Contacts of the strand formed by residues 214 - 218 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145E SER 4.2 0.2 + - - -
146E THR* 3.4 7.6 - - + +
147E PHE* 2.8 27.2 + - - -
210E LYS 3.6 15.5 + - - -
211E TRP* 3.1 49.4 + + + +
212E ASN 3.1 18.9 - - - -
213E GLY* 1.3 79.6 - - - +
215E ARG* 1.3 66.9 + - - +
320E GLU* 4.5 8.7 + - - -
210F LYS 5.7 1.1 - - - -
214F HIS* 3.1 35.6 + + - -
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Residues in contact with ARG 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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119E TYR* 5.8 1.0 + - - -
132E PHE* 3.9 19.7 - - - -
135E GLU* 2.8 21.8 + - - +
136E ASN* 5.0 2.6 - - - +
139E ARG* 3.4 24.7 - - - +
147E PHE* 3.2 7.2 - - + +
149E TYR* 3.5 24.9 + - + -
213E GLY 4.1 0.6 + - - +
214E HIS* 1.3 77.2 + - - +
216E ILE* 1.3 64.5 + - - +
279E LEU* 3.7 19.5 - - - +
281E GLU* 3.0 32.2 + - + +
282E PHE* 3.8 19.2 - - + -
320E GLU* 3.7 9.0 - - - +
139F ARG* 5.3 2.6 - - - +
212F ASN* 3.3 25.4 + - - +
213F GLY* 4.7 8.7 - - - -
214F HIS* 5.3 1.0 + - - -
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Residues in contact with ILE 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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146E THR* 3.9 15.3 - - + -
147E PHE 2.8 11.3 + - - +
148E VAL* 3.2 9.5 - - + -
149E TYR* 2.7 33.1 + - - +
203E ILE* 3.6 28.9 - - + -
211E TRP* 3.4 36.8 - - + -
214E HIS* 4.6 1.6 - - + -
215E ARG* 1.3 79.5 - - - +
217E ALA* 1.3 66.3 + - - +
218E LEU* 3.4 8.6 + - + +
282E PHE* 4.0 3.6 - - - -
320E GLU* 4.1 22.7 - - + +
321E ALA 4.9 2.0 - - - +
324E LEU* 4.1 18.6 - - + -
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Residues in contact with ALA 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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149E TYR* 3.6 7.6 - - - -
216E ILE* 1.3 75.1 - - - +
218E LEU* 1.3 60.0 + - - +
219E THR* 2.8 12.0 + - + +
277E PHE* 4.1 14.6 - - + -
282E PHE* 3.6 20.1 - - + -
317E VAL* 3.2 39.3 + - + +
320E GLU* 4.9 2.9 + - - +
321E ALA* 3.5 16.6 + - - +
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Residues in contact with LEU 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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17E GLN* 5.7 2.9 - - - +
78E PHE* 5.9 0.7 - - + -
148E VAL* 3.4 42.6 - - + -
149E TYR 2.6 21.2 + - - +
150E ALA* 4.1 6.3 - - + -
151E GLY 3.2 17.0 + - - -
190E LEU* 3.2 21.5 - - + +
195E ASP 5.5 0.4 - - - +
196E VAL* 4.7 20.2 - - + -
199E ALA* 3.9 27.1 - - + -
200E LEU* 5.0 11.0 - - + -
203E ILE* 5.4 2.7 - - + -
216E ILE* 3.4 9.3 + - + +
217E ALA* 1.3 69.8 - - - +
219E THR* 1.3 58.8 + - - +
220E PHE* 4.4 13.2 - - + -
321E ALA* 4.7 3.6 - - + -
324E LEU* 5.6 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