Contacts of the helix formed by residues 253 - 269 (chain P) in PDB entry 3HX0
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 ASN 253 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251P ASN* 3.1 13.6 + - - +
252P HIS* 1.3 84.0 - - - +
254P LEU* 1.3 54.9 + - - +
255P HIS* 3.0 10.1 - - - -
256P ILE* 2.7 42.3 + - + +
257P THR* 2.8 20.8 + - + -
286P LEU* 3.6 42.2 + - + +
289P PHE* 4.5 7.9 + - - +
291P LYS 4.6 3.8 + - - -
292P PRO* 3.3 4.9 - - - +
293P VAL* 2.9 30.0 + - - +
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Residues in contact with LEU 254 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251P ASN* 2.9 25.9 - - + +
252P HIS 3.5 2.8 + - - -
253P ASN* 1.3 76.5 - - - +
255P HIS* 1.3 58.1 + - - +
257P THR* 3.8 4.3 - - - +
258P GLU* 2.8 50.7 + - + +
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Residues in contact with HIS 255 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252P HIS 3.7 19.9 + - - -
253P ASN* 3.8 3.4 - - - -
254P LEU* 1.3 78.6 + - - +
256P ILE* 1.3 80.0 + - + +
258P GLU* 4.3 12.8 - - - +
259P LYS* 4.4 5.2 + - - +
292P PRO* 4.9 7.0 - - + -
293P VAL 5.4 0.4 + - - -
316P ILE* 4.0 21.8 - - + +
317P LEU* 3.5 24.6 - - + +
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Residues in contact with ILE 256 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253P ASN* 2.7 34.0 + - + +
255P HIS* 1.3 91.8 - - + +
257P THR* 1.3 66.7 + - + +
258P GLU 3.1 2.0 + - - -
259P LYS* 3.1 14.7 + - - +
260P LEU* 3.1 31.3 + - + +
286P LEU* 4.4 6.7 - - + -
293P VAL* 3.8 17.5 - - + +
313P ILE* 4.1 26.2 - - + +
316P ILE* 4.5 12.8 - - + +
317P LEU* 3.5 32.8 - - + -
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Residues in contact with THR 257 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251P ASN* 3.2 34.9 + - - +
253P ASN* 2.8 24.3 + - + +
254P LEU* 3.8 5.7 - - - +
256P ILE* 1.3 72.8 - - - +
258P GLU* 1.3 65.4 + - - +
260P LEU* 2.8 11.5 + - - -
261P GLU* 2.7 45.8 + - - +
283P ILE* 3.9 26.2 - - + +
286P LEU* 3.9 16.6 - - + -
287P LYS* 4.1 2.4 + - - +
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Residues in contact with GLU 258 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254P LEU* 2.8 41.8 + - + +
255P HIS* 4.3 9.9 - - - +
257P THR* 1.3 84.1 + - - +
259P LYS* 1.3 60.6 + - - +
261P GLU* 3.5 7.4 + - - +
262P VAL* 3.0 29.8 + - + +
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Residues in contact with LYS 259 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255P HIS 4.4 5.1 + - - +
256P ILE 3.1 8.0 + - - +
258P GLU* 1.3 80.5 - - - +
260P LEU* 1.3 62.0 + - - +
262P VAL* 3.4 8.6 + - - +
263P LEU* 3.2 17.5 + - - +
316P ILE* 4.2 12.1 - - + -
321P HIS 6.2 0.4 - - - -
322P LEU* 4.2 13.7 - - + +
325P LEU* 3.6 33.2 - - + +
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Residues in contact with LEU 260 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256P ILE* 3.1 24.1 + - + +
257P THR* 2.8 10.1 + - - +
259P LYS* 1.3 73.1 - - - +
261P GLU* 1.3 53.2 + - - +
262P VAL 3.0 1.6 - - - -
263P LEU* 2.8 9.6 + - + +
264P ALA* 2.7 34.5 + - - +
279P TYR* 4.2 11.0 - - + -
282P ALA* 6.0 0.4 - - + -
283P ILE* 3.5 24.5 - - + +
286P LEU* 3.8 29.2 - - + -
309P MET* 4.5 24.9 - - + -
312P LYS* 4.9 11.2 - - + -
313P ILE* 5.0 5.8 - - + -
316P ILE* 4.8 6.7 - - + -
322P LEU* 4.6 15.5 - - + -
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Residues in contact with GLU 261 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257P THR* 2.7 27.6 + - - +
258P GLU* 4.0 6.5 + - - +
260P LEU* 1.3 73.1 - - - +
262P VAL* 1.3 58.6 + - + +
264P ALA* 3.7 3.4 - - - -
265P LYS* 3.0 57.1 + - - +
