Contacts of the strand formed by residues 244 - 249 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179F LYS* 3.4 19.4 - - - +
91G ASN* 3.0 30.9 + - - +
186G THR* 3.8 0.7 + - - +
187G ARG* 3.4 2.4 - - - -
188G ASN* 2.8 47.1 + - - +
189G ASN* 4.7 4.8 + - - +
242G GLY 3.5 1.5 + - - +
243G ASP* 1.3 74.9 - - - +
245G PHE* 1.3 64.3 + - - +
246G GLU* 2.7 32.2 + - - +
256G ALA* 3.6 9.4 - - - +
257G ALA 3.5 4.9 - - - +
258G THR* 3.7 23.6 + - + +
1264G PO4 4.4 7.1 + - - -
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Residues in contact with PHE 245 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104G ILE* 3.0 46.0 - - + -
137G LEU* 4.2 13.5 - - + +
185G MET* 4.3 11.2 - - + -
186G THR 3.2 15.5 - - - -
187G ARG* 3.4 32.5 - - + -
192G VAL* 4.4 1.8 - - + -
237G VAL* 3.4 10.8 - - + -
238G ALA 3.7 14.1 - - - -
239G VAL* 4.0 11.2 - - + -
243G ASP* 3.4 25.4 - - + -
244G ARG* 1.3 77.9 - - - +
246G GLU* 1.3 60.3 + - - +
256G ALA* 3.2 4.7 - - - +
257G ALA* 2.7 38.5 + - + +
259G PHE* 3.9 15.0 - + + -
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Residues in contact with GLU 246 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179F LYS* 3.3 22.2 + - - -
180F ASN* 4.9 3.3 - - - +
137G LEU* 5.0 0.2 - - - -
185G MET* 3.3 4.5 - - - -
186G THR* 2.7 39.2 + - - +
244G ARG* 2.7 25.3 + - - +
245G PHE* 1.3 74.3 - - - +
247G ALA* 1.3 61.8 + - - +
248G HIS* 3.2 26.1 - - + +
254G SER* 4.1 8.0 + - - -
255G VAL 3.1 18.8 - - - +
256G ALA* 3.7 6.5 - - + -
1264G PO4 3.0 38.1 + - - +
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Residues in contact with ALA 247 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106G ALA* 3.6 24.2 - - + -
137G LEU* 3.5 26.8 - - + +
183G MET* 5.0 0.2 - - - -
184G LYS 3.5 5.2 - - - +
185G MET* 4.1 5.2 - - + -
246G GLU* 1.3 74.1 - - - +
248G HIS* 1.3 63.1 + - - +
249G ILE* 4.1 3.1 - - + -
254G SER* 3.1 9.0 - - - -
255G VAL* 2.8 41.9 + - + +
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Residues in contact with HIS 248 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182G ALA 3.4 2.4 - - - +
183G MET* 3.3 4.0 - - - -
184G LYS* 2.8 45.3 + - + +
186G THR* 4.9 5.2 - - + -
246G GLU* 3.2 33.0 - - + +
247G ALA* 1.3 76.2 - - - +
249G ILE* 1.3 61.9 + - - +
250G GLU 3.9 0.6 + - - -
253G GLY 3.7 4.7 - - - +
254G SER* 3.6 13.1 - - - -
1264G PO4 3.1 35.2 + - - -
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Residues in contact with ILE 249 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106G ALA* 4.7 4.7 - - + -
107G GLU 3.5 28.0 - - - +
108G ILE* 4.5 3.4 - - + -
135G PRO* 3.8 22.0 - - + -
136G ALA 4.6 2.0 - - - +
181G CYS* 3.8 21.5 - - + +
182G ALA 3.4 3.6 - - - +
183G MET* 3.9 9.4 - - + -
233G LEU* 3.7 25.8 - - + -
247G ALA* 5.2 0.7 - - + -
248G HIS* 1.3 75.7 - - - +
250G GLU* 1.3 64.5 + - - +
251G GLY 3.3 0.2 + - - -
252G ILE* 3.0 42.0 + - + -
253G GLY 2.9 20.7 + - - +
255G VAL* 5.1 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