Contacts of the strand formed by residues 244 - 249 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179G LYS* 3.9 11.7 - - - +
91J ASN* 3.6 29.1 + - - +
186J THR* 3.7 1.2 + - - +
187J ARG* 3.5 2.3 - - - -
188J ASN* 2.9 45.8 + - - +
189J ASN* 4.7 11.6 + - - +
242J GLY 4.7 1.3 - - - +
243J ASP* 1.3 75.1 - - - +
245J PHE* 1.3 64.6 + - - +
246J GLU* 2.8 37.8 + - - +
256J ALA* 3.9 10.9 - - - +
257J ALA 3.5 4.0 - - - +
258J THR* 3.7 24.4 + - + +
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Residues in contact with PHE 245 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104J ILE* 3.0 45.1 - - + -
137J LEU* 4.4 13.0 - - + +
185J MET* 4.2 12.8 - - + -
186J THR 3.4 12.6 - - - -
187J ARG* 3.6 28.9 - - + -
192J VAL* 4.4 2.2 - - + -
237J VAL* 3.5 12.8 - - + -
238J ALA 3.8 13.5 - - - -
239J VAL* 3.9 11.0 - - + -
243J ASP* 3.5 22.9 - - + -
244J ARG* 1.3 77.0 - - - +
246J GLU* 1.3 61.8 + - - +
256J ALA* 3.2 4.9 - - - +
257J ALA* 2.8 39.2 + - + +
259J PHE* 3.8 16.4 - + + -
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Residues in contact with GLU 246 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179G LYS* 3.4 18.0 + - - -
180G ASN* 5.2 1.9 - - - +
137J LEU* 5.2 0.4 - - - -
184J LYS 4.0 0.7 - - - +
185J MET* 3.2 4.0 - - - -
186J THR* 2.8 44.7 + - - +
244J ARG* 2.8 35.3 + - - +
245J PHE* 1.3 76.1 - - - +
247J ALA* 1.3 62.9 + - - +
248J HIS* 3.6 32.3 + - + +
254J SER* 4.0 13.2 + - - -
255J VAL 3.2 10.9 - - - +
256J ALA* 4.4 2.6 - - + +
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Residues in contact with ALA 247 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106J ALA* 3.8 21.5 - - + -
137J LEU* 3.8 24.6 - - + +
183J MET* 4.8 1.3 - - + -
184J LYS 3.3 8.3 - - - +
185J MET* 4.1 6.3 - - + -
246J GLU* 1.3 75.0 - - - +
248J HIS* 1.3 62.6 + - - +
249J ILE* 5.2 2.7 - - + -
254J SER* 3.1 8.7 - - - -
255J VAL* 2.8 39.4 + - + +
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Residues in contact with HIS 248 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182J ALA 3.4 1.7 - - - +
183J MET* 3.2 7.8 - - - +
184J LYS* 2.8 43.1 + - + +
186J THR* 5.8 6.3 - - + -
246J GLU* 3.6 33.9 - - + +
247J ALA* 1.3 79.6 - - - +
249J ILE* 1.3 63.4 + - - +
250J GLU 4.0 0.4 - - - +
253J GLY 3.6 4.5 + - - +
254J SER* 3.9 12.0 - - - -
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Residues in contact with ILE 249 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106J ALA* 4.7 4.7 - - + -
107J GLU 3.5 28.3 - - - +
108J ILE* 4.4 3.1 - - + -
135J PRO* 3.7 23.1 - - + -
136J ALA 4.4 2.7 - - - +
181J CYS* 4.0 17.3 - - + +
182J ALA 3.5 4.0 - - - +
183J MET* 4.1 8.5 - - + -
233J LEU* 3.8 23.3 - - + -
247J ALA* 4.2 1.1 - - + +
248J HIS* 1.3 77.5 - - - +
250J GLU* 1.3 59.7 + - - +
251J GLY 3.3 0.7 + - - -
252J ILE* 2.9 37.7 + - + -
253J GLY 2.8 39.9 + - - +
255J VAL* 4.9 4.0 - - + -
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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