Contacts of the helix formed by residues 246 - 257 (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 SER 246 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244B TYR 3.3 3.4 + - - -
245B PRO* 1.3 68.6 - - - +
247B GLU* 1.3 65.5 + - - +
248B PHE 2.9 6.1 - - - -
249B SER* 2.9 15.1 + - - +
250B THR* 2.8 34.8 + - - -
279B ARG* 5.5 2.6 + - - -
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Residues in contact with GLU 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245B PRO* 3.1 17.7 - - + -
246B SER* 1.3 79.7 + - - +
248B PHE* 1.3 58.1 + - - +
250B THR* 3.8 10.6 - - - -
251B TYR* 3.1 27.0 + - - +
272B LEU* 3.0 38.0 - - + +
273B PHE* 3.8 12.0 - - + -
275B ASN* 4.8 2.4 - - - +
276B LEU* 2.9 29.2 + - + +
279B ARG* 2.5 45.0 + - - +
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Residues in contact with PHE 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B LEU* 3.8 28.3 - - + -
105B VAL* 4.0 18.2 - - + -
106B LEU* 4.1 6.3 - - + -
203B LEU* 4.3 15.9 - - + -
204B MET* 3.9 20.6 - - + -
207B ASN* 3.2 31.6 - - - -
241B CYS* 4.2 5.6 - - + -
244B TYR* 4.4 3.4 - - + -
245B PRO* 3.2 39.0 + - + +
246B SER 2.9 0.6 - - - -
247B GLU* 1.3 79.4 - - - +
249B SER* 1.3 62.4 + - - +
251B TYR* 3.9 3.7 - + - +
252B LEU* 3.4 30.5 + - - +
273B PHE* 3.5 29.2 - + - -
276B LEU* 4.4 4.7 - - + -
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Residues in contact with SER 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237B ILE* 3.5 22.6 + - - +
238B GLU* 4.4 7.6 - - - +
241B CYS* 3.4 21.1 - - - +
246B SER* 2.9 16.7 + - - -
248B PHE* 1.3 76.8 - - - +
250B THR* 1.3 62.0 + - - +
252B LEU 3.5 0.7 + - - -
253B ASN* 2.8 41.9 + - - -
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Residues in contact with THR 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246B SER* 2.8 22.4 + - - -
247B GLU* 3.9 9.9 - - - -
249B SER* 1.3 75.0 - - - +
251B TYR* 1.3 60.1 + - - +
253B ASN* 3.7 7.0 - - - +
254B PHE* 2.8 30.7 + - + +
268B TYR* 3.9 18.2 - - + +
272B LEU* 3.8 22.4 - - + -
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Residues in contact with TYR 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B ILE* 4.1 13.0 - - + -
196B LEU* 2.7 48.6 + - - +
199B LEU* 3.4 16.4 - - + +
200B GLY* 3.5 23.6 - - - -
203B LEU* 4.8 2.7 - - + -
247B GLU 3.1 20.5 + - - +
248B PHE* 4.0 5.2 - - + +
249B SER 3.3 0.2 - - - -
250B THR* 1.3 78.1 - - - +
252B LEU* 1.3 67.1 + - + +
254B PHE* 3.2 5.4 + - - +
255B CYS* 3.0 32.2 + - - -
269B LEU* 3.5 37.2 - - + -
272B LEU* 4.2 8.5 - - + -
273B PHE* 3.5 28.5 - + + -
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Residues in contact with LEU 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197B GLU* 3.8 15.9 - - + +
200B GLY* 3.7 31.2 - - - +
201B TYR* 3.7 23.3 - - + -
204B MET* 4.2 9.9 - - + -
237B ILE* 3.6 19.5 - - + -
240B LEU* 4.1 17.3 - - + -
241B CYS* 3.9 20.2 - - - -
248B PHE 3.4 19.0 + - - +
249B SER 4.0 0.9 - - - +
251B TYR* 1.3 78.8 - - + +
253B ASN* 1.3 67.3 + - - +
255B CYS* 3.2 3.9 + - - +
256B ARG* 2.8 28.8 + - - +
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Residues in contact with ASN 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237B ILE* 3.2 28.0 - - - +
249B SER* 2.8 35.1 + - - +
250B THR* 3.7 6.3 - - - +
252B LEU* 1.3 76.6 - - - +
254B PHE* 1.3 64.3 + - - +
256B ARG* 3.2 4.3 + - - +
257B SER* 3.2 22.9 + - - -
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Residues in contact with PHE 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250B THR* 2.8 20.1 + - + +
251B TYR 3.4 3.8 - - - +
253B ASN* 1.3 76.1 - - - +
255B CYS* 1.3 66.9 + - - +
257B SER* 2.6 25.4 + - - -
258B LEU* 3.6 38.6 + - + +
264B PRO* 4.7 0.9 - - + -
265B ASP* 3.9 31.0 - - + -
268B TYR* 4.0 25.1 - + + -
269B LEU* 3.5 38.1 - - + -
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Residues in contact with CYS 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193B ARG* 4.4 8.7 - - - +
196B LEU* 3.4 45.5 - - - -
197B GLU* 4.0 21.7 - - + +
251B TYR* 3.0 30.3 + - - +
252B LEU* 3.6 8.5 - - - +
254B PHE* 1.3 78.5 - - - +
256B ARG* 1.3 59.4 + - - +
257B SER 2.9 5.7 + - - -
258B LEU* 3.0 25.4 + - - +
269B LEU* 4.5 8.5 - - - -
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Residues in contact with ARG 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182B ILE* 3.3 28.4 - - + +
183B ASN* 5.8 2.1 + - - -
197B GLU* 3.6 26.4 + - + +
201B TYR* 2.7 37.2 + - - -
213B TRP* 5.6 1.2 - - - -
232B LYS* 4.1 11.7 + - - +
233B MET 5.7 1.8 + - - -
235B THR 4.4 10.9 + - - -
236B PRO* 5.4 1.4 - - - +
237B ILE* 3.7 37.1 - - - +
240B LEU* 5.7 2.2 - - - +
252B LEU* 2.8 16.9 + - - +
253B ASN* 3.2 6.5 + - - +
255B CYS* 1.3 75.4 - - - +
257B SER* 1.3 58.6 + - - +
258B LEU 3.5 2.5 - - - +
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Residues in contact with SER 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253B ASN 3.2 8.7 + - - -
254B PHE* 2.6 29.0 + - - -
255B CYS 2.9 0.6 + - - -
256B ARG* 1.3 77.6 - - - +
258B LEU* 1.3 65.8 + - - +
259B ARG* 3.7 5.0 + - - +
262B ASP* 4.7 1.6 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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