Contacts of the strand formed by residues 244 - 249 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179K LYS* 3.7 14.8 - - - +
91L ASN* 3.3 30.3 + - - +
186L THR* 3.8 1.0 + - - +
187L ARG* 3.5 1.8 - - - -
188L ASN* 2.9 42.5 + - - +
189L ASN* 4.8 11.6 + - - +
242L GLY 3.5 1.5 + - - +
243L ASP* 1.3 73.0 - - - +
245L PHE* 1.3 64.6 + - - +
246L GLU* 2.8 35.1 + - - +
256L ALA* 3.9 8.0 - - - +
257L ALA 3.6 3.6 - - - +
258L THR* 3.6 24.3 + - + +
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Residues in contact with PHE 245 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104L ILE* 3.1 42.4 - - + -
137L LEU* 4.2 11.9 - - + +
185L MET* 4.6 11.9 - - + -
186L THR 3.4 13.2 - - - -
187L ARG* 3.5 33.7 - - + -
192L VAL* 4.4 0.9 - - + -
237L VAL* 3.6 10.5 - - + -
238L ALA 3.8 14.1 - - - -
239L VAL* 3.8 11.9 - - + -
243L ASP* 3.5 22.7 - - + -
244L ARG* 1.3 73.4 - - - +
246L GLU* 1.3 60.7 + - - +
255L VAL 4.0 0.2 - - - +
256L ALA* 3.2 4.7 - - - +
257L ALA* 2.8 38.8 + - + +
259L PHE* 3.7 23.1 - + + -
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Residues in contact with GLU 246 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179K LYS* 2.7 27.5 + - - -
180K ASN* 4.7 2.8 - - - +
137L LEU* 5.1 0.4 - - - -
184L LYS 3.8 0.5 - - - +
185L MET* 3.3 5.0 - - - +
186L THR* 2.9 45.4 + - - +
244L ARG* 2.8 29.6 + - - +
245L PHE* 1.3 75.2 - - - +
247L ALA* 1.3 65.7 + - - +
248L HIS* 3.5 29.2 - - + +
254L SER* 3.7 15.8 + - - -
255L VAL 3.3 8.2 - - - +
256L ALA* 4.1 4.1 - - + +
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Residues in contact with ALA 247 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106L ALA* 3.8 21.5 - - + -
137L LEU* 3.6 26.6 - - + +
183L MET* 4.9 0.2 - - - -
184L LYS 3.2 7.2 - - - +
185L MET* 4.2 5.8 - - + -
246L GLU* 1.3 76.5 - - - +
248L HIS* 1.3 64.0 + - - +
249L ILE* 4.2 2.4 + - + -
254L SER* 3.1 7.4 - - - -
255L VAL* 2.8 41.6 + - + +
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Residues in contact with HIS 248 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182L ALA 3.5 1.4 - - - +
183L MET* 3.2 4.5 - - - +
184L LYS* 2.8 54.4 + - + +
186L THR* 5.4 7.7 + - + +
246L GLU* 3.5 35.4 - - + +
247L ALA* 1.3 78.8 - - - +
249L ILE* 1.3 64.1 + - - +
250L GLU 4.0 1.1 - - - +
253L GLY 3.7 4.7 + - - +
254L SER* 3.8 12.4 - - - -
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Residues in contact with ILE 249 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106L ALA* 4.5 6.3 - - + -
107L GLU 3.5 29.6 - - - +
108L ILE* 4.3 3.6 - - + -
135L PRO* 3.8 21.1 - - + -
136L ALA 4.4 2.2 - - - +
181L CYS* 4.0 20.2 - - + +
182L ALA 3.5 2.2 - - - +
183L MET* 3.8 8.1 - - + -
233L LEU* 3.7 26.2 - - + -
247L ALA* 5.3 0.7 - - + -
248L HIS* 1.3 77.2 - - - +
250L GLU* 1.3 69.0 + - - +
251L GLY 3.3 0.2 + - - -
252L ILE* 2.9 43.5 + - + -
253L GLY 2.8 21.7 + - - +
255L VAL* 5.0 3.8 - - + -
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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