Contacts of the helix formed by residues 251 - 263 (chain B) in PDB entry 1G9Y
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 ARG 251 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A LEU* 4.2 22.8 - - - +
135A LEU 5.2 5.7 + - - -
137A ASP* 2.7 42.4 + - - -
247B GLN* 2.9 33.7 + - + +
248B LYS* 2.8 23.9 + - - +
250B GLN* 1.3 99.1 + - + +
252B ARG* 1.3 62.7 + - - -
253B TRP* 3.1 21.0 + - + +
254B PHE* 3.1 20.8 + - + +
255B LEU* 3.9 2.1 + - - +
413C A 4.2 2.4 + - - -
414C C 3.0 23.4 + - - -
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Residues in contact with ARG 252 (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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248B LYS 4.6 1.1 - - - -
249B THR* 2.8 23.7 + - + +
250B GLN 3.4 1.6 + - - -
251B ARG* 1.3 77.2 - - - +
253B TRP* 1.3 57.8 + - - +
255B LEU* 2.9 13.6 + - - +
256B ASP* 2.8 55.3 + - - +
267B VAL* 3.5 41.9 + - + +
269B ASP* 2.8 44.3 + - - +
274B SER* 4.1 5.6 - - - +
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Residues in contact with TRP 253 (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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96A LYS* 3.9 15.7 - - + -
97A LEU* 3.6 31.2 - - + -
250B GLN 3.9 8.2 + - - -
251B ARG* 3.8 26.0 - - + +
252B ARG* 1.3 77.4 - - - +
254B PHE* 1.3 85.2 + + + +
256B ASP* 3.7 12.3 + - - +
257B LYS* 2.8 53.3 + - + +
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Residues in contact with PHE 254 (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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96A LYS* 4.2 18.4 - - + -
97A LEU* 3.7 28.3 - - + -
212B TYR* 3.7 35.0 - + - -
213B LEU* 5.7 2.0 - - + -
216B PHE* 3.2 44.4 - + - -
247B GLN* 5.3 3.4 - - + -
251B ARG* 3.1 12.5 + - + +
252B ARG 3.1 0.6 - - - -
253B TRP* 1.3 104.3 - + + +
255B LEU* 1.3 68.9 + - + +
257B LYS* 3.5 8.5 - - + +
258B LEU* 3.1 39.2 + - + +
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Residues in contact with LEU 255 (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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245B VAL* 3.7 33.4 - - + +
247B GLN* 4.1 24.0 - - + +
251B ARG 4.5 2.9 - - - +
252B ARG* 2.9 11.7 + - - +
254B PHE* 1.3 84.6 - - + +
256B ASP* 1.3 65.7 + - - +
258B LEU* 3.0 17.5 + - + +
259B VAL* 3.2 10.2 + - - +
267B VAL* 3.6 22.5 - - + +
274B SER* 3.5 45.3 - - - +
275B ASP* 3.8 8.7 - - - +
276B TYR* 3.9 10.5 - - + +
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Residues in contact with ASP 256 (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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252B ARG* 2.8 54.9 + - - +
253B TRP* 3.7 10.9 + - - +
255B LEU* 1.3 74.5 - - - +
257B LYS* 1.3 64.0 + - - +
259B VAL* 3.0 20.9 + - - +
260B ASP* 3.4 6.1 + - - +
267B VAL* 3.6 13.5 - - - +
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Residues in contact with LYS 257 (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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96A LYS* 4.0 21.2 - - - +
253B TRP* 2.8 42.8 + - + +
254B PHE* 3.5 9.9 - - + +
256B ASP* 1.3 77.6 - - - +
258B LEU* 1.3 57.1 + - - +
260B ASP* 3.0 12.8 + - + +
261B GLU* 2.5 64.3 + - + +
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Residues in contact with LEU 258 (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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209B PHE* 4.2 3.6 - - + -
213B LEU* 4.0 29.8 - - + -
245B VAL* 4.1 33.4 - - + -
254B PHE* 3.1 28.0 + - + +
255B LEU* 3.0 14.1 + - + +
257B LYS* 1.3 73.8 - - - +
259B VAL* 1.3 60.4 + - - +
261B GLU* 3.9 17.7 - - - +
262B ILE* 2.8 56.2 + - + +
276B TYR* 4.3 20.6 - - + -
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Residues in contact with VAL 259 (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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255B LEU 3.7 1.1 - - - +
256B ASP* 3.0 10.2 + - - +
258B LEU* 1.3 77.2 - - - +
260B ASP* 1.3 58.8 + - - +
263B GLY* 2.9 27.0 + - - -
264B VAL* 3.6 6.0 + - - +
265B GLY 3.7 16.2 - - - +
266B TYR* 3.8 11.0 - - - -
267B VAL* 3.7 24.0 - - + +
276B TYR* 3.7 29.2 - - + -
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Residues in contact with ASP 260 (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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256B ASP 3.4 4.1 + - - +
257B LYS* 3.0 15.8 + - + +
259B VAL* 1.3 81.5 - - - +
261B GLU* 1.3 67.4 + - - +
263B GLY* 3.5 10.8 + - - -
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Residues in contact with GLU 261 (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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96A LYS* 4.2 7.8 + - - -
205B TYR* 3.6 15.2 - - - -
209B PHE* 3.3 37.6 - - + -
257B LYS* 2.5 56.6 + - + +
258B LEU* 3.9 14.8 - - - +
260B ASP* 1.3 81.5 - - - +
262B ILE* 1.3 64.0 + - - +
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Residues in contact with ILE 262 (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 THR* 4.5 5.5 - - - +
205B TYR* 2.6 40.8 + - - +
209B PHE* 4.1 9.6 - - + -
213B LEU* 4.2 1.6 - - + -
243B PHE* 4.3 2.2 - - + -
258B LEU* 2.8 40.9 + - + +
261B GLU* 1.3 73.7 - - - +
263B GLY* 1.3 60.8 + - - +
264B VAL* 3.3 17.0 + - + +
276B TYR* 3.3 44.6 - - + +
278B LEU* 4.5 3.8 - - + -
287B PHE* 4.0 34.3 - - + -
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Residues in contact with GLY 263 (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 THR* 6.0 1.6 - - - -
259B VAL* 2.9 16.6 + - - -
260B ASP* 3.8 8.5 - - - -
261B GLU 3.3 2.2 - - - -
262B ILE* 1.3 77.4 - - - +
264B VAL* 1.3 61.4 + - - +
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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