Contacts of the helix formed by residues 251 - 264 (chain O) in PDB entry 5G04
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 ALA 251 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249O ASP 3.0 9.5 + - - +
250O PHE* 1.3 71.3 - - - +
252O GLU* 1.3 72.0 + - - +
254O HIS* 3.0 32.8 + - - +
277O TYR* 3.3 15.7 - - + -
280O ARG* 4.2 9.6 - - + +
281O LEU* 3.8 36.1 - - + +
282O ILE 5.2 0.9 - - - +
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Residues in contact with GLU 252 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D PHE* 3.6 36.8 - - + -
19D ASN 5.5 2.9 - - - +
20D LEU* 4.7 13.9 - - + +
213O GLU* 5.5 0.5 - - - +
216O LEU* 3.5 18.1 - - + +
250O PHE* 3.3 30.9 - - + -
251O ALA* 1.3 86.9 + - - +
253O ALA* 1.3 55.7 + - - +
254O HIS 3.2 0.2 - - - -
255O TYR* 3.0 18.0 + - - +
256O LEU 3.0 12.3 + - - -
277O TYR* 4.1 12.3 - - + +
281O LEU* 4.1 13.0 - - - +
282O ILE 5.7 0.2 - - - +
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Residues in contact with ALA 253 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216O LEU* 3.7 5.8 - - - +
240O LEU* 3.4 31.8 - - + +
243O LEU* 4.1 8.1 - - + -
244O LEU* 3.8 27.0 - - + +
250O PHE* 3.4 27.8 + - + +
251O ALA 3.1 0.6 + - - -
252O GLU* 1.3 74.8 - - - +
254O HIS* 1.3 63.7 + - - +
256O LEU 3.7 0.2 + - - -
257O SER* 3.3 18.9 + - - -
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Residues in contact with HIS 254 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ASN* 4.4 6.2 + - - -
39A LEU* 3.4 34.3 - - + +
393C GLU* 5.6 0.2 + - - -
244O LEU* 3.5 15.0 - - + +
248O PRO 4.3 8.7 + - - -
250O PHE 4.3 8.3 - - - -
251O ALA* 3.0 24.4 + - - +
253O ALA* 1.3 76.4 - - - +
255O TYR* 1.3 57.0 + - - +
257O SER* 3.3 10.3 - - - -
258O TYR* 3.0 26.7 + - - +
273O SER* 3.9 12.6 + - - +
276O HIS* 3.4 40.8 - + + +
277O TYR* 3.7 21.5 - - + -
280O ARG* 5.0 6.3 - - + +
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Residues in contact with TYR 255 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D VAL* 4.5 1.6 - - - +
13D THR* 3.4 39.8 + - + +
17D TRP* 2.8 33.3 + - - -
18D PHE* 3.6 32.3 - + + -
251O ALA 3.8 0.8 + - - -
252O GLU 3.0 11.2 + - - +
254O HIS* 1.3 76.2 - - - +
256O LEU* 1.3 60.1 + - - +
258O TYR* 3.1 41.0 + + - +
259O LEU* 2.8 38.8 + - + +
274O LEU* 4.6 3.8 - - + -
277O TYR* 3.5 45.0 - + + -
278O PHE* 4.7 0.7 - + - -
306O ASN* 3.9 5.3 + - - -
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Residues in contact with LEU 256 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D PHE* 4.4 5.8 - - + -
215O PHE* 4.8 0.2 - - + -
216O LEU* 3.7 33.9 - - + -
219O GLN* 3.7 30.7 - - + -
220O ALA* 3.6 29.4 - - + -
223O LEU* 3.6 16.1 - - + +
236O LEU* 3.9 17.9 - - + +
240O LEU* 3.6 19.3 - - + -
252O GLU 3.0 9.0 + - - +
253O ALA 3.9 0.9 - - - +
254O HIS 3.5 0.2 - - - -
255O TYR* 1.3 71.2 - - - +
257O SER* 1.3 55.9 + - - +
259O LEU* 3.5 11.5 + - + +
260O ASN* 2.8 35.0 + - - +
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Residues in contact with SER 257 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ASN* 5.2 4.3 + - - -
237O GLN* 4.0 15.6 + - - +
240O LEU* 3.0 28.6 - - - +
241O ASN* 4.9 4.5 + - - -
253O ALA 3.3 7.5 + - - -
254O HIS* 3.3 13.0 - - - -
256O LEU* 1.3 72.5 - - - +
258O TYR* 1.3 51.6 + - - +
260O ASN* 3.0 7.4 + - - +
261O ASN* 2.4 52.4 + - - +
273O SER* 3.8 8.1 - - - -
