Contacts of the helix formed by residues 242 - 259 (chain B) in PDB entry 1QQG
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 ASP 242 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B ASP* 3.4 12.8 - - - +
78B SER* 2.6 41.4 + - - +
79B LYS* 4.7 3.5 - - - +
219B ASN* 3.5 13.9 - - - -
240B VAL* 3.3 2.4 + - - +
241B ASP* 1.3 82.3 - - - +
243B SER* 1.3 65.5 + - - +
244B VAL* 3.2 7.4 + - - +
245B VAL* 3.1 24.2 + - - +
246B ALA* 3.1 21.8 + - - +
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Residues in contact with SER 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B SER* 5.9 0.3 - - - -
216B HIS* 4.4 4.3 - - - -
218B GLU* 3.0 33.9 + - - +
219B ASN* 3.8 3.2 - - - +
242B ASP* 1.3 72.5 - - - +
244B VAL* 1.3 67.4 + - - +
246B ALA* 3.8 0.9 - - - +
247B GLN* 3.0 31.1 + - - +
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Residues in contact with VAL 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ALA* 4.2 7.4 - - + +
77B ASP* 3.7 22.7 - - - +
78B SER* 3.5 29.2 - - - +
242B ASP* 3.1 8.7 - - - +
243B SER* 1.3 80.9 + - - +
245B VAL* 1.3 64.2 + - - +
247B GLN* 3.1 16.0 + - - +
248B ASN* 3.1 14.2 + - + +
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Residues in contact with VAL 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ARG* 5.7 4.9 - - - -
76B ALA 4.3 13.5 - - - +
77B ASP* 4.5 3.6 - - + -
164B TRP* 4.4 14.6 - - + +
240B VAL* 3.9 14.4 - - + -
241B ASP* 3.7 19.1 - - + +
242B ASP* 3.1 40.0 + - - +
244B VAL* 1.3 76.4 - - - +
246B ALA* 1.3 56.7 + - - +
248B ASN* 3.3 6.4 + - + +
249B MET* 2.9 37.9 + - + +
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Residues in contact with ALA 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B HIS* 3.7 9.7 - - + +
218B GLU 3.6 24.0 - - - +
220B PHE 3.6 22.2 - - - +
221B PHE* 4.2 3.9 - - - -
240B VAL* 3.7 17.2 - - + +
242B ASP 3.1 11.9 + - - +
243B SER 3.8 1.6 - - - +
244B VAL 3.2 0.2 - - - -
245B VAL* 1.3 76.4 - - - +
247B GLN* 1.3 62.0 + - - +
249B MET* 3.5 6.6 + - - +
250B HIS* 3.2 21.7 + - - +
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Residues in contact with GLN 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B HIS* 3.7 30.8 + - + +
243B SER 3.0 18.7 + - - +
244B VAL* 3.1 6.6 + - - +
246B ALA* 1.3 74.9 - - - +
248B ASN* 1.3 58.8 + - - +
250B HIS* 3.3 2.9 + - - +
251B GLU* 2.8 53.3 + - + +
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Residues in contact with ASN 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ARG* 5.5 6.8 - - - +
76B ALA 5.8 2.7 - - - +
162B GLU* 5.7 1.2 + - - -
164B TRP* 4.1 18.1 - - - +
244B VAL* 3.1 13.0 + - + +
245B VAL* 3.3 11.0 + - + +
247B GLN* 1.3 73.8 - - - +
249B MET* 1.3 67.3 + - + +
251B GLU* 4.0 9.7 - - - +
252B THR* 2.9 54.6 + - - -
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Residues in contact with MET 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B TRP* 3.6 57.0 - - + +
166B VAL* 4.0 6.3 - - + -
185B LEU* 3.5 31.2 - - + -
221B PHE* 3.9 28.9 - - + -
240B VAL* 3.7 30.5 - - - -
245B VAL* 2.9 24.6 + - + +
246B ALA 3.5 5.8 - - - +
247B GLN 3.3 0.2 - - - -
248B ASN* 1.3 76.2 - - - +
250B HIS* 1.3 61.5 + - - +
252B THR* 4.1 0.3 - - - -
253B ILE* 3.1 31.8 + - + +
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Residues in contact with HIS 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B CYS* 3.2 46.7 + - - -
215B GLY* 4.2 3.3 - - - -
216B HIS* 3.7 30.7 - + - +
221B PHE* 3.8 16.1 - - + -
246B ALA 3.2 10.9 + - - +
247B GLN 3.4 9.0 - - - +
248B ASN 3.2 0.2 - - - -
249B MET* 1.3 79.2 - - - +
251B GLU* 1.3 65.5 + - + +
253B ILE* 3.9 0.2 - - - -
254B LEU* 2.8 59.0 + - + +
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Residues in contact with GLU 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B GLN* 2.8 54.7 + - + +
