Contacts of the helix formed by residues 247 - 259 (chain B) in PDB entry 4QGC
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 LYS 247 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217B ASP* 5.2 8.1 + - - -
245B ILE* 3.5 10.3 - - - +
246B ARG* 1.3 82.6 - - + +
248B ALA* 1.3 65.2 + - - +
249B SER* 3.3 24.7 + - - +
250B ASP* 3.2 37.0 + - - +
251B VAL* 3.8 0.9 + - - +
275B GLU* 5.0 3.6 - - - +
279B ARG* 3.8 24.9 - - - +
282B GLU* 3.5 13.9 - - - +
283B ILE* 3.8 11.0 - - - +
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Residues in contact with ALA 248 (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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247B LYS* 1.3 72.5 - - - +
249B SER* 1.3 61.2 + - - +
251B VAL* 3.1 13.0 + - - +
252B HIS* 3.1 41.7 + - + -
282B GLU* 3.0 53.4 + - + +
286B ALA* 4.3 2.2 - - + +
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Residues in contact with SER 249 (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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247B LYS* 3.3 32.0 + - - +
248B ALA* 1.3 75.3 - - - +
250B ASP* 1.3 66.1 + - - +
251B VAL 3.3 0.2 - - - -
252B HIS* 3.6 14.5 + - - +
253B GLU* 3.1 32.0 + - - +
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Residues in contact with ASP 250 (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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220B ALA* 3.4 30.3 - - + +
221B VAL* 4.3 1.9 - - - +
244B PHE 4.2 2.9 - - - +
245B ILE* 3.7 21.1 - - + -
246B ARG* 3.1 28.2 + - - +
247B LYS* 3.4 38.5 + - - +
248B ALA 3.1 0.4 - - - -
249B SER* 1.3 78.6 + - - +
251B VAL* 1.3 62.4 + - - +
253B GLU* 3.3 7.1 + - - +
254B VAL* 3.2 25.8 + - - +
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Residues in contact with VAL 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B ILE* 3.7 20.9 - - + -
247B LYS 3.9 5.8 - - - +
248B ALA* 3.1 8.4 + - - +
250B ASP* 1.3 74.8 - - - +
252B HIS* 1.3 60.4 + - + +
254B VAL* 3.2 8.7 + - - +
255B ARG* 2.8 31.7 + - - +
267B ILE* 4.2 15.6 - - + +
269B SER* 3.4 22.7 - - - +
283B ILE* 4.3 8.1 - - + +
286B ALA* 3.5 30.7 - - + +
287B SER* 3.7 16.6 - - - +
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Residues in contact with HIS 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B ALA* 3.1 34.9 + - + -
249B SER* 3.6 13.4 - - - +
250B ASP 3.3 0.2 - - - -
251B VAL* 1.3 75.9 - - + +
253B GLU* 1.3 56.7 + - + +
255B ARG* 3.4 11.5 + - + +
256B LYS* 2.8 29.8 + - - +
285B GLU* 5.6 1.6 + - - -
286B ALA* 3.7 22.0 - - + +
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Residues in contact with GLU 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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220B ALA* 3.9 21.7 + - - +
221B VAL* 3.8 20.4 + - + +
249B SER* 3.1 23.8 + - - +
250B ASP* 3.6 5.8 - - - +
251B VAL 3.2 0.2 - - - -
252B HIS* 1.3 76.0 - - + +
254B VAL* 1.3 60.6 + - - +
256B LYS* 3.2 17.2 + - + +
257B VAL* 2.9 34.4 + - + +
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Residues in contact with VAL 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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220B ALA 5.7 0.7 - - - +
221B VAL* 3.7 18.4 - - + -
229B LEU* 4.1 29.6 - - + -
240B VAL* 4.6 7.6 - - + -
242B ALA* 4.3 18.2 - - + -
245B ILE* 4.7 4.0 - - + -
250B ASP 3.2 15.6 + - - +
251B VAL* 3.2 8.9 + - - +
253B GLU* 1.3 76.2 - - - +
255B ARG* 1.3 62.8 + - - +
257B VAL* 3.2 3.1 + - - +
258B LEU* 3.0 28.2 + - + +
267B ILE* 3.9 24.2 - - + -
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Residues in contact with ARG 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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251B VAL* 2.8 17.3 + - - +
252B HIS* 3.4 14.6 - - + +
254B VAL* 1.3 78.2 - - - +
256B LYS* 1.3 61.1 + - - +
258B LEU* 3.5 6.3 + - - +
259B GLY* 3.1 19.9 + - - +
263B LYS* 4.9 13.4 + - - +
265B ILE 4.0 7.1 + - - -
267B ILE* 3.5 27.6 - - + +
286B ALA 2.9 27.7 + - - -
287B SER* 4.2 3.2 - - - +
288B ASP* 2.9 39.8 + - - +
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Residues in contact with LYS 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 HIS 2.8 18.6 + - - +
253B GLU* 3.2 18.1 + - + +
255B ARG* 1.3 78.1 - - - +
257B VAL* 1.3 65.3 + - + +
259B GLY* 3.1 15.0 + - - -
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Residues in contact with VAL 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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221B VAL* 4.0 21.5 - - + -
226B ILE* 4.1 33.7 - - + +
229B LEU* 3.7 31.9 - - + -
230B LYS* 4.4 15.0 - - + +
233B VAL* 5.4 0.9 - - - +
253B GLU* 2.9 21.2 + - + +
254B VAL 3.2 4.7 + - - +
256B LYS* 1.3 77.0 - - + +
258B LEU* 1.3 65.9 + - - +
259B GLY* 3.3 1.2 + - - -
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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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229B LEU* 4.0 28.3 - - + +
232B GLY 6.0 0.2 - - - -
233B VAL* 3.8 28.7 - - + +
240B VAL* 4.4 11.7 - - + -
254B VAL* 3.0 21.5 + - + +
255B ARG* 3.8 6.5 - - - +
257B VAL* 1.3 76.3 - - - +
259B GLY* 1.3 64.7 + - - +
260B GLU 3.8 0.2 + - - -
261B LYS* 4.1 3.5 + - - +
262B GLY* 3.2 36.3 + - - +
263B LYS* 5.7 0.2 - - - -
265B ILE* 4.3 20.9 - - + +
267B ILE* 3.8 34.1 - - + -
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Residues in contact with GLY 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 ARG 3.1 14.0 + - - +
256B LYS* 3.1 14.9 + - - -
257B VAL 4.1 1.6 - - - -
258B LEU* 1.3 79.0 - - - +
260B GLU* 1.3 62.6 + - - -
262B GLY 3.7 0.2 - - - -
263B LYS* 3.3 23.2 + - - +
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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