Contacts of the helix formed by residues 253 - 268 (chain C) in PDB entry 5HP1
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 253 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251C SER* 4.9 2.2 - - - +
252C TRP* 1.3 76.3 - - - +
254C VAL* 1.3 67.9 + - - +
255C ASN* 3.4 13.7 + - - +
256C ASP* 2.9 25.8 + - - +
257C ILE* 3.4 21.8 + - - +
289C LEU 3.5 6.3 + - - -
290C THR* 3.1 26.7 - - - +
291C GLU 3.1 7.9 - - - -
292C VAL* 3.6 17.9 - - + -
293C ILE* 4.6 3.8 - - - -
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Residues in contact with VAL 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253C THR* 1.3 75.2 - - - +
255C ASN* 1.3 66.7 + - - +
257C ILE* 3.0 14.6 + - - +
258C GLN* 3.1 39.1 + - + +
283C LEU* 3.7 15.1 - - + +
285C GLY 5.9 0.7 - - - +
287C LYS* 4.3 19.7 - - + +
288C ALA 3.5 15.5 - - - +
289C LEU* 3.4 24.8 + - + +
291C GLU 3.0 9.0 + - - +
293C ILE* 3.5 24.9 - - + -
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Residues in contact with ASN 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253C THR* 3.4 4.4 + - - +
254C VAL* 1.3 78.9 - - - +
256C ASP* 1.3 63.4 + - - +
258C GLN* 3.5 12.5 + - - +
259C LYS* 2.3 70.5 + - - +
289C LEU* 3.1 46.9 + - + +
29E G 3.5 18.7 + - - +
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Residues in contact with ASP 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247C PRO* 5.4 6.5 - - + +
249C LYS* 4.3 9.5 - - - +
251C SER 3.5 7.8 - - - +
252C TRP* 3.5 33.2 - - + -
253C THR* 2.9 36.6 + - - +
254C VAL 3.2 0.6 - - - -
255C ASN* 1.3 78.6 - - - +
257C ILE* 1.3 58.3 + - - +
259C LYS* 3.6 11.9 + - - +
260C LEU* 2.9 29.7 + - - +
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Residues in contact with ILE 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252C TRP* 4.3 12.8 - - + -
253C THR 3.4 16.4 - - - +
254C VAL 3.0 7.0 + - - +
256C ASP* 1.3 73.6 - - - +
258C GLN* 1.3 58.9 + - - +
260C LEU* 3.6 12.1 - - + +
261C VAL* 2.7 38.0 + - + +
279C LEU* 3.4 31.4 - - + +
282C LEU* 3.7 33.0 - - + -
283C LEU* 3.6 18.4 - - + -
293C ILE* 4.7 15.7 - - + -
295C LEU* 4.5 10.1 - - + -
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Residues in contact with GLN 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254C VAL* 3.1 33.1 + - - +
255C ASN* 3.8 15.3 + - - +
257C ILE* 1.3 76.0 - - - +
259C LYS* 1.3 63.1 + - - +
261C VAL* 4.0 1.9 - - - +
262C GLY 3.0 19.6 + - - -
283C LEU* 3.5 26.4 - - + +
289C LEU* 4.0 8.9 - - - +
28E G 3.1 43.9 + - + +
29E G 3.5 28.3 + - - +
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Residues in contact with LYS 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247C PRO* 5.3 12.8 - - + -
255C ASN* 2.3 55.9 + - - +
256C ASP* 3.8 11.6 + - - +
258C GLN* 1.3 74.8 - - - +
260C LEU* 1.3 57.6 + - - +
262C GLY* 3.8 0.7 - - - -
263C LYS* 2.9 37.2 + - + +
29E G 3.5 28.0 - - - +
30E G 3.8 15.6 - - - +
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Residues in contact with LEU 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246C LEU* 3.6 26.5 - - + -
247C PRO* 5.3 11.6 - - + +
252C TRP* 4.9 16.2 - - + -
256C ASP 2.9 19.0 + - - +
257C ILE* 3.2 15.2 + - + +
259C LYS* 1.3 76.5 - - - +
261C VAL* 1.3 62.5 + - - +
263C LYS* 3.1 7.5 + - - +
264C LEU* 3.0 49.5 + - + +
279C LEU* 3.7 31.9 - - + -
303C LEU* 3.9 24.2 - - + -
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Residues in contact with VAL 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257C ILE* 2.7 24.8 + - + +
258C GLN* 4.1 2.5 - - - +
260C LEU* 1.3 72.2 - - + +
