Contacts of the strand formed by residues 244 - 249 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179B LYS* 3.7 11.9 - - - +
91E ASN* 3.5 29.3 + - - +
186E THR* 3.8 1.0 + - - +
187E ARG* 3.5 2.4 - - - -
188E ASN* 2.8 45.7 + - - +
189E ASN* 4.7 12.4 + - - +
242E GLY 4.8 1.1 - - - +
243E ASP* 1.3 74.3 - - - +
245E PHE* 1.3 63.7 + - - +
246E GLU* 2.8 39.4 + - - +
256E ALA* 3.9 10.4 - - - +
257E ALA 3.4 4.7 - - - +
258E THR* 3.5 25.1 + - + +
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Residues in contact with PHE 245 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104E ILE* 3.0 45.1 - - + -
137E LEU* 4.4 13.9 - - + +
185E MET* 4.3 13.0 - - + -
186E THR 3.4 13.0 - - - -
187E ARG* 3.6 29.4 - - + -
192E VAL* 4.4 2.2 - - + -
237E VAL* 3.5 13.0 - - + -
238E ALA 3.8 13.0 - - - -
239E VAL* 3.9 10.3 - - + -
243E ASP* 3.5 23.8 - - + -
244E ARG* 1.3 78.2 - - - +
246E GLU* 1.3 60.6 + - - +
255E VAL 4.5 0.2 - - - -
256E ALA* 3.1 5.5 - - - +
257E ALA* 2.7 38.0 + - + +
259E PHE* 3.9 15.0 - + + -
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Residues in contact with GLU 246 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179B LYS* 3.4 17.1 + - - -
180B ASN* 5.1 2.6 - - - +
137E LEU* 5.3 0.2 - - - -
184E LYS 3.9 1.0 - - - +
185E MET* 3.3 3.3 - - - +
186E THR* 2.9 45.5 + - - +
244E ARG* 2.8 34.4 + - - +
245E PHE* 1.3 75.6 - - - +
247E ALA* 1.3 61.7 + - - +
248E HIS* 3.6 32.9 + - + +
254E SER* 3.9 13.3 + - - -
255E VAL 3.2 9.0 - - - +
256E ALA* 4.3 3.0 - - + +
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Residues in contact with ALA 247 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106E ALA* 3.8 28.9 - - + -
137E LEU* 3.8 17.1 - - + +
183E MET* 4.8 2.0 - - + -
184E LYS 3.3 8.3 - - - +
185E MET* 4.1 7.2 - - + +
246E GLU* 1.3 75.0 - - - +
248E HIS* 1.3 64.4 + - - +
249E ILE* 4.2 2.5 - - + -
254E SER* 3.1 8.8 - - - -
255E VAL* 2.8 38.0 + - + +
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Residues in contact with HIS 248 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182E ALA 3.4 1.9 - - - +
183E MET* 3.2 7.8 - - - +
184E LYS* 2.8 44.8 + - + +
186E THR* 5.9 4.9 - - + -
246E GLU* 3.6 34.6 - - + +
247E ALA* 1.3 78.6 - - - +
249E ILE* 1.3 62.2 + - - +
250E GLU 4.0 0.9 - - - +
253E GLY 3.7 4.7 + - - +
254E SER* 3.9 12.4 - - - -
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Residues in contact with ILE 249 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106E ALA* 4.7 4.9 - - + -
107E GLU 3.6 26.9 - - - +
108E ILE* 4.5 3.4 - - + -
135E PRO* 3.8 22.7 - - + -
136E ALA 4.6 2.0 - - - +
181E CYS* 3.8 20.0 - - + +
182E ALA 3.4 4.0 - - - +
183E MET* 4.1 8.3 - - + -
233E LEU* 3.8 24.9 - - + -
247E ALA* 5.3 1.3 - - + +
248E HIS* 1.3 78.1 - - - +
250E GLU* 1.3 66.9 + - - +
251E GLY 3.2 0.7 + - - -
252E ILE* 2.9 46.0 + - + -
253E GLY* 2.8 22.8 + - - +
255E 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