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Residues in contact with TYR 258 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D VAL* 4.1 4.9 - - + +
254O HIS 3.0 14.8 + - - +
255O TYR* 3.1 50.9 + + - +
257O SER* 1.3 72.8 - - - +
259O LEU* 1.3 64.3 + - + +
261O ASN* 3.6 3.7 + - - +
262O LEU* 2.7 62.0 + - + +
270O SER* 3.3 21.3 - - - -
273O SER* 3.7 17.0 - - - -
274O LEU* 3.5 29.7 - - + +
306O ASN* 4.2 8.1 + - - -
310O LEU* 3.5 21.6 - - + +
313O ARG* 3.8 15.2 + - - -
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Residues in contact with LEU 259 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D VAL* 4.4 14.6 - - + -
13D THR* 3.7 25.6 - - + -
18D PHE* 4.7 0.4 - - + -
220O ALA* 4.3 12.8 - - + +
223O LEU* 4.0 22.2 - - + +
224O LYS* 5.9 1.1 - - + +
255O TYR* 2.8 48.6 + - + +
256O LEU* 3.8 26.0 - - + +
258O TYR* 1.3 85.3 - - + +
260O ASN* 1.3 54.0 + - - +
262O LEU* 3.6 6.1 - - + +
263O ARG* 2.8 33.8 + - - +
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Residues in contact with ASN 260 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A PRO* 4.3 2.8 - - - +
223O LEU* 4.2 7.8 - - - +
233O PRO* 3.3 12.4 + - - +
236O LEU* 3.3 20.0 - - + +
237O GLN* 3.4 38.8 - - - +
256O LEU 2.8 19.7 + - - +
257O SER* 3.0 8.6 + - - +
259O LEU* 1.3 74.5 - - - +
261O ASN* 1.3 61.5 + - - +
263O ARG* 2.6 34.5 + - - +
264O VAL* 3.2 26.9 + - - +
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Residues in contact with ASN 261 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A PRO* 3.4 32.7 - - - +
237O GLN* 3.7 6.0 + - - +
257O SER* 2.4 39.7 + - - +
258O TYR 3.7 3.5 + - - +
260O ASN* 1.3 69.3 - - - +
262O LEU* 1.3 54.0 + - - +
264O VAL* 3.1 7.5 - - - +
265O GLN 3.1 6.4 + - - -
266O ASP* 2.7 34.7 + - + -
269O SER* 3.2 21.8 + - - -
270O SER* 3.7 18.8 - - - +
273O SER* 3.0 23.9 + - - -
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Residues in contact with LEU 262 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D VAL* 4.2 11.2 - - + -
258O TYR* 2.7 52.3 + - + +
259O LEU* 3.6 8.3 - - + +
261O ASN* 1.3 69.2 - - - +
263O ARG* 1.3 64.2 + - - +
264O VAL 3.1 1.1 - - - -
265O GLN* 3.1 14.6 + - - +
266O ASP 4.7 0.9 - - - +
270O SER* 3.0 32.3 - - - -
310O LEU* 3.6 9.4 - - + -
313O ARG* 3.9 20.2 - - + -
314O PHE* 3.5 21.3 - - + -
502O GLN* 3.9 11.8 + - - +
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Residues in contact with ARG 263 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223O LEU* 3.6 28.2 - - + +
227O GLU* 3.7 47.7 + - + +
230O ALA* 4.7 4.8 - - - +
231O LEU 2.9 21.3 + - - -
232O THR* 3.4 6.4 + - - -
233O PRO* 3.2 36.3 - - + +
236O LEU* 3.8 8.9 - - - +
259O LEU 2.8 21.0 + - - +
260O ASN* 2.6 30.1 + - - +
262O LEU* 1.3 71.3 - - - +
264O VAL* 1.3 58.5 + - + +
265O GLN 3.3 1.1 + - - -
500O ASN 5.8 0.2 - - - +
501O SER* 5.5 2.3 - - - -
502O GLN* 3.6 31.6 + - - +
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Residues in contact with VAL 264 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A HIS* 3.8 15.9 - - + +
30A HIS* 6.4 0.2 - - + -
31A HIS* 3.0 53.7 + - + +
32A PRO* 3.6 13.0 - - + -
116A ALA* 4.0 0.5 - - - +
233O PRO* 3.4 27.4 - - + -
260O ASN 3.2 10.3 + - - +
261O ASN* 3.1 18.2 - - - +
262O LEU 3.1 1.4 - - - -
263O ARG* 1.3 77.4 - - + +
265O GLN* 1.3 65.2 + - - +
266O ASP* 3.3 17.5 - - - +
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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