248B ASN* 4.0 9.4 - - - +
250B HIS* 1.3 83.5 - - + +
252B THR* 1.3 58.4 + - - +
254B LEU* 3.9 6.9 - - + +
255B GLU* 3.0 30.3 + - - +
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Residues in contact with THR 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B LYS* 5.3 2.5 - - - +
162B GLU* 3.8 20.9 + - + +
164B TRP* 3.7 25.5 - - + -
187B LEU* 4.1 7.2 - - + -
248B ASN* 2.9 40.3 + - - -
251B GLU* 1.3 70.5 - - - +
253B ILE* 1.3 61.1 + - - +
255B GLU* 3.4 7.0 + - - +
256B ALA* 3.0 25.6 + - - +
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Residues in contact with ILE 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B TRP* 4.2 10.5 - - + -
185B LEU* 4.1 16.2 - - + -
187B LEU* 4.1 17.0 - - + -
192B ILE* 3.7 31.9 - - + -
208B LEU* 4.7 5.6 - - + -
211B ILE* 4.8 2.5 - - + -
214B CYS* 4.4 11.2 - - + -
221B PHE* 3.6 26.9 - - + -
223B ILE* 5.3 0.4 - - + -
249B MET* 3.1 22.1 + - + +
250B HIS 4.1 1.8 - - - +
252B THR* 1.3 72.3 - - - +
254B LEU* 1.3 65.5 + - - +
256B ALA* 3.0 8.9 + - - +
257B MET* 2.9 35.7 + - - +
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Residues in contact with LEU 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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214B CYS* 4.3 3.3 - - - -
250B HIS* 2.8 46.6 + - + +
251B GLU* 3.9 6.5 - - + +
253B ILE* 1.3 75.9 - - - +
255B GLU* 1.3 56.4 + - - +
257B MET* 2.8 46.1 + - + +
258B ARG* 2.8 64.4 + - + +
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Residues in contact with GLU 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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212A ARG* 2.7 39.0 + - - -
251B GLU 3.0 20.2 + - - +
252B THR* 3.5 7.2 - - - +
254B LEU* 1.3 78.6 - - - +
256B ALA* 1.3 56.3 + - - +
258B ARG* 4.4 7.9 + - - +
259B ALA* 2.9 32.0 + - + +
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Residues in contact with ALA 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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161B LYS* 4.5 11.4 - - - +
187B LEU* 4.2 18.8 - - + -
188B THR 4.9 0.7 - - - +
189B SER* 4.6 3.3 - - - +
208B LEU* 3.6 22.3 - - + +
252B THR 3.0 14.3 + - - +
253B ILE* 3.0 10.1 + - - +
255B GLU* 1.3 77.9 - - - +
257B MET* 1.3 61.2 + - - +
259B ALA* 3.7 11.6 + - - +
260B MET* 3.4 17.0 + - - +
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Residues in contact with MET 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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208B LEU* 4.2 28.0 - - + +
211B ILE* 3.3 44.0 - - + +
212B ARG 4.4 3.1 - - - +
213B ARG* 4.3 13.5 - - - -
214B CYS* 4.3 7.2 - - - +
253B ILE* 2.9 26.2 + - - +
254B LEU* 2.8 31.1 + - + +
256B ALA* 1.3 74.8 - - - +
258B ARG* 1.3 59.8 + - + +
260B MET* 3.1 28.8 - - - +
261B SER 4.6 0.2 + - - -
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Residues in contact with ARG 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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211A ILE 5.7 0.4 - - - -
212A ARG* 3.4 57.1 + - + +
213A ARG* 3.6 46.4 - - - +
214A CYS 5.7 1.2 + - - -
254B LEU* 2.8 59.2 + - + +
255B GLU* 3.9 7.1 + - - +
257B MET* 1.3 72.6 - - + +
259B ALA* 1.3 56.4 + - - +
260B MET 2.9 9.0 + - - -
261B SER* 2.8 27.7 + - - -
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Residues in contact with ALA 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A ARG* 3.5 11.4 - - - +
255B GLU* 2.9 29.7 + - + +
256B ALA* 3.9 10.8 - - - +
257B MET 3.3 0.6 - - - -
258B ARG* 1.3 74.8 - - - +
260B MET* 1.3 60.7 + - - +
261B SER 3.2 0.9 - - - -
262B ASP* 3.1 23.1 + - + +
263B GLU* 3.7 15.3 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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