Contacts of the helix formed by residues 265 - 274 (chain B) in PDB entry 1GQF
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 PHE 265 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215B LEU* 3.2 35.9 - - + -
218B ALA* 4.1 6.3 - - + -
219B SER* 3.7 25.4 - - - -
230B PHE* 3.3 48.9 - + - -
261B LEU 3.9 15.3 - - - -
262B THR 2.9 16.4 + - - +
263B ALA 2.9 0.2 + - - -
264B HIS* 1.3 79.4 - - + +
266B ARG* 1.3 68.0 + - - +
267B GLY* 3.3 1.9 + - - -
270B CYS* 3.8 10.7 - - + +
273B LEU* 4.0 12.8 - - + -
278B LYS* 3.4 35.4 - - + +
280B PHE* 3.9 12.8 - + + -
327B PHE* 3.8 5.4 - - + -
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Residues in contact with ARG 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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384A LYS* 6.3 0.8 - - - +
259B LYS* 3.8 16.0 - - - +
263B ALA* 2.8 27.3 + - - +
264B HIS 3.3 0.6 - - - -
265B PHE* 1.3 80.6 - - - +
267B GLY* 1.3 69.2 + - - +
268B ASP* 3.4 0.9 - - - +
269B ARG* 2.7 47.8 + - - +
270B CYS 3.1 2.9 + - - -
322B PRO* 3.5 42.0 + - + +
323B VAL* 4.2 5.5 + - - +
324B GLU* 3.0 44.2 + - - +
327B PHE* 4.0 5.1 - - + -
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Residues in contact with GLY 267 (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 PHE 3.3 4.0 + - - -
266B ARG* 1.3 68.0 - - - +
268B ASP* 1.3 52.4 + - - +
269B ARG 2.5 14.7 + - - -
270B CYS 2.9 14.2 + - - -
271B LYS* 3.3 2.9 + - - +
274B LEU* 3.3 40.4 - - - +
278B LYS* 5.0 4.4 - - - +
324B GLU* 2.9 19.6 + - - -
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Residues in contact with ASP 268 (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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384A LYS* 5.1 12.5 + - - +
266B ARG 3.1 0.2 + - - -
267B GLY* 1.3 68.0 - - - +
269B ARG* 1.3 93.7 + - - +
271B LYS* 5.3 1.8 - - - -
324B GLU* 3.6 17.8 - - - +
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Residues in contact with ARG 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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219B SER* 3.6 12.6 + - - +
220B GLU* 5.4 1.7 - - - +
263B ALA* 3.7 21.1 - - - +
264B HIS* 3.4 19.1 - - - +
266B ARG* 2.7 40.4 + - - +
267B GLY 2.5 2.4 + - - -
268B ASP* 1.3 102.8 + - - +
270B CYS* 1.2 66.1 - - - +
271B LYS 3.8 1.1 - - - -
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Residues in contact with CYS 270 (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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219B SER* 3.4 30.5 - - - +
224B HIS* 4.2 2.2 - - - -
265B PHE* 3.8 27.8 - - - +
266B ARG 3.1 1.2 + - - -
267B GLY* 2.9 8.1 + - - +
269B ARG* 1.2 86.0 - - - +
271B LYS* 1.2 64.3 + - - +
272B THR* 3.1 13.0 - - - -
273B LEU* 3.0 49.6 + - + +
274B LEU* 3.7 5.4 + - - +
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Residues in contact with LYS 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 GLY 3.3 2.8 + - - +
268B ASP* 6.0 1.1 - - - -
269B ARG 3.8 0.8 - - - +
270B CYS* 1.2 75.9 - - - +
272B THR* 1.3 58.3 + - + +
273B LEU 3.1 4.9 + - - -
274B LEU* 3.2 39.5 + - + +
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Residues in contact with THR 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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219B SER 4.9 0.5 + - - -
221B GLU 3.3 18.9 + - - -
222B ASP* 3.0 31.6 - - + +
224B HIS* 3.2 24.0 + - - +
225B THR* 3.3 11.9 + - - +
270B CYS* 4.1 6.1 - - - -
271B LYS* 1.3 75.7 + - + +
273B LEU* 1.3 57.5 + - - +
274B LEU 3.5 0.7 - - - -
276B LYS* 3.2 25.6 + - - +
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Residues in contact with LEU 273 (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 HIS* 3.2 42.0 - - + +
227B ALA* 4.8 0.7 - - + -
229B CYS* 4.4 11.2 - - - +
230B PHE* 3.7 32.3 - - + -
265B PHE* 4.0 15.3 - - + -
270B CYS* 3.0 30.7 + - - +
272B THR* 1.3 77.6 - - - +
274B LEU* 1.3 60.6 + - - +
276B LYS* 2.9 37.5 + - + +
277B PRO 5.2 0.4 - - - +
278B LYS* 3.0 28.9 + - + -
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Residues in contact with LEU 274 (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 GLY* 3.3 44.4 - - - +
270B CYS 3.7 2.6 + - - +
271B LYS* 3.2 37.3 + - + +
272B THR 3.5 0.6 - - - -
273B LEU* 1.3 78.6 - - - +
275B GLU* 1.3 85.1 - - + +
276B LYS* 3.1 12.1 + - - +
278B LYS* 4.8 2.2 - - - +
326B ASP* 5.5 1.6 - - - +
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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