Contacts of the helix formed by residues 249 - 261 (chain B) in PDB entry 5HNK
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 249 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209B VAL* 3.9 27.5 - - - +
245B ASN* 2.6 23.3 + - - +
246B LEU 3.1 13.5 + - - -
247B ASN 3.3 0.6 - - - -
248B ALA* 1.3 78.0 + - - +
250B GLU* 1.3 63.2 + - - +
251B GLU 3.4 2.7 - - - -
252B LEU* 3.3 17.8 + - - +
253B LEU* 2.9 26.3 + - - +
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Residues in contact with GLU 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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231B ILE* 3.7 31.4 - - + +
234B LEU* 4.0 24.2 - - + +
247B ASN 4.9 2.0 + - - +
248B ALA 3.6 3.2 + - - -
249B SER* 1.3 75.5 - - - +
251B GLU* 1.3 65.8 + - + +
253B LEU* 3.3 6.5 + - - +
254B PHE* 3.1 40.6 + - + -
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Residues in contact with GLU 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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248B ALA 5.4 0.6 + - - -
249B SER 3.4 0.2 - - - -
250B GLU* 1.3 81.2 - - + +
252B LEU* 1.3 62.6 + - - +
254B PHE* 3.6 6.7 + - - +
255B ARG* 3.1 38.0 + - - +
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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
----------------------------------------------------------
197B ALA 4.3 2.9 - - - +
207B ARG* 3.5 44.4 - - + +
208B GLY 4.0 5.4 - - - +
209B VAL* 4.0 29.8 - - + +
249B SER* 3.3 20.5 + - - +
250B GLU 3.3 0.4 - - - -
251B GLU* 1.3 78.5 - - - +
253B LEU* 1.3 61.1 + - + +
255B ARG* 3.8 22.8 - - - +
256B ASN* 2.9 58.8 + - - +
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Residues in contact with LEU 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B ALA* 4.0 7.3 - - - +
198B ILE* 3.9 38.8 - - + +
209B VAL* 4.2 12.8 - - + -
227B VAL* 4.1 16.3 - - + +
230B ILE* 4.7 11.2 - - + -
231B ILE* 4.1 24.9 - - + -
234B LEU* 4.8 5.2 - - + -
246B LEU* 3.8 24.0 - - + +
249B SER* 2.9 24.6 + - - +
250B GLU 3.3 3.8 + - - +
252B LEU* 1.3 77.0 - - + +
254B PHE* 1.3 65.0 + - - +
256B ASN* 3.5 3.1 + - - +
257B LEU* 3.0 25.1 + - - +
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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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228B LEU* 4.0 25.6 - - + -
231B ILE* 3.7 35.8 - - + +
250B GLU* 3.1 38.5 + - + +
251B GLU* 4.0 6.7 - - - +
253B LEU* 1.3 76.4 - - - +
255B ARG* 1.3 64.4 + - - +
257B LEU* 3.3 9.4 + - + +
258B ILE* 3.3 28.7 + - + +
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Residues in contact with ARG 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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78B HIS* 3.4 29.0 + - + +
79B LEU* 3.5 36.9 - - - +
81B GLU* 5.3 2.2 + - - -
207B ARG* 5.7 3.8 + - - +
251B GLU* 3.1 22.8 + - - +
252B LEU* 3.8 36.1 - - - +
254B PHE* 1.3 79.1 - - - +
256B ASN* 1.3 70.0 + - - +
258B ILE* 3.2 20.9 + - - +
259B LEU* 3.2 18.9 + - + +
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Residues in contact with ASN 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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79B LEU* 5.5 0.5 - - - +
197B ALA* 2.9 36.9 + - - +
200B GLY* 4.3 2.2 - - - -
206B ILE* 3.3 26.0 - - + +
207B ARG 3.0 25.5 + - - +
208B GLY* 4.2 1.4 - - - -
252B LEU* 2.9 31.2 + - - +
253B LEU 3.9 1.8 - - - +
255B ARG* 1.3 84.2 + - - +
257B LEU* 1.3 57.1 + - - +
259B LEU* 3.1 12.0 + - - +
260B VAL* 2.9 34.7 + - + +
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Residues in contact with LEU 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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193B ILE* 3.6 30.5 - - + +
194B SER* 5.0 2.2 - - - +
197B ALA* 4.0 16.1 - - + +
227B VAL* 4.1 20.2 - - + -
228B LEU* 3.7 39.3 - - + -
253B LEU 3.0 15.9 + - - +
254B PHE* 3.6 10.5 - - + +
255B ARG 3.2 0.2 - - - -
256B ASN* 1.3 75.5 - - - +
258B ILE* 1.3 57.8 + - + +
260B VAL* 4.2 0.9 - - - -
261B ASP* 2.9 45.8 + - + +
265B TYR* 4.6 4.9 - - + +
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Residues in contact with ILE 258 (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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74B PHE* 3.6 37.8 - - + -
75B ARG* 5.0 2.9 + - - -
78B HIS* 4.0 35.2 - - + +
254B PHE* 3.6 19.1 - - + +
255B ARG* 3.2 10.2 + - - +
257B LEU* 1.3 76.6 - - + +
259B LEU* 1.3 62.1 + - + +
260B VAL 3.7 0.2 + - - -
261B ASP 4.2 2.3 + - - +
265B TYR* 3.7 45.6 - - + +
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Residues in contact with LEU 259 (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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74B PHE* 6.0 0.4 - - + -
75B ARG* 2.9 76.9 + - + +
78B HIS* 4.2 12.6 - - + -
79B LEU* 3.8 32.5 - - + -
82B TYR* 5.0 2.2 - - + -
206B ILE* 4.0 21.5 - - + -
255B ARG* 3.2 16.1 + - + +
256B ASN* 3.1 26.3 + - - +
258B ILE* 1.3 78.6 - - + +
260B VAL* 1.3 59.0 + - + +
261B ASP 5.4 0.2 - - - -
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Residues in contact with VAL 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B ASP* 5.7 4.8 - - + +
158B THR* 4.5 7.3 - - - +
193B ILE* 3.5 37.3 - - + +
196B LYS* 3.9 33.9 - - + +
197B ALA* 3.9 11.9 - - + +
200B GLY* 6.0 0.9 - - - -
201B ASP* 6.1 1.1 - - + -
206B ILE* 4.8 14.4 - - + -
256B ASN* 2.9 23.8 + - + +
257B LEU 4.0 2.7 - - - +
259B LEU* 1.3 82.5 - - + +
261B ASP* 1.3 63.7 + - - +
262B LEU* 2.8 15.1 + - - +
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Residues in contact with ASP 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ARG* 5.7 0.7 - - - -
190B GLU* 5.1 6.8 - - - +
193B ILE* 3.5 31.1 - - + +
257B LEU* 2.9 27.1 + - + +
258B ILE 4.2 1.8 + - - -
259B LEU 3.8 0.8 - - - -
260B VAL* 1.3 71.8 - - - +
262B LEU* 1.3 62.2 + - - +
263B PRO* 3.5 10.0 - - - +
264B THR* 2.7 37.9 + - - +
265B TYR* 3.3 31.3 + - + +
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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