Contacts of the strand formed by residues 244 - 249 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91F ASN* 3.1 34.8 + - - +
186F THR 3.8 0.9 - - - +
187F ARG* 3.5 1.7 - - - -
188F ASN* 2.8 47.3 + - - +
189F ASN* 4.5 13.9 + - - +
242F GLY 3.5 1.8 + - - +
243F ASP* 1.3 74.1 - - - +
245F PHE* 1.3 62.8 + - - +
246F GLU* 3.2 35.5 + - + +
256F ALA* 3.6 15.4 - - - +
257F ALA 3.5 7.2 - - - -
258F THR* 3.7 23.6 - - + +
179I LYS* 3.6 10.9 - - - +
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Residues in contact with PHE 245 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104F ILE* 2.9 46.2 - - + -
137F LEU* 4.1 13.0 - - + +
185F MET* 4.3 11.9 - - - -
186F THR 3.5 11.9 - - - -
187F ARG* 3.4 33.0 - - + -
192F VAL* 4.4 2.2 - - + -
237F VAL* 3.5 10.1 - - + -
238F ALA 3.7 13.2 - - - -
239F VAL* 3.9 11.9 - - + -
243F ASP* 3.5 27.4 - - + -
244F ARG* 1.3 73.2 - - - +
246F GLU* 1.3 60.4 + - - +
255F VAL 4.0 0.2 - - - +
256F ALA* 3.2 5.0 - - - +
257F ALA* 2.7 38.0 + - + +
259F PHE* 3.8 15.7 - + + -
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Residues in contact with GLU 246 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184F LYS 3.9 1.0 - - - +
185F MET* 3.4 3.9 - - - -
186F THR* 2.9 44.8 + - - +
189F ASN* 4.8 8.9 - - - +
244F ARG* 3.2 26.3 + - + +
245F PHE* 1.3 76.2 - - - +
247F ALA* 1.3 68.0 + - - +
248F HIS* 5.9 1.3 - - + -
254F SER* 4.4 11.4 + - - -
255F VAL 3.3 9.7 - - - +
256F ALA* 3.9 6.9 - - + +
179I LYS* 2.9 26.4 + - - -
180I ASN* 5.3 0.5 - - - +
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Residues in contact with ALA 247 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106F ALA* 3.7 29.6 - - + -
137F LEU* 3.8 16.9 - - + +
183F MET* 4.9 0.9 - - + -
184F LYS 3.4 5.2 - - - +
185F MET* 4.0 9.6 - - + -
246F GLU* 1.3 77.4 - - - +
248F HIS* 1.3 62.0 + - - +
249F ILE* 4.9 2.2 - - + -
254F SER* 3.1 8.2 - - - -
255F VAL* 2.9 38.6 + - + +
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Residues in contact with HIS 248 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182F ALA 3.6 2.5 - - - +
183F MET* 3.3 4.9 - - - +
184F LYS* 2.9 41.3 + - + +
246F GLU* 5.2 1.8 - - + +
247F ALA* 1.3 74.6 - - - +
249F ILE* 1.3 66.4 + - - +
250F GLU* 4.2 24.1 - - + +
251F GLY 5.4 1.8 - - - -
253F GLY* 3.5 18.3 + - - -
254F SER* 4.1 11.0 - - - -
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Residues in contact with ILE 249 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106F ALA* 4.6 5.8 - - + -
107F GLU 3.6 27.6 - - - +
108F ILE* 4.5 3.1 - - + -
135F PRO* 3.8 20.9 - - + -
136F ALA 4.5 2.5 - - - +
181F CYS* 4.1 13.2 - - + +
182F ALA 3.5 4.7 - - - +
183F MET* 4.0 8.7 - - + -
233F LEU* 3.8 28.3 - - + -
247F ALA* 4.9 1.6 - - + -
248F HIS* 1.3 83.2 - - - +
250F GLU* 1.3 64.8 + - - +
251F GLY 3.4 0.7 + - - -
252F ILE* 3.1 28.5 + - + -
253F GLY 2.8 39.2 + - - +
255F VAL* 4.9 3.6 - - + -
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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