Contacts of the helix formed by residues 228 - 247 (chain A) in PDB entry 5NKS
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 PRO 228 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204A ILE* 5.7 0.9 - - + -
208A GLU* 4.8 11.7 - - + -
224A VAL 3.7 5.1 - - - +
225A LEU 3.7 10.5 - - - +
226A SER 3.2 9.9 - - - +
227A HIS* 1.3 93.2 - - - +
229A GLU* 1.3 60.4 + - - +
230A GLU* 3.5 17.9 - - + +
231A VAL* 2.9 47.4 + - + +
232A GLU* 3.9 1.0 + - - +
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Residues in contact with GLU 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A HIS 3.6 1.6 + - - -
228A PRO* 1.3 70.8 - - - +
230A GLU* 1.3 73.6 + - + +
232A GLU* 3.1 10.4 + - - +
233A ALA* 3.0 21.1 + - + +
257A SER* 3.7 18.5 + - - +
258A LYS* 3.6 12.4 + - - +
259A GLY* 2.9 32.3 + - - +
308A ASN* 3.2 32.5 + - - +
310A ASP* 5.2 4.9 - - - +
313A THR* 5.4 0.3 + - - -
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Residues in contact with GLU 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A PRO* 3.1 22.4 + - + +
229A GLU* 1.3 85.2 + - + +
231A VAL* 1.3 62.3 + - + +
233A ALA* 4.2 6.2 - - - +
234A GLU* 3.1 25.3 + - - +
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Residues in contact with VAL 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A GLU* 4.2 18.4 - - + +
201A ASN* 3.3 28.2 + - + +
204A ILE* 3.7 40.6 - - + -
205A VAL* 3.9 22.9 - - + +
227A HIS 4.2 6.5 - - - -
228A PRO* 2.9 38.2 + - + +
230A GLU* 1.3 75.2 - - + +
232A GLU* 1.3 62.1 + - + +
234A GLU* 4.2 2.4 - - - +
235A ALA* 3.2 16.3 + - - +
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Residues in contact with GLU 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A ALA* 3.4 21.0 - - + +
200A GLU* 4.4 7.2 - - + +
228A PRO 4.9 0.7 - - - +
229A GLU* 3.1 10.7 + - - +
231A VAL* 1.3 80.1 - - + +
233A ALA* 1.3 66.2 + - - +
235A ALA 3.2 1.6 + - - -
236A VAL* 2.9 30.0 + - + +
252A VAL* 5.9 0.7 - - - +
253A THR 5.2 0.2 - - - +
254A LYS 3.2 11.6 - - - +
255A VAL* 3.6 2.1 - - - -
256A MET* 2.9 29.2 + - - +
257A SER* 2.8 29.8 + - - +
260A ALA* 3.4 23.0 - - + +
305A PRO* 4.1 17.3 - - + +
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Residues in contact with ALA 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A GLU* 3.0 16.4 + - + +
230A GLU* 4.2 6.1 - - - +
232A GLU* 1.3 76.0 - - - +
234A GLU* 1.3 58.3 + - - +
236A VAL* 3.3 2.1 + - - +
237A TYR* 2.9 30.4 + - - +
259A GLY* 3.7 29.8 - - - +
260A ALA* 4.2 11.6 - - - +
263A ALA* 4.6 3.8 - - + +
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Residues in contact with GLU 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A ASN* 2.9 32.7 + - - +
204A ILE* 5.8 4.9 - - + -
230A GLU 3.1 18.6 + - - +
231A VAL* 4.2 3.1 - - - +
233A ALA* 1.3 77.6 - - - +
235A ALA* 1.3 60.6 + - - +
237A TYR* 3.3 7.8 + - + +
238A ARG* 2.8 61.9 + - - +
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Residues in contact with ALA 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A MET* 3.3 23.2 - - + +
199A ALA* 3.4 7.9 - - - +
200A GLU 3.4 34.8 - - - +
201A ASN 3.6 1.6 - - - +
231A VAL 3.2 17.0 + - - +
232A GLU 3.2 1.8 + - - -
234A GLU* 1.3 86.8 + - - +
236A VAL* 1.3 58.0 + - - +
238A ARG* 3.3 1.1 + - - +
239A ALA* 2.8 27.0 + - - +
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Residues in contact with VAL 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A ALA* 3.6 21.1 - - + -
232A GLU* 2.9 25.2 + - + +
233A ALA* 3.7 5.2 - - - +
235A ALA* 1.3 75.6 - - - +
237A TYR* 1.3 65.2 + - - +
239A ALA* 3.2 3.9 + - - +
240A VAL* 2.9 28.6 + - + +
252A VAL* 3.9 22.4 - - + -
260A ALA* 3.9 19.1 - - + +
263A ALA* 3.9 20.6 - - + -
264A ILE* 3.9 22.7 - - + -
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Residues in contact with TYR 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A ALA 2.9 17.8 + - - +
234A GLU* 3.6 7.4 - - + +
236A VAL* 1.3 80.3 - - - +
238A ARG* 1.3 53.3 + - - +
240A VAL* 3.5 7.9 + - + +
241A THR* 2.7 51.3 + - - -
263A ALA* 4.6 18.1 - - + +
266A GLN* 5.2 8.3 - - + -
270A ARG* 4.5 28.2 + - - -
