Contacts of the strand formed by residues 214 - 219 (chain E) in PDB entry 2WNU
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 ILE 214 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98E SER* 3.9 15.7 - - - -
99E ALA 3.4 16.4 - - - +
100E THR* 4.0 7.4 - - + -
115E PHE* 3.7 5.0 - - - -
119E ILE* 4.0 11.4 - - + -
145E TYR* 3.1 8.0 - - - +
146E HIS* 2.9 46.0 + - + +
213E SER* 1.3 73.7 - - - +
215E PHE* 1.3 64.6 + - - +
216E SER* 3.8 18.2 - - - +
162F VAL* 4.3 5.2 - - + -
164F PHE* 3.6 24.9 - - + -
178F GLY 3.5 23.3 - - - +
179F VAL* 3.9 13.5 - - + -
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Residues in contact with PHE 215 (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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97E PHE* 3.8 28.9 - + - -
98E SER* 3.4 0.9 - - - -
99E ALA* 2.9 30.9 + - - +
115E PHE* 3.4 40.8 - + + -
126E TYR* 4.0 9.0 - + - -
131E GLY 3.6 19.1 - - - -
143E PHE* 4.2 19.7 - + + -
144E THR 3.4 11.7 - - - -
145E TYR* 4.3 0.4 - + + -
157E LEU* 5.1 1.6 - - + -
195E VAL* 4.1 10.1 - - + -
196E PHE* 4.1 22.4 - - - -
197E LEU* 3.8 27.1 - - + -
214E ILE* 1.3 71.9 - - - +
216E SER* 1.3 73.9 + - - +
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Residues in contact with SER 216 (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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97E PHE* 2.9 17.9 - - - -
98E SER* 2.5 24.9 + - - -
143E PHE* 3.6 1.9 - - - -
144E THR* 2.9 47.8 + - - +
145E TYR* 4.8 0.2 - - - +
214E ILE* 3.8 12.5 - - - +
215E PHE* 1.3 80.9 - - - +
217E GLY* 1.3 59.5 + - - +
218E PHE* 5.8 0.2 - - - -
139F TYR* 5.1 3.4 - - - -
178F GLY 4.7 2.1 + - - -
179F VAL* 4.5 3.6 - - - -
180F LEU* 3.8 9.6 - - - -
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Residues in contact with GLY 217 (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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96E ALA* 3.3 1.0 - - - -
97E PHE* 2.9 51.8 + - - -
133E PHE* 6.3 0.2 - - - -
141E TYR* 5.5 0.4 - - - -
142E TYR 3.1 13.0 - - - -
143E PHE* 3.9 6.3 - - - -
144E THR* 5.5 0.2 - - - -
216E SER* 1.3 75.2 - - - +
218E PHE* 1.3 67.4 + - - +
180F LEU* 3.4 1.6 - - - +
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Residues in contact with PHE 218 (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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217D PHE* 3.9 11.7 - + - -
95E ILE* 3.4 12.1 - - - +
96E ALA* 3.8 12.1 - - + -
141E TYR* 3.3 11.3 - - - +
142E TYR* 2.9 67.0 + + + -
144E THR* 5.3 2.2 - - + -
216E SER 5.6 0.2 - - - -
217E GLY* 1.3 78.0 - - - +
219E LEU* 1.3 71.1 + - - +
220E LEU* 3.5 24.9 - - + -
139F TYR* 4.1 29.2 - + - -
180F LEU* 3.5 17.9 - - + -
212F PHE* 4.5 1.6 - + - -
214F LEU* 3.7 33.9 - - + -
215F PHE* 4.8 1.1 - - + -
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Residues in contact with LEU 219 (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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93E GLN* 3.4 25.1 - - + +
95E ILE* 3.0 28.9 + - + +
137E VAL* 4.7 2.5 - - + +
139E GLY* 4.5 0.9 - - - -
140E LEU 3.4 17.0 - - - +
141E TYR* 3.5 38.1 - - + +
218E PHE* 1.3 77.9 - - - +
220E LEU* 1.3 62.5 + - - +
221E PHE 3.4 20.4 - - - +
222E PRO* 3.8 32.1 - - + -
214F LEU* 4.8 3.1 - - - +
215F PHE* 3.4 24.4 - - + -
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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