Contacts of the helix formed by residues 255 - 264 (chain A) in PDB entry 1QMU
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 GLY 255 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A ASN* 3.1 23.2 + - - -
147A PHE* 3.3 9.6 - - - +
148A PRO 5.0 1.4 - - - +
149A ASP* 4.4 1.2 + - - -
192A ASP* 5.0 7.8 - - - +
252A VAL* 4.3 10.8 + - - -
253A PRO 3.4 3.6 - - - -
254A GLY* 1.3 83.3 - - - +
256A MET* 1.3 64.0 + - - -
257A GLN 3.4 2.5 - - - -
258A ASP* 4.1 6.2 + - - +
259A TRP* 3.7 11.6 + - - +
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Residues in contact with MET 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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70A ILE* 3.9 22.0 - - + -
73A MET* 3.9 11.2 - - + +
116A MET* 3.9 17.7 - - - +
144A ASN* 3.0 13.5 + - - +
147A PHE* 3.4 44.6 - - + -
165A VAL* 4.1 13.2 - - - -
169A LEU* 5.0 1.1 - - + -
179A ASN* 3.1 44.4 - - + +
255A GLY* 1.3 71.8 - - - -
257A GLN* 1.3 63.5 + - - +
259A TRP* 3.2 2.4 + - - +
260A ASN* 2.8 41.9 + - - +
268A GLU* 3.5 3.4 - - - +
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Residues in contact with GLN 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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144A ASN* 4.5 1.5 + - - +
179A ASN* 4.2 2.2 - - - +
188A ASN* 3.1 21.0 + - - +
189A TYR 3.3 4.4 - - - -
190A PRO* 3.0 35.2 - - + +
192A ASP* 3.2 24.7 + - - +
255A GLY 3.4 0.2 - - - -
256A MET* 1.3 80.1 - - - +
258A ASP* 1.3 75.3 + - - +
260A ASN* 3.5 15.1 - - - +
261A TYR* 3.8 5.7 + - - +
268A GLU* 3.3 37.1 + - + +
270A THR* 2.6 35.0 + - - +
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Residues in contact with ASP 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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149A ASP* 5.7 4.7 - - - +
150A GLN* 4.1 1.5 + - + +
190A PRO* 3.3 12.0 - - - +
191A PHE* 3.2 25.0 - - + +
192A ASP* 2.8 33.2 + - + +
193A ASP* 4.0 8.9 - - - +
255A GLY* 4.1 7.1 + - - +
256A MET 3.4 0.2 - - - -
257A GLN* 1.3 99.0 + - - +
259A TRP* 1.3 69.7 + - - +
261A TYR* 3.3 6.6 + - - +
262A LEU* 3.0 34.2 + - + +
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Residues in contact with TRP 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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147A PHE* 3.6 21.8 - + + -
148A PRO* 3.3 51.2 + - + +
166A MET* 3.9 36.1 - - + -
169A LEU* 3.7 36.6 - - + -
170A LYS* 4.0 25.6 - - - -
255A GLY 3.7 10.3 + - - +
256A MET 3.2 9.1 + - - +
258A ASP* 1.3 80.1 - - - +
260A ASN* 1.3 73.2 + - - +
262A LEU* 4.8 2.0 - - - -
263A ASN* 2.9 56.8 + - + +
264A THR* 4.2 8.3 - - + -
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Residues in contact with ASN 260 (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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68A LYS* 2.8 25.3 + - - -
169A LEU* 3.1 22.7 - - - +
256A MET* 2.8 30.3 + - - +
257A GLN 3.5 8.5 - - - +
259A TRP* 1.3 88.6 - - - +
261A TYR* 1.3 56.9 + - - +
264A THR* 2.8 39.9 + - - +
266A CYS* 3.6 16.5 - - - +
268A GLU* 3.2 35.4 + - + -
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Residues in contact with TYR 261 (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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190A PRO* 5.4 4.0 - - + -
191A PHE* 4.0 15.7 - + + -
204A SER* 4.6 2.2 - - - -
205A PRO* 3.6 18.3 - - + +
206A ASP* 2.5 40.5 + - + -
210A PHE* 3.7 31.4 - + + -
257A GLN 3.8 6.5 + - - +
258A ASP* 3.3 9.6 + - - +
259A TRP 3.3 0.2 - - - -
260A ASN* 1.3 78.8 - - - +
262A LEU* 1.3 76.0 + - + +
264A THR 3.0 19.2 - - - +
266A CYS 3.3 9.4 - - - +
267A PHE* 3.6 15.9 - + - -
268A GLU 5.4 0.9 - - - +
331A HIS* 3.0 61.4 + + - +
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Residues in contact with LEU 262 (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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148A PRO 5.8 2.2 - - - +
150A GLN* 3.4 48.5 - - + +
191A PHE* 3.9 16.6 - - + -
258A ASP* 3.0 23.8 + - + +
259A TRP* 5.3 0.9 - - - -
261A TYR* 1.3 99.1 - - + +
263A ASN* 1.3 72.0 + - - +
331A HIS* 4.9 4.3 - - + -
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Residues in contact with ASN 263 (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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148A PRO* 5.7 1.8 - - - +
170A LYS* 3.6 21.0 + - - +
259A TRP* 2.9 64.3 + - + +
262A LEU* 1.3 92.2 - - - +
264A THR* 1.3 66.5 + - - +
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Residues in contact with THR 264 (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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169A LEU* 3.7 36.6 - - + +
170A LYS* 4.6 8.5 - - + -
174A PHE 5.6 0.2 - - - -
259A TRP* 4.2 11.9 - - + -
260A ASN* 2.8 20.3 + - - +
261A TYR 3.0 19.4 - - - +
263A ASN* 1.3 85.5 - - - +
265A ASN* 1.3 64.4 + - - +
266A CYS* 3.1 23.0 + - - +
331A HIS* 4.4 3.3 + - - -
334A THR* 6.0 0.4 - - - -
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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