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Residues in contact with ARG 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A MET* 3.5 30.9 + - + +
176A CYS 5.5 3.8 + - - -
178A ASP* 2.9 40.5 + - - +
181A MET* 4.8 2.2 - - - +
201A ASN* 3.3 26.1 - - - +
234A GLU* 2.8 50.3 + - - +
235A ALA* 3.7 5.4 - - - +
237A TYR* 1.3 74.9 - - - +
239A ALA* 1.3 65.5 + - - +
241A THR* 3.2 8.1 + - - -
242A ILE* 3.1 36.4 + - + +
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Residues in contact with ALA 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A MET* 3.8 16.1 - - - +
181A MET* 4.3 12.1 - - - -
185A PHE* 3.9 2.4 - - - -
197A VAL* 4.1 20.4 - - + -
235A ALA 2.8 17.9 + - - +
236A VAL* 3.7 5.4 - - - +
238A ARG* 1.3 77.2 - - - +
240A VAL* 1.3 57.2 - - - +
242A ILE* 3.2 2.6 + - - +
243A ALA* 2.9 31.0 + - - +
250A LEU* 3.6 15.4 - - + +
252A VAL* 5.8 0.2 - - + -
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Residues in contact with VAL 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A VAL* 2.9 35.1 + - + +
237A TYR* 3.6 10.5 - - + +
239A ALA* 1.3 69.4 - - - +
241A THR* 1.3 59.7 + - - +
243A ALA* 3.8 1.2 - - - +
244A LYS* 2.8 30.1 + - + +
250A LEU* 3.5 19.2 - - + +
263A ALA* 4.9 4.9 - - + +
264A ILE* 5.3 0.9 - - - -
267A ALA* 3.6 32.5 - - + -
270A ARG* 3.8 18.2 - - - +
272A VAL* 4.2 12.2 - - + +
274A VAL* 4.3 11.9 - - + -
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Residues in contact with THR 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A TYR* 2.7 41.5 + - - -
238A ARG* 3.2 8.6 + - - -
240A VAL* 1.3 80.5 - - - +
242A ILE* 1.3 60.1 + - + +
244A LYS* 3.8 6.1 - - - +
245A GLN* 3.0 36.7 + - + +
270A ARG* 5.5 2.5 + - - +
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Residues in contact with ILE 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A ASP* 3.8 40.8 - - + +
181A MET* 3.8 18.2 - - + -
182A TYR* 3.7 40.5 - - + +
185A PHE* 3.7 14.4 - - + -
238A ARG* 3.1 23.6 + - + +
239A ALA 3.8 3.6 - - - +
241A THR* 1.3 77.2 - - + +
243A ALA* 1.3 60.5 + - - +
245A GLN* 3.3 7.4 + - - +
246A ALA* 2.9 27.5 + - - +
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Residues in contact with ALA 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A PHE* 3.7 17.7 - - + -
239A ALA 2.9 17.2 + - - +
240A VAL* 3.8 2.9 - - - +
242A ILE* 1.3 77.7 - - - +
244A LYS* 1.3 57.4 + - - +
246A ALA 3.2 1.2 + - - -
247A ASN* 2.9 24.1 + - - -
248A CYS* 3.0 31.7 + - + +
249A PRO 5.1 0.2 - - - -
250A LEU* 3.7 24.2 - - + -
272A VAL* 5.6 3.1 - - + -
273A VAL 5.6 0.4 - - - +
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Residues in contact with LYS 244 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240A VAL* 2.8 18.9 + - + +
241A THR* 3.8 7.4 - - - +
243A ALA* 1.3 76.3 - - - +
245A GLN* 1.3 72.2 + - - +
247A ASN* 3.1 14.3 + - - +
270A ARG* 5.1 12.8 - - + +
272A VAL* 3.9 35.1 - - + +
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Residues in contact with GLN 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A TYR* 3.8 27.3 + - + +
241A THR* 3.0 29.4 + - + +
242A ILE* 3.3 5.8 + - - +
244A LYS* 1.3 87.6 - - - +
246A ALA* 1.3 59.3 + - - +
247A ASN* 3.5 1.0 + - - +
495A PRO* 5.5 3.3 - - - +
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Residues in contact with ALA 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A TYR* 4.4 14.6 - - + +
185A PHE* 4.1 20.0 - - + -
186A SER* 3.9 20.4 - - - +
189A ARG* 2.8 30.0 + - - +
242A ILE 2.9 17.3 + - - +
243A ALA 3.9 2.9 - - - +
244A LYS 3.2 0.2 - - - -
245A GLN* 1.3 77.3 - - - +
247A ASN* 1.3 67.4 + - - +
248A CYS* 4.2 3.9 - - + +
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Residues in contact with ASN 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A ARG* 3.2 18.9 - - - +
243A ALA 2.9 5.9 + - - -
244A LYS* 3.1 12.8 + - - +
245A GLN 3.3 1.7 - - - +
246A ALA* 1.3 78.3 - - - +
248A CYS* 1.3 58.1 + - - +
482A ILE* 3.0 39.6 + - - +
485A ARG* 3.5 30.7 + - - +
486A ASN* 2.8 34.9 + - - +
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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