Contacts of the strand formed by residues 244 - 249 (chain N) 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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179M LYS* 3.5 15.8 - - - +
91N ASN* 3.5 30.1 + - - +
186N THR* 3.7 1.4 + - - +
187N ARG* 3.5 2.1 - - - -
188N ASN* 2.8 45.6 + - - +
189N ASN* 4.7 12.3 + - - +
242N GLY 3.5 1.3 + - - +
243N ASP* 1.3 72.7 - - - +
245N PHE* 1.3 65.2 + - - +
246N GLU* 2.8 34.7 + - - +
256N ALA* 3.9 9.7 - - - +
257N ALA 3.5 5.2 - - - +
258N THR* 3.7 23.4 + - + +
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Residues in contact with PHE 245 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104N ILE* 3.0 46.0 - - + -
137N LEU* 4.6 13.7 - - + -
185N MET* 4.2 13.2 - - + -
186N THR 3.4 12.1 - - - -
187N ARG* 3.6 30.1 - - + -
192N VAL* 4.4 2.0 - - + -
237N VAL* 3.5 12.8 - - + -
238N ALA 3.8 12.8 - - - -
239N VAL* 4.0 9.9 - - + -
243N ASP* 3.5 24.7 - - + -
244N ARG* 1.3 78.2 - - - +
246N GLU* 1.3 62.0 + - - +
256N ALA* 3.2 5.5 - - - +
257N ALA* 2.8 38.9 + - + +
259N PHE* 3.9 15.0 - + + -
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Residues in contact with GLU 246 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179M LYS* 3.4 17.2 + - - -
180M ASN* 5.0 2.4 - - - +
137N LEU* 5.3 0.4 - - - -
184N LYS 3.9 0.5 - - - +
185N MET* 3.3 3.7 - - - -
186N THR* 2.8 48.2 + - - +
244N ARG* 2.8 33.9 + - - +
245N PHE* 1.3 76.6 - - - +
247N ALA* 1.3 63.9 + - - +
248N HIS* 3.6 31.9 + - + +
254N SER* 3.9 14.2 + - - -
255N VAL 3.2 9.3 - - - +
256N ALA* 4.3 2.4 - - + +
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Residues in contact with ALA 247 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106N ALA* 3.8 21.3 - - + -
137N LEU* 3.8 25.0 - - + +
183N MET* 4.9 1.8 - - + -
184N LYS 3.3 7.6 - - - +
185N MET* 4.1 7.0 - - + -
246N GLU* 1.3 74.0 - - - +
248N HIS* 1.3 63.4 + - - +
249N ILE* 5.3 2.5 - - + -
254N SER* 3.1 8.8 - - - -
255N VAL* 2.9 37.7 + - + +
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Residues in contact with HIS 248 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182N ALA 3.5 1.0 - - - +
183N MET* 3.2 7.4 - - - +
184N LYS* 2.8 45.6 + - + +
186N THR* 5.9 5.6 - - + -
246N GLU* 3.6 35.0 - - + +
247N ALA* 1.3 79.7 - - - +
249N ILE* 1.3 63.0 + - - +
250N GLU 4.0 0.4 - - - -
253N GLY 3.7 4.4 + - - +
254N SER* 3.9 12.2 - - - -
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Residues in contact with ILE 249 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106N ALA* 4.7 5.6 - - + -
107N GLU 3.6 26.7 - - - +
108N ILE* 4.5 3.8 - - + -
135N PRO* 3.8 22.9 - - + -
136N ALA 4.5 1.8 - - - +
181N CYS* 3.9 17.7 - - + +
182N ALA 3.5 4.3 - - - +
183N MET* 4.0 8.1 - - + -
233N LEU* 3.8 24.5 - - + -
247N ALA* 5.3 1.6 - - + +
248N HIS* 1.3 77.2 - - - +
250N GLU* 1.3 68.4 + - - +
251N GLY 3.3 0.7 + - - -
252N ILE* 3.0 31.7 + - + -
253N GLY 2.8 36.1 + - - +
255N VAL* 5.0 4.3 - - + -
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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
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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