Contacts of the strand formed by residues 214 - 218 (chain F) in PDB entry 2VUU
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 HIS 214 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212E ASN 4.3 4.0 + - - -
213E GLY* 3.6 17.6 + - - -
214E HIS* 3.1 53.4 + + - -
215E ARG 5.3 0.8 + - - -
145F SER 4.2 0.2 + - - -
146F THR* 3.4 6.5 - - + +
147F PHE* 2.8 32.6 + - - -
210F LYS 3.4 25.8 + - - -
211F TRP* 3.0 43.1 + + + +
212F ASN 3.8 8.4 + - - -
213F GLY* 1.3 79.9 - - - +
215F ARG* 1.3 61.6 + - - +
320F GLU* 5.6 1.6 + - - -
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Residues in contact with ARG 215 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139E ARG* 2.8 41.0 + - - +
140E GLN* 4.4 0.4 - - - +
142E GLY* 4.7 5.0 - - - -
119F TYR* 5.9 0.4 + - - -
132F PHE* 3.7 16.8 - - - -
135F GLU* 2.8 25.5 + - - +
139F ARG* 3.4 28.3 - - - +
147F PHE* 3.2 7.4 - - + -
149F TYR* 3.7 14.2 + - + -
213F GLY 4.9 0.4 - - - +
214F HIS* 1.3 78.6 + - - +
216F ILE* 1.3 62.0 + - - +
279F LEU* 3.7 19.5 - - - +
281F GLU* 3.0 40.6 + - - +
282F PHE* 3.9 17.8 - - + -
320F GLU* 4.6 7.4 - - - +
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Residues in contact with ILE 216 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146F THR* 3.6 23.3 - - + -
147F PHE 2.8 9.5 + - - +
148F VAL* 3.4 10.7 - - + -
149F TYR* 2.7 32.9 + - - +
203F ILE* 4.1 18.8 - - + -
211F TRP* 3.5 39.9 - - + -
215F ARG* 1.3 81.5 - - - +
217F ALA* 1.3 67.3 + - - +
218F LEU* 3.5 5.2 + - + -
282F PHE* 4.1 3.4 - - - -
320F GLU* 4.3 18.4 - - + +
321F ALA* 4.8 2.7 - - - +
324F LEU* 4.1 20.9 - - + -
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Residues in contact with ALA 217 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149F TYR* 3.5 8.1 - - - -
216F ILE* 1.3 75.6 - - - +
218F LEU* 1.3 60.8 + - - +
219F THR* 2.9 25.7 + - + +
277F PHE* 4.4 8.5 - - + -
282F PHE* 3.9 19.3 - - + -
317F VAL* 3.9 26.1 - - + +
320F GLU* 5.6 1.8 - - - +
321F ALA* 3.5 17.7 + - - +
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Residues in contact with LEU 218 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17F GLN* 5.3 3.8 - - - +
78F PHE* 5.9 0.2 - - + -
148F VAL* 3.7 39.0 - - + -
149F TYR 2.5 18.1 + - - +
150F ALA* 3.9 10.8 - - + -
151F GLY 3.1 8.0 + - - -
190F LEU* 3.1 30.7 - - + +
195F ASP 5.4 0.4 - - - +
196F VAL* 4.5 27.4 - - + -
199F ALA* 3.8 26.7 - - + -
200F LEU* 5.0 6.7 - - + -
203F ILE* 5.5 3.4 - - + -
216F ILE* 3.5 7.1 + - + -
217F ALA* 1.3 70.0 - - - +
219F THR* 1.3 59.2 + - - +
220F PHE* 4.2 14.4 - - + -
321F ALA* 4.6 4.5 - - + -
324F LEU* 6.1 1.3 - - + -
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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