Contacts of the strand formed by residues 244 - 249 (chain M) in PDB entry 2WQT
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 244 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91M ASN* 3.4 30.3 + - - +
186M THR* 3.7 1.4 + - - +
187M ARG* 3.5 1.9 - - - -
188M ASN* 2.8 46.3 + - - +
189M ASN* 4.7 11.6 + - - +
242M GLY 4.8 1.1 - - - +
243M ASP* 1.3 74.7 - - - +
245M PHE* 1.3 63.7 + - - +
246M GLU* 2.8 38.1 + - - +
256M ALA* 3.9 10.4 - - - +
257M ALA 3.5 4.5 - - - +
258M THR* 3.6 24.4 + - + +
179O LYS* 3.8 11.3 - - - +
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Residues in contact with PHE 245 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104M ILE* 3.1 45.8 - - + -
137M LEU* 4.4 13.2 - - + +
185M MET* 4.2 13.0 - - + -
186M THR 3.3 14.6 - - - -
187M ARG* 3.6 29.6 - - + -
192M VAL* 4.3 2.0 - - + -
237M VAL* 3.5 12.6 - - + -
238M ALA 3.8 13.7 - - - -
239M VAL* 4.0 10.1 - - + -
243M ASP* 3.5 24.7 - - + -
244M ARG* 1.3 76.9 - - - +
246M GLU* 1.3 61.3 + - - +
255M VAL 4.6 0.2 - - - -
256M ALA* 3.2 4.5 - - - +
257M ALA* 2.8 38.9 + - + +
259M PHE* 3.9 16.2 - + + -
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Residues in contact with GLU 246 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137M LEU* 5.2 0.4 - - - -
184M LYS 4.0 0.5 - - - +
185M MET* 3.2 4.5 - - - -
186M THR* 2.8 48.5 + - - +
244M ARG* 2.8 34.7 + - - +
245M PHE* 1.3 76.4 - - - +
247M ALA* 1.3 63.3 + - - +
248M HIS* 3.6 31.6 + - + +
254M SER* 3.9 12.1 + - - -
255M VAL 3.2 8.4 - - - +
256M ALA* 4.3 2.8 - - + +
179O LYS* 3.1 20.6 + - - -
180O ASN* 5.1 1.6 - - - +
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Residues in contact with ALA 247 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106M ALA* 3.8 20.6 - - + -
137M LEU* 3.8 24.6 - - + +
183M MET* 4.8 2.2 - - + -
184M LYS 3.3 8.3 - - - +
185M MET* 4.1 7.2 - - + -
246M GLU* 1.3 75.1 - - - +
248M HIS* 1.3 63.0 + - - +
249M ILE* 5.2 2.0 - - + -
254M SER* 3.2 8.1 - - - -
255M VAL* 2.9 38.0 + - + +
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Residues in contact with HIS 248 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182M ALA 3.5 1.7 - - - +
183M MET* 3.2 6.9 - - - +
184M LYS* 2.8 42.5 + - + +
186M THR* 5.9 4.7 - - + -
246M GLU* 3.6 34.8 - - + +
247M ALA* 1.3 80.1 - - - +
249M ILE* 1.3 63.6 + - - +
250M GLU 4.0 0.4 - - - -
253M GLY 3.6 4.4 + - - +
254M SER* 3.9 12.6 - - - -
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Residues in contact with ILE 249 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106M ALA* 4.6 5.8 - - + -
107M GLU 3.6 28.0 - - - +
108M ILE* 4.5 3.1 - - + -
135M PRO* 3.8 21.8 - - + -
136M ALA 4.5 2.5 - - - +
181M CYS* 3.9 17.5 - - + +
182M ALA 3.5 4.5 - - - +
183M MET* 4.0 8.1 - - + -
233M LEU* 3.7 24.7 - - + -
247M ALA* 5.2 0.7 - - + -
248M HIS* 1.3 78.3 - - - +
250M GLU* 1.3 62.8 + - - +
251M GLY 3.4 0.5 + - - -
252M ILE* 3.0 32.3 + - + -
253M GLY* 2.8 38.1 + - - +
255M VAL* 4.9 4.7 - - + -
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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