Contacts of the helix formed by residues 242 - 259 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A ASP* 3.2 11.5 - - - +
78A SER* 2.7 43.4 + - - +
79A LYS* 3.3 12.1 + - - +
219A ASN* 3.6 13.0 - - - -
240A VAL* 3.2 13.4 - - - +
241A ASP* 1.3 78.0 - - - +
243A SER* 1.3 61.1 + - - +
244A VAL* 3.0 18.1 + - - +
245A VAL* 3.0 29.1 + - - +
246A ALA 3.3 1.0 + - - -
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Residues in contact with SER 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A SER* 5.8 0.7 - - - -
216A HIS* 4.7 3.3 - - - -
218A GLU* 3.2 32.9 - - - +
219A ASN* 3.9 3.4 - - - +
242A ASP* 1.3 72.8 - - - +
244A VAL* 1.3 70.0 + - - +
246A ALA* 3.9 0.7 - - - +
247A GLN* 3.0 29.1 + - - +
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Residues in contact with VAL 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ALA* 3.8 9.0 - - + +
77A ASP* 3.7 21.1 - - - +
78A SER* 3.7 29.2 - - - +
242A ASP* 3.0 8.7 + - - +
243A SER* 1.3 81.9 - - - +
245A VAL* 1.3 59.6 + - - +
247A GLN* 3.9 8.4 - - - +
248A ASN* 3.2 23.0 + - + +
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Residues in contact with VAL 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ARG* 6.1 2.0 - - - -
76A ALA 4.6 11.2 + - - +
77A ASP* 4.6 4.9 - - + -
164A TRP* 4.2 22.0 - - + +
240A VAL* 3.7 22.7 - - + -
241A ASP* 3.9 10.8 - - + +
242A ASP* 3.0 41.7 + - - +
244A VAL* 1.3 76.5 - - - +
246A ALA* 1.3 57.6 + - - +
248A ASN* 3.4 6.1 + - - +
249A MET* 3.0 27.2 + - + +
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Residues in contact with ALA 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A HIS* 3.8 8.2 - - + +
218A GLU 3.8 17.5 - - - +
220A PHE 3.4 27.4 - - - +
221A PHE* 4.1 5.9 - - + -
240A VAL* 3.7 21.7 - - + +
242A ASP 3.3 5.8 + - - +
243A SER 3.4 2.7 + - - +
245A VAL* 1.3 71.7 - - - +
247A GLN* 1.3 65.8 + - - +
249A MET* 3.2 7.6 + - - +
250A HIS* 3.0 23.6 + - - +
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Residues in contact with GLN 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A HIS* 3.6 33.1 + - + +
243A SER* 3.0 20.2 + - - +
244A VAL* 3.9 7.6 - - - +
246A ALA* 1.3 75.1 - - - +
248A ASN* 1.3 58.4 + - - +
250A HIS* 3.2 5.4 - - - +
251A GLU* 2.9 53.2 + - + +
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Residues in contact with ASN 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ARG* 4.7 8.7 - - - +
76A ALA 5.6 4.5 - - - +
162A GLU* 5.7 0.2 + - - -
164A TRP* 4.1 16.6 - - - +
244A VAL* 3.2 17.1 + - + +
245A VAL* 3.6 7.6 - - - +
246A ALA 3.2 0.2 - - - -
247A GLN* 1.3 80.2 - - - +
249A MET* 1.3 60.7 + - - +
251A GLU* 3.8 11.6 - - - +
252A THR* 2.6 46.0 + - - -
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Residues in contact with MET 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A TRP* 3.6 55.2 - - + +
166A VAL* 3.9 7.4 - - + -
185A LEU* 3.3 33.7 - - + -
221A PHE* 3.8 23.8 - - + -
240A VAL* 3.6 29.8 - - - -
245A VAL* 3.0 19.8 + - - +
246A ALA* 3.2 5.8 + - - +
248A ASN* 1.3 75.0 - - - +
250A HIS* 1.3 65.8 + - - +
252A THR* 3.7 0.2 - - - -
253A ILE* 2.9 35.4 + - + +
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Residues in contact with HIS 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A CYS* 3.1 36.0 + - - -
215A GLY* 3.9 9.6 - - - -
216A HIS* 3.1 32.8 - + - +
221A PHE* 3.7 16.1 - - + -
246A ALA 3.0 13.1 + - - +
247A GLN 3.2 9.4 - - - +
249A MET* 1.3 76.1 - - - +
251A GLU* 1.3 56.0 + - + +
253A ILE* 3.9 0.9 - - - +
254A LEU* 2.8 60.9 + - + +
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Residues in contact with GLU 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A GLN* 2.9 53.3 + - + +
