
269B LEU* 1.3 70.4 + - + +
271B GLN* 3.8 5.4 - - + +
272B LEU* 2.9 58.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 269 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B ILE* 4.0 8.1 - - + -
196B LEU* 4.2 25.6 - - + -
251B TYR* 3.5 41.1 - - + -
254B PHE* 3.5 41.1 - - + -
255B CYS* 4.5 2.2 - - - -
265B ASP 3.3 13.4 + - - +
266B TYR* 2.9 10.8 + - - +
268B TYR* 1.3 88.3 - - + +
270B ARG* 1.3 67.4 + - - +
272B LEU* 3.2 24.4 - - + +
273B PHE* 3.4 15.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 270 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B ASP* 3.2 31.9 - - - +
113B ILE* 3.9 23.8 - - + +
114B SER* 3.2 28.2 + - - +
117B GLU* 2.2 40.2 + - - +
266B TYR* 2.7 18.8 + - - +
267B SER* 2.9 43.1 + - - +
269B LEU* 1.3 72.6 - - - +
271B GLN* 1.3 64.7 + - - +
273B PHE* 2.9 17.2 + - - +
274B ARG* 2.9 34.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 271 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A ARG* 6.3 0.8 - - - +
284A TYR* 3.7 47.8 + - + -
267B SER* 2.6 23.0 + - - +
268B TYR* 3.8 5.8 - - + +
270B ARG* 1.3 73.4 - - - +
272B LEU* 1.3 62.3 + - - +
274B ARG* 3.3 35.6 - - - +
275B ASN* 2.5 64.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 272 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B GLU* 3.0 41.9 - - + +
250B THR* 3.8 27.8 - - + -
251B TYR* 4.1 17.9 - - + +
268B TYR* 2.9 46.6 + - + +
269B LEU* 3.2 24.0 - - + +
270B ARG 3.0 0.2 + - - -
271B GLN* 1.3 79.2 - - - +
273B PHE* 1.3 65.2 + - + +
275B ASN* 3.7 7.3 + - - +
276B LEU 3.4 6.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 273 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B LEU* 3.6 35.2 - - + +
109B ALA* 4.0 17.7 - - + -
110B ASP* 5.8 3.4 - - + +
113B ILE* 4.1 8.7 - - + -
203B LEU* 3.9 24.0 - - + -
247B GLU* 3.8 20.4 - - + -
248B PHE* 3.5 28.9 - + - -
251B TYR* 3.5 44.9 - + + -
269B LEU 3.4 15.9 - - - -
270B ARG* 2.9 7.3 + - - +
272B LEU* 1.3 77.7 - - + +
274B ARG* 1.3 60.7 + - + +
276B LEU* 3.3 6.8 + - + +
277B PHE* 3.0 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 274 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A GLN* 6.2 0.9 - - - +
274A ARG* 3.0 52.5 - - - +
110B ASP* 3.2 33.6 + - + +
270B ARG* 2.9 35.4 + - - +
271B GLN* 3.3 36.6 + - - +
273B PHE* 1.3 74.3 - - + +
275B ASN* 1.3 66.2 + - - +
277B PHE* 2.8 20.3 + - - +
278B HIS* 2.9 12.5 + - - +
284B TYR* 5.0 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 275 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A HIS* 4.8 12.0 + - + -
284A TYR* 4.6 6.7 + - - -
247B GLU* 4.8 1.8 - - - +
271B GLN* 2.5 51.8 + - - +
272B LEU* 4.0 9.5 - - - +
274B ARG* 1.3 74.0 - - - +
276B LEU* 1.3 58.9 + - - +
278B HIS* 3.0 11.1 + - - +
279B ARG* 2.9 40.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 276 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B LEU* 4.5 2.5 - - + -
106B LEU* 3.7 31.4 - - + -
245B PRO* 3.7 35.9 - - + -
247B GLU* 2.9 40.6 - - + +
248B PHE* 4.4 6.1 - - + -
272B LEU 3.4 5.1 + - - +
273B PHE* 3.3 8.2 + - + +
274B ARG 3.1 0.8 - - - -
275B ASN* 1.3 79.8 - - - +
277B PHE* 1.3 62.9 + - - +
279B ARG* 3.7 14.0 - - + +
280B GLN* 3.2 41.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 277 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B LYS* 3.7 31.6 - - + -
106B LEU* 3.7 26.9 - - + +
107B LEU* 4.0 22.0 - - + -
273B PHE 3.0 11.0 + - - +
274B ARG* 2.8 15.1 + - - +
276B LEU* 1.3 75.7 - - - +
278B HIS* 1.3 65.2 + - - +
280B GLN* 3.2 13.0 + - - +
281B GLY 3.3 7.1 + - - -
282B PHE* 3.7 24.4 + + + -
283B SER 3.5 25.4 - - - -
284B TYR* 3.7 43.3 - + - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 278 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A HIS* 5.8 9.4 - - + +
274B ARG 2.9 9.5 + - - +
275B ASN* 3.3 12.6 - - - +
277B PHE* 1.3 77.8 - - - +
279B ARG* 1.3 59.3 + - + +
281B GLY* 2.8 23.1 + - - -
284B TYR* 4.2 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 279 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B PRO* 5.7 1.2 - - - +
246B SER* 5.5 2.6 + - - -
247B GLU* 2.5 38.2 + - - +
275B ASN* 2.9 22.5 + - + +
276B LEU* 3.7 21.0 - - + +
278B HIS* 1.3 73.9 - - + +
280B GLN* 1.3 62.8 + - + +
281B GLY* 3.2 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 280 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B LEU* 4.0 14.8 - - + +
245B PRO* 4.9 3.8 - - - +
276B LEU* 3.2 36.9 + - + +
277B PHE 3.5 5.4 - - - +
278B HIS 3.0 1.2 + - - -
279B ARG* 1.3 78.2 - - - +
281B GLY* 1.3 62.9 + - - +
282B PHE* 3.2 39.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 281 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B PHE 3.3 0.6 + - - -
278B HIS 2.8 16.5 + - - -
279B ARG 3.2 2.0 + - - -
280B GLN* 1.3 77.9 - - - +
282B PHE* 1.3 68.3 + - - +
----------------------------------------------------------
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