Contacts of the strand formed by residues 169 - 171 (chain E) in PDB entry 2X86
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 ASN 169 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168E PHE* 1.3 79.1 - - - +
170E VAL* 1.3 65.2 + - - +
171E TYR* 3.7 3.5 + - - +
209E ARG* 3.0 52.8 + - + +
210E ASP 3.0 10.9 + - - +
211E PHE* 3.4 25.5 - - + -
212E VAL* 2.9 23.5 + - - +
243E PHE* 5.1 2.8 - - - -
273E GLN* 5.5 0.5 + - - -
276E THR* 4.2 4.7 + - - +
400E NAP 4.2 3.7 + - - -
401E ADP 3.4 19.5 + - - -
402E BMA 4.9 1.9 + - - -
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Residues in contact with VAL 170 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E PHE* 3.6 22.5 - - + -
11E ILE* 4.1 9.2 - - + -
167E TYR* 3.7 30.1 - - + -
168E PHE 4.0 0.7 - - - +
169E ASN* 1.3 74.3 + - - +
171E TYR* 1.3 63.0 + - - +
175E GLU* 4.5 1.0 - - - +
183E SER* 4.1 9.0 - - - -
212E VAL* 3.3 19.5 - - + +
214E VAL* 3.8 27.6 - - + -
217E VAL* 3.9 13.2 - - + -
400E NAP 3.3 30.6 + - - +
402E BMA 5.4 0.5 + - - -
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Residues in contact with TYR 171 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E PHE* 3.5 10.1 - - - -
169E ASN 3.8 9.0 - - - +
170E VAL* 1.3 75.3 - - - +
172E GLY* 1.3 59.4 + - - +
175E GLU* 4.1 0.2 - - - -
183E SER* 3.5 26.5 - - - +
185E ALA* 4.6 4.7 - - + -
211E PHE* 3.7 22.6 + + + -
212E VAL 3.2 33.0 + - - -
213E TYR* 3.6 18.5 + + - +
214E VAL 2.9 23.6 + - - -
246E VAL* 6.4 0.2 - - + -
293E LYS 4.6 1.0 + - - -
294E THR 3.6 11.4 + - - -
295E VAL* 3.8 6.2 - - - -
298E GLY* 3.2 26.0 - - - -
299E VAL* 3.6 35.7 + - + -
302E TYR* 4.0 13.9 - + - -
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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
------------------------------------------------------------
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