248A ASN* 3.8 10.9 - - - +
250A HIS* 1.3 76.8 - - + +
252A THR* 1.3 54.6 + - - +
254A LEU* 3.1 8.3 + - - +
255A GLU* 2.8 37.3 + - - +
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Residues in contact with THR 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A LYS* 5.3 2.9 + - - +
162A GLU* 3.8 20.6 + - + -
164A TRP* 3.6 26.6 - - + -
187A LEU* 4.0 5.3 - - + +
248A ASN* 2.6 36.4 + - - -
249A MET 3.7 2.5 - - - -
251A GLU* 1.3 78.3 - - - +
253A ILE* 1.3 60.1 + - - +
255A GLU* 3.5 7.8 + - - +
256A ALA* 3.2 18.7 + - - +
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Residues in contact with ILE 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A TRP* 4.2 7.9 - - + -
185A LEU* 4.2 14.1 - - + -
187A LEU* 4.2 16.2 - - + -
192A ILE* 3.7 31.2 - - + -
208A LEU* 5.0 2.7 - - + -
211A ILE* 4.7 5.2 - - + -
214A CYS* 4.3 14.1 - - + -
221A PHE* 3.4 35.0 - - + -
223A ILE* 5.2 0.2 - - + -
249A MET* 2.9 25.4 + - + +
250A HIS 3.9 1.8 - - - +
252A THR* 1.3 70.7 - - - +
254A LEU* 1.3 62.8 + - - +
256A ALA* 2.8 24.2 + - - +
257A MET* 2.9 20.7 + - + +
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Residues in contact with LEU 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A CYS* 4.4 4.7 - - - +
250A HIS* 2.8 47.9 + - + +
251A GLU* 3.6 6.1 - - - +
253A ILE* 1.3 71.5 - - - +
255A GLU* 1.3 58.3 + - - +
257A MET* 2.8 45.8 + - + +
258A ARG* 2.9 57.4 + - + +
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Residues in contact with GLU 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A GLU 2.8 17.4 + - - +
252A THR* 3.6 8.5 - - - +
254A LEU* 1.3 76.6 - - - +
256A ALA* 1.3 54.1 + - - +
258A ARG* 4.4 7.9 + - - +
259A ALA* 2.7 43.7 + - + +
212B ARG* 2.7 40.2 + - - -
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Residues in contact with ALA 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A LYS* 4.7 8.7 - - - +
187A LEU* 4.1 16.4 - - + -
188A THR 5.0 0.9 - - - +
189A SER 4.5 2.9 - - - +
208A LEU* 3.7 23.2 - - + +
252A THR 3.2 12.1 + - - +
253A ILE* 2.8 17.6 + - - +
255A GLU* 1.3 77.0 - - - +
257A MET* 1.3 61.8 + - - +
259A ALA* 4.2 5.2 - - - +
260A MET* 3.4 22.9 + - - +
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Residues in contact with MET 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A LEU* 4.4 26.7 - - + +
211A ILE* 3.8 39.7 - - + +
212A ARG 4.1 11.9 - - - +
213A ARG* 4.4 5.4 - - - -
214A CYS* 4.1 21.5 - - - +
253A ILE* 2.9 20.3 + - + +
254A LEU* 2.8 22.7 + - + +
256A ALA* 1.3 78.1 - - - +
258A ARG* 1.3 62.6 + - + +
260A MET* 3.2 31.1 + - + +
261A SER* 4.3 1.4 + - - -
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Residues in contact with ARG 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A LEU* 2.9 53.7 + - + +
255A GLU* 4.0 5.6 + - - +
257A MET* 1.3 72.2 - - + +
259A ALA* 1.3 61.8 + - - +
260A MET 3.0 6.1 + - - -
261A SER* 3.0 24.7 + - - -
262A ASP* 3.5 0.3 - - - +
212B ARG* 2.9 61.6 + - - +
213B ARG* 3.6 44.3 - - - +
214B CYS 5.8 0.6 + - - -
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Residues in contact with ALA 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255A GLU* 2.7 35.6 + - + +
256A ALA* 4.2 7.0 - - - +
257A MET 3.4 0.2 - - - -
258A ARG* 1.3 72.3 - - - +
260A MET* 1.3 63.1 + - - +
261A SER 3.2 0.4 - - - -
262A ASP* 3.2 22.0 + - + +
212B ARG* 3.1 13.4 - - - +
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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
------------------------------------------------------------
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