Contacts of the helix formed by residues 265 - 282 (chain B) in PDB entry 1G4C
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 265 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263B SER 3.9 1.2 + - - -
264B LEU* 1.3 74.6 - - - +
266B PRO* 1.3 78.5 - - + +
267B GLU* 3.3 3.8 - - + +
268B GLU* 2.9 27.5 + - + +
269B LEU* 2.9 19.4 + - - +
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Residues in contact with PRO 266 (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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265B ALA* 1.3 89.1 - - + +
267B GLU* 1.3 57.5 + - - +
269B LEU* 3.2 4.9 + - - +
270B LEU* 3.0 25.8 + - - +
298B ILE* 4.2 2.3 - - + +
301B PHE* 3.7 39.5 - - + -
304B GLU* 3.9 10.1 - - - +
306B ILE* 3.5 34.5 - - + -
311B LEU* 3.8 12.7 - - + +
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Residues in contact with GLU 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B ALA* 3.3 2.7 - - + +
266B PRO* 1.3 79.9 - - - +
268B GLU* 1.3 59.5 + - - +
270B LEU* 3.4 16.4 + - + +
271B ASN* 3.1 33.6 + - - +
306B ILE* 4.8 1.6 - - - +
308B THR* 2.6 38.4 + - - +
310B ARG* 3.8 33.8 + - - +
311B LEU* 3.8 11.1 - - + +
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Residues in contact with GLU 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B SER 4.9 0.2 - - - +
264B LEU* 3.5 25.6 - - + +
265B ALA* 2.9 40.0 + - + +
267B GLU* 1.3 75.2 - - - +
269B LEU* 1.3 65.8 + - - +
271B ASN* 3.3 22.6 + - - +
272B HIS* 3.2 23.5 + - + +
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Residues in contact with LEU 269 (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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203B ALA* 3.7 29.4 - - + -
205B ILE* 4.4 5.8 - - + -
228B ILE* 4.1 24.0 - - + -
260B LEU* 3.7 23.6 - - + -
262B THR* 4.7 4.3 - - + +
264B LEU* 4.0 14.1 - - + +
265B ALA 2.9 11.6 + - - +
266B PRO* 3.4 9.4 - - + +
268B GLU* 1.3 77.2 - - - +
270B LEU* 1.3 57.8 + - - +
272B HIS* 3.0 3.9 + - - -
273B THR* 2.8 32.1 + - + -
298B ILE* 3.8 23.6 - - + -
301B PHE* 4.1 13.7 - - + -
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Residues in contact with LEU 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B PRO 3.0 13.0 + - - +
267B GLU* 3.6 10.5 - - + +
269B LEU* 1.3 72.4 - - - +
271B ASN* 1.3 67.5 + - - +
273B THR* 3.1 13.5 + - - +
274B GLN* 2.8 50.5 + - + +
296B LEU 5.8 3.4 - - - +
298B ILE* 3.9 17.7 - - + +
310B ARG* 3.6 55.6 - - + +
311B LEU* 4.2 17.7 - - + -
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Residues in contact with ASN 271 (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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267B GLU 3.1 17.3 + - - -
268B GLU* 3.4 20.2 - - - +
269B LEU 3.2 0.4 - - - -
270B LEU* 1.3 74.2 - - - +
272B HIS* 1.3 62.4 + - + +
274B GLN* 3.9 3.1 - - - +
275B ARG* 3.0 28.1 + - - +
310B ARG* 2.8 42.3 + - - +
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Residues in contact with HIS 272 (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 ILE* 3.9 25.6 - - + -
229B PRO* 3.5 30.4 - - + +
264B LEU* 3.6 23.3 - - + +
268B GLU* 3.2 23.2 + - + +
269B LEU 3.0 7.8 + - - +
271B ASN* 1.3 78.7 - - + +
273B THR* 1.3 66.3 + - - +
275B ARG* 3.2 30.3 + - - +
276B ILE* 3.0 27.8 + - - +
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Residues in contact with THR 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B ILE* 4.4 10.5 - - + -
225B LEU* 4.2 20.4 - - + -
228B ILE* 4.6 0.2 - - + -
269B LEU* 2.8 33.2 + - + +
270B LEU* 3.1 27.9 + - - +
272B HIS* 1.3 77.8 - - - +
274B GLN* 1.3 56.0 + - - +
276B ILE* 3.3 9.3 + - - +
277B GLU* 3.0 31.4 + - - +
296B LEU* 3.6 24.5 + - + +
298B ILE* 4.3 9.8 - - + +
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Residues in contact with GLN 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU* 3.9 26.2 - - - +