262C GLY* 1.3 64.2 + - - +
264C LEU* 3.3 8.6 + - - +
265C ASN* 3.0 38.7 + - - +
276C VAL* 4.2 13.3 - - + +
279C LEU* 3.6 33.0 - - + -
280C SER* 3.9 24.9 - - - +
283C LEU* 4.7 9.6 - - + -
6E C 5.6 1.3 - - - +
7E C 4.7 11.7 - - - +
28E G 6.0 2.5 - - - +
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Residues in contact with GLY 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258C GLN 3.0 16.5 + - - -
259C LYS 3.8 0.7 - - - -
261C VAL* 1.3 78.4 - - - +
263C LYS* 1.3 61.3 + - - +
265C ASN* 3.2 14.6 - - - +
266C TRP 3.1 16.6 + - - -
29E G 4.2 11.0 - - - -
30E G 3.2 28.1 + - - +
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Residues in contact with LYS 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244C ILE* 4.4 19.9 - - + +
245C VAL* 3.0 48.1 + - - +
246C LEU* 5.2 7.9 - - + -
247C PRO* 4.8 8.3 - - + -
259C LYS* 2.9 22.7 + - + +
260C LEU* 3.1 6.9 + - - +
262C GLY* 1.3 74.7 - - - +
264C LEU* 1.3 61.5 + - - +
266C TRP* 3.2 8.9 + - + +
267C ALA* 3.0 21.4 + - - +
30E G 3.5 25.5 - - - +
31E G 3.7 22.9 + - - +
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Residues in contact with LEU 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246C LEU* 4.8 13.7 - - + -
260C LEU* 3.0 43.7 + - + +
261C VAL* 3.7 4.9 - - - +
262C GLY 3.3 0.2 - - - -
263C LYS* 1.3 73.8 - - - +
265C ASN* 1.3 66.5 + - - +
267C ALA* 2.9 8.1 + - - +
268C SER* 2.9 22.2 + - - -
274C ILE* 3.7 26.1 - - + +
276C VAL* 3.9 9.6 - - + -
279C LEU* 3.7 15.3 - - + -
303C LEU* 5.1 0.2 - - + -
306C ASN* 3.5 46.2 - - + +
310C LEU* 5.1 9.0 - - + -
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Residues in contact with ASN 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261C VAL* 3.0 36.6 + - - +
262C GLY* 3.2 13.1 - - - +
264C LEU* 1.3 75.4 - - - +
266C TRP* 1.3 62.8 + - - +
268C SER* 2.6 26.9 + - - -
269C GLN* 4.0 1.9 + - - +
276C VAL* 4.4 3.5 - - - +
353C LYS* 3.0 30.7 + - - +
5E C 5.7 1.3 - - - +
6E C 3.5 41.4 + - - +
7E C 4.8 1.4 - - - -
29E G 4.9 4.8 - - - +
30E G 5.8 0.4 - - - +
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Residues in contact with TRP 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230C MET 4.5 7.2 - - - -
231C GLY 4.4 10.1 - - - -
232C TYR* 3.9 20.9 - + - -
241C VAL* 3.4 27.0 - - + +
242C GLN 5.0 0.8 + - - -
244C ILE* 3.9 20.5 - - + +
262C GLY 3.1 3.8 + - - -
263C LYS* 3.2 9.6 + - - +
265C ASN* 1.3 78.2 - - - +
267C ALA* 1.3 62.2 + - - +
269C GLN* 2.8 56.3 + - - +
30E G 3.9 26.7 + - + +
31E G 3.4 64.6 - - + -
32E G 5.1 0.2 - - - -
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Residues in contact with ALA 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241C VAL* 6.1 0.9 - - - -
244C ILE* 4.5 14.6 - - + -
263C LYS 3.0 11.6 + - - +
264C LEU* 2.9 13.4 + - - +
266C TRP* 1.3 76.0 - - - +
268C SER* 1.3 62.5 + - - +
269C GLN* 3.0 7.3 + - - -
270C ILE* 3.2 4.0 + - - +
271C TYR* 3.0 30.5 + - + +
274C ILE* 4.6 5.2 - - + -
310C LEU* 4.0 28.9 - - + -
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Residues in contact with SER 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264C LEU 2.9 10.6 + - - -
265C ASN* 2.6 22.2 + - - -
267C ALA* 1.3 76.5 - - - +
269C GLN* 1.3 52.2 + - - +
270C ILE 3.1 0.4 - - - -
271C TYR 3.9 12.5 - - - +
272C PRO* 5.2 0.2 - - - +
274C ILE* 4.0 16.6 - - - -
338C THR* 6.5 0.2 - - - -
351C THR* 2.7 30.7 + - - -
352C GLY* 3.6 5.9 + - - -
353C LYS* 4.1 30.9 + - - +
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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