Contacts of the strand formed by residues 175 - 179 (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 PHE 175 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159E SER* 3.3 24.7 - - - -
167E MET* 3.3 33.7 - - + -
168E GLU 3.1 9.2 - - - -
169E LEU* 3.5 19.3 - - + -
174E THR* 1.3 75.2 + - - +
176E GLU* 1.3 61.7 + - - +
236E LEU* 4.0 21.5 - - + -
238E ARG* 3.9 31.2 - - + -
239E ARG 2.9 10.5 + - - +
240E VAL* 3.2 20.3 - - + -
241E THR* 3.1 22.9 + - - -
339E PHE* 4.4 7.2 - + - -
350E TRP* 3.8 35.4 - + - -
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Residues in contact with GLU 176 (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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167E MET* 4.7 1.3 - - - -
168E GLU* 2.6 43.1 + - - +
170E MET* 2.9 46.0 - - + +
174E THR* 4.0 1.9 + - - +
175E PHE* 1.3 75.5 - - - +
177E TRP* 1.3 59.1 + - - +
178E HIS* 3.1 28.5 + - + +
241E THR* 3.3 29.0 - - - +
243E VAL* 3.7 11.7 - - + +
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Residues in contact with TRP 177 (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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157E PHE* 3.6 31.9 - + - -
164E LEU 2.6 23.4 + - - -
165E PHE* 3.9 20.3 - + - +
166E GLN* 3.3 27.8 - - + +
167E MET* 3.7 18.9 - - + -
176E GLU* 1.3 73.0 - - - +
178E HIS* 1.3 70.4 + - - +
179E ALA* 3.4 23.6 - - + +
181E PHE* 4.1 9.9 - + - -
189E TRP* 4.1 15.5 - + - -
225E PRO* 4.0 15.3 - - + -
228E VAL* 3.9 12.3 - - + -
229E CYS* 4.0 13.7 - - - -
241E THR 3.3 6.3 + - - -
242E TYR* 3.5 36.2 - + - -
243E VAL 3.2 19.9 + - - -
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Residues in contact with HIS 178 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164E LEU* 4.1 6.6 - - - +
166E GLN 4.4 1.0 + - - -
168E GLU* 3.7 23.3 + - + -
170E MET* 4.2 3.2 - - - +
176E GLU* 3.1 37.6 + - + +
177E TRP* 1.3 83.0 + - - +
179E ALA* 1.3 63.6 + - - +
243E VAL* 2.9 46.2 - - + +
245E VAL* 3.7 15.9 - - + +
249E GLU* 3.5 33.1 + - - +
251E LYS* 4.5 2.2 - - - -
247H LYS* 6.2 1.8 - - + -
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Residues in contact with ALA 179 (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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164E LEU* 4.0 5.8 - - + +
177E TRP* 3.4 28.5 - - + +
178E HIS* 1.3 76.1 - - - +
180E PRO* 1.3 69.2 - - + +
181E PHE* 3.9 9.4 - - + -
242E TYR* 2.7 29.3 + - - +
243E VAL 3.0 6.3 + - - -
244E GLN* 3.1 4.5 - - - -
245E VAL* 2.9 23.5 + - - +
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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