270B LEU* 2.8 43.5 + - + +
271B ASN* 4.0 3.4 - - - +
273B THR* 1.3 70.3 + - - +
275B ARG* 1.3 67.3 + - - +
277B GLU* 3.2 21.0 + - - +
278B LEU* 3.0 23.9 + - - +
310B ARG* 2.8 34.5 + - - +
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Residues in contact with ARG 275 (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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224B ALA* 4.9 7.1 + - - +
227B ASP* 5.4 3.0 + - - +
228B ILE* 4.4 11.3 - - - +
229B PRO* 5.2 1.2 - - - +
271B ASN 3.0 19.8 + - - +
272B HIS* 3.4 35.5 + - - +
274B GLN* 1.3 77.4 - - - +
276B ILE* 1.3 80.3 + - - +
278B LEU* 3.1 7.8 + - - +
279B GLN* 2.8 79.9 + - + +
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Residues in contact with ILE 276 (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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221B ALA* 4.6 6.1 - - - +
224B ALA* 3.9 44.9 - - + +
225B LEU* 3.9 21.1 - - + +
228B ILE* 3.9 12.1 - - + -
272B HIS 3.0 20.3 + - - +
273B THR* 3.5 6.7 - - - +
275B ARG* 1.3 94.5 - - - +
277B GLU* 1.3 62.0 + - - +
279B GLN* 4.2 7.6 - - - +
280B GLN* 2.8 35.8 + - + +
294B LEU* 4.2 5.8 - - + -
296B LEU* 3.6 16.8 - - + -
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Residues in contact with GLU 277 (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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273B THR 3.0 15.8 + - - +
274B GLN* 3.2 29.9 + - - +
276B ILE* 1.3 76.3 - - - +
278B LEU* 1.3 58.9 + - - +
281B GLY* 2.9 31.0 + - - -
282B ARG* 4.0 1.2 + - - +
294B LEU* 3.7 23.6 - - - +
295B ASP* 3.4 12.6 - - - +
296B LEU* 2.8 48.1 + - + +
362B MG 4.0 3.1 - - - -
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Residues in contact with LEU 278 (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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274B GLN 3.0 12.6 + - - +
275B ARG* 3.1 10.5 + - - +
277B GLU* 1.3 78.1 - - - +
279B GLN* 1.3 66.3 + - + +
280B GLN 3.6 0.3 + - - -
282B ARG* 3.5 54.3 - - + +
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Residues in contact with GLN 279 (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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224B ALA* 6.1 0.3 - - - +
275B ARG* 2.8 66.3 + - + +
276B ILE* 4.0 6.1 - - - +
278B LEU* 1.3 76.0 - - + +
280B GLN* 1.3 74.6 + - - +
282B ARG 5.1 0.7 + - - -
283B VAL* 5.5 2.6 - - - +
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Residues in contact with GLN 280 (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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217B GLN* 3.0 25.2 - - + +
220B ALA* 3.9 27.5 - - - +
221B ALA* 4.8 9.0 - - - +
224B ALA* 4.9 6.3 - - + +
276B ILE* 2.8 34.1 + - + +
279B GLN* 1.3 88.7 + - + +
281B GLY* 1.3 59.9 + - - +
282B ARG 3.6 1.8 - - - -
283B VAL* 3.9 14.2 - - - +
294B LEU* 4.0 13.2 - - + -
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Residues in contact with GLY 281 (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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217B GLN* 3.8 2.7 - - - -
277B GLU 2.9 18.1 + - - -
280B GLN* 1.3 77.9 - - - +
282B ARG* 1.3 61.0 + - - +
283B VAL 3.1 9.3 + - - -
286B ALA* 3.7 4.7 - - - +
292B ALA* 4.3 4.2 - - - +
293B THR* 2.8 36.3 + - - -
294B LEU* 3.9 13.2 - - - +
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Residues in contact with ARG 282 (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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277B GLU 4.7 0.4 - - - +
278B LEU* 3.5 50.0 + - + +
279B GLN 5.1 0.4 - - - -
280B GLN 3.6 1.0 - - - -
281B GLY* 1.3 80.2 - - - +
283B VAL* 1.3 60.1 + - - +
286B ALA 3.3 22.8 + - - +
287B GLU* 3.4 29.9 + - - +
288B ARG 3.8 9.8 + - - -
289B TRP* 3.7 41.1 - - - +
292B ALA* 4.9 13.2 - - - -
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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