283P ILE* 3.5 27.0 - - + +
287P LYS* 2.9 29.2 + - - -
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Residues in contact with VAL 262 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258P GLU* 3.0 22.2 - - + +
259P LYS* 3.5 11.0 - - - +
260P LEU 3.0 1.0 - - - -
261P GLU* 1.3 78.4 - - + +
263P LEU* 1.3 59.0 + - - +
265P LYS* 4.3 5.4 - - + +
266P ALA* 3.2 24.4 + - - +
325P LEU* 3.8 17.0 - - + -
328P ILE* 4.7 5.7 - - + +
332P VAL* 5.7 0.2 - - - +
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Residues in contact with LEU 263 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259P LYS 3.2 9.4 + - - +
260P LEU* 2.8 10.2 + - + +
262P VAL* 1.3 79.5 - - - +
264P ALA* 1.3 64.2 + - - +
266P ALA* 3.2 7.6 + - + +
267P TYR* 3.0 44.7 + - + +
279P TYR* 3.4 34.1 - - + +
312P LYS* 4.4 12.3 - - + -
322P LEU* 4.4 9.2 - - + -
324P LYS* 4.0 31.0 - - + -
325P LEU* 4.1 7.8 - - + +
328P ILE* 4.5 18.6 - - + -
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Residues in contact with ALA 264 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260P LEU 2.7 19.0 + - - +
261P GLU* 3.7 10.5 - - - +
262P VAL 3.4 0.2 - - - -
263P LEU* 1.3 69.4 - - - +
265P LYS* 1.3 54.4 + - + +
267P TYR* 2.6 28.7 + - - +
268P SER* 2.8 17.5 + - - -
276P ALA* 3.9 11.3 - - + +
279P TYR* 3.7 31.1 - - + -
280P ALA* 5.0 2.0 - - + +
283P ILE* 4.1 5.4 - - + -
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Residues in contact with LYS 265 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261P GLU* 3.0 45.6 + - + +
262P VAL* 4.4 5.6 - - + +
264P ALA* 1.3 80.2 - - + +
266P ALA* 1.3 62.1 + - - +
268P SER* 3.2 17.5 + - - -
269P VAL* 3.2 24.6 + - + +
332P VAL* 5.5 0.9 - - - -
336P GLU* 4.9 14.6 - - - +
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Residues in contact with ALA 266 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262P VAL 3.2 18.8 + - - +
263P LEU* 3.3 11.7 - - + +
264P ALA 3.0 1.0 - - - -
265P LYS* 1.3 79.5 - - - +
267P TYR* 1.3 59.1 + - + +
269P VAL* 4.1 2.9 - - - +
270P GLN* 3.1 32.1 + - - +
328P ILE* 4.3 14.1 - - + -
332P VAL* 4.0 34.5 - - + +
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Residues in contact with TYR 267 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263P LEU* 3.0 38.4 + - + +
264P ALA* 2.6 16.7 + - - +
266P ALA* 1.3 73.6 - - - +
268P SER* 1.3 62.1 + - - +
270P GLN* 3.5 19.3 + - - +
271P GLY 3.5 0.2 + - - -
272P ASP* 3.0 50.9 + - + +
275P ARG* 3.4 35.3 + - + -
276P ALA* 4.3 7.4 - - + +
279P TYR* 3.7 18.4 - + - -
1S G 3.3 18.2 + - - -
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Residues in contact with SER 268 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264P ALA 2.8 10.4 + - - -
265P LYS* 3.2 14.3 + - - -
267P TYR* 1.3 72.9 - - - +
269P VAL* 1.3 64.2 + - - +
270P GLN 2.8 10.3 + - - -
271P GLY* 2.9 17.2 + - - -
272P ASP 4.7 2.2 - - - -
273P LYS* 4.7 5.0 + - - +
276P ALA* 3.9 16.8 - - - +
346P THR* 3.6 6.4 + - - -
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Residues in contact with VAL 269 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265P LYS* 3.4 19.1 - - + +
266P ALA* 4.1 9.6 - - - +
268P SER* 1.3 82.3 - - - +
270P GLN* 1.3 60.3 + - + +
271P GLY 3.3 1.8 - - - -
332P VAL* 4.4 11.9 - - + +
335P LEU* 4.3 18.1 - - + +
336P GLU* 3.9 35.0 - - + +
339P SER* 3.4 30.5 - - - +
346P THR* 3.5 20.9 + - - +
349P ALA* 5.3 1.6 - - - +
350P GLN* 5.2 0.3 - - - +
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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
------------------------------------------------------------
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