Contacts of the helix formed by residues 237 - 244 (chain A) in PDB entry 1QQJ
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 237 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A HIS* 5.1 1.0 - - - -
141A PHE* 6.2 3.1 - - + -
195A LEU* 2.9 32.9 + - + +
197A ASP* 2.9 35.0 + - + +
199A GLU* 2.7 34.7 + - - +
235A SER* 3.9 10.4 + - - +
236A ALA* 1.3 73.5 - - - +
238A ASP* 1.3 57.7 + - - +
240A GLN* 3.7 14.5 + - - +
241A GLN* 2.9 30.1 + - - +
361A SER* 3.7 9.7 - - - -
363A LEU* 3.7 33.3 - - + +
383A PHE* 4.2 11.7 - - + -
2004A CAC 2.8 32.1 + - - +
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Residues in contact with ASP 238 (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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180A MET* 3.7 32.7 - - + +
181A ARG 4.9 0.9 + - - -
193A CYS* 3.4 26.0 - - - +
194A ARG* 2.8 32.3 + - - +
195A LEU* 3.4 23.5 + - + +
237A ARG* 1.3 72.7 + - - +
239A ILE* 1.3 68.5 + - - +
241A GLN* 3.6 5.4 + - - +
242A TRP* 3.5 20.3 + - - +
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Residues in contact with ILE 239 (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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176A PRO* 4.2 14.8 - - + +
177A MET 3.9 24.7 - - - +
178A GLY* 4.0 8.5 - - - +
179A GLN 3.8 19.5 - - - +
180A MET* 3.8 20.0 - - + -
193A CYS* 4.3 3.8 - - + -
236A ALA* 3.2 25.4 + - + +
238A ASP* 1.3 74.9 + - - +
240A GLN* 1.3 67.4 + - - +
241A GLN 3.4 0.2 + - - -
242A TRP* 3.4 4.2 + - - +
243A GLU* 3.2 23.9 + - + +
251A LEU* 4.1 18.2 - - + +
252A GLY 3.8 19.7 - - - +
336B ASN* 5.2 1.6 - - + -
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Residues in contact with GLN 240 (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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235A SER* 4.5 3.6 - - - -
236A ALA 2.8 15.8 + - - +
237A ARG* 3.7 19.1 + - - +
239A ILE* 1.3 77.2 - - - +
241A GLN* 1.3 64.4 + - - +
243A GLU* 3.2 15.8 + - - +
244A TYR* 3.0 48.4 + - + +
249A PRO* 3.7 21.4 - - + +
252A GLY* 4.1 6.8 - - - +
253A LYS* 3.5 22.5 - - - +
2004A CAC 3.0 36.1 + - - +
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Residues in contact with GLN 241 (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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141A PHE* 3.6 34.8 - - + +
237A ARG 2.9 22.0 + - - +
238A ASP* 4.0 7.0 - - - +
239A ILE 3.3 0.6 - - - -
240A GLN* 1.3 74.4 - - - +
242A TRP* 1.3 61.4 + - - +
244A TYR* 3.5 37.4 + - - -
245A VAL* 5.1 1.4 + - - +
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Residues in contact with TRP 242 (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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179A GLN* 2.9 42.2 + - - -
180A MET* 4.1 4.0 - - - -
181A ARG* 3.5 55.2 - - + +
184A ASN* 5.5 1.1 - - - -
188A PRO* 3.5 16.0 - - + +
238A ASP 3.5 12.8 + - - +
239A ILE 3.4 3.7 + - - +
240A GLN 3.2 0.4 - - - -
241A GLN* 1.3 80.8 - - - +
243A GLU* 1.3 57.8 - - + +
245A VAL 5.2 0.2 + - - -
150B PRO* 3.5 27.4 - - + -
151B ASN* 3.0 43.4 + - + +
154B HIS* 3.8 21.8 - + + -
155B LEU* 3.6 19.5 - - + +
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Residues in contact with GLU 243 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239A ILE* 3.2 16.4 + - + +
240A GLN* 3.2 14.2 + - - +
242A TRP* 1.3 80.5 - - + +
244A TYR* 1.3 71.1 + - + +
245A VAL 3.5 3.4 + - - +
247A LEU 5.3 0.5 + - - -
248A GLY 4.5 2.5 - - - +
249A PRO* 4.0 1.0 - - - +
250A PHE* 2.9 25.7 + - + +
251A LEU* 2.9 34.6 + - - +
252A GLY* 2.8 27.8 + - - -
151B ASN* 3.3 14.9 + - - +
155B LEU* 4.6 20.6 - - + +
157B VAL* 4.8 10.4 - - - +
332B HIS* 5.0 4.0 + - + +
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Residues in contact with TYR 244 (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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141A PHE* 5.8 4.5 - - - +
240A GLN* 3.0 35.6 + - + +
241A GLN* 3.5 42.0 + - - -
242A TRP 3.6 0.8 - - - -
243A GLU* 1.3 78.0 - - + +
245A VAL* 1.3 82.2 + - + +
246A PRO 3.6 1.0 - - - -
247A LEU 3.3 1.4 + - - -
248A GLY* 2.8 51.7 + - - +
249A PRO* 3.9 9.9 - - + -
2001A ACT 4.5 21.2 + - + +
246B PRO* 3.7 33.1 - - + +
247B LEU* 5.7 0.9 - - + -
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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