Contacts of the strand formed by residues 164 - 169 (chain E) in PDB entry 3ZP0
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 164 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126E TRP* 3.8 11.9 - - + -
129E HIS* 3.4 28.0 - - + +
154E LEU* 3.6 22.7 - - + -
161E TYR* 3.2 35.2 - - + +
162E PRO 4.0 0.2 - - - +
163E THR* 1.3 71.5 - - - +
165E LYS* 1.3 63.0 + - - +
166E ARG* 3.6 28.9 - - + +
245E PHE 4.9 2.5 - - - +
246E GLU* 3.0 8.3 - - - +
247E SER* 2.6 41.2 + - - +
251E PHE* 4.2 19.1 - - + -
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Residues in contact with LYS 165 (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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163E THR* 3.7 26.3 + - + +
164E ILE* 1.3 78.2 - - - +
166E ARG* 1.3 70.9 + - - +
245E PHE 3.4 4.9 - - - +
246E GLU* 3.9 26.4 - - + +
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Residues in contact with ARG 166 (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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121E ILE* 3.3 40.7 - - + +
122E PRO* 5.6 0.4 - - - +
125E SER* 2.7 49.7 + - - -
126E TRP* 3.7 27.6 - - + -
164E ILE* 3.6 21.9 - - + -
165E LYS* 1.3 85.3 - - - +
167E SER* 1.3 60.9 + - - +
243E ILE 3.8 0.7 - - - +
244E ASN* 3.5 1.9 - - - +
245E PHE* 2.6 52.4 + - + +
251E PHE* 5.9 0.7 - - + -
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Residues in contact with SER 167 (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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121E ILE* 5.9 3.0 - - - +
166E ARG* 1.3 76.6 - - - +
168E TYR* 1.3 66.3 + - - +
169E ASN* 4.3 1.6 + - - +
242E ALA* 4.4 6.9 - - - +
243E ILE 3.3 5.3 + - - -
244E ASN* 3.0 24.7 + - - -
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Residues in contact with TYR 168 (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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118E ILE* 4.0 8.1 - - - +
119E GLN 5.3 1.3 - - - -
120E ILE* 3.6 48.5 - - + +
121E ILE* 5.0 10.1 - - + -
167E SER* 1.3 76.2 + - - +
169E ASN* 1.3 85.0 + - - +
170E ASN* 3.8 4.2 - - - -
171E THR* 4.2 7.1 + - - -
172E ASN* 3.2 23.6 + - - -
176E LEU* 3.5 27.6 - - + -
178E VAL* 5.8 0.2 - - + -
237E LEU* 4.1 6.5 - - + +
242E ALA* 3.3 2.8 - - - -
243E ILE* 2.8 48.2 + - + +
245E PHE* 5.8 0.8 - - - -
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Residues in contact with ASN 169 (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 SER* 4.4 1.5 + - - +
168E TYR* 1.3 92.3 - - - +
170E ASN* 1.3 69.3 + - - +
171E THR* 2.9 24.1 + - - +
240E ASN* 4.2 22.0 + - - +
241E ASP 3.6 5.6 - - - -
242E ALA* 3.8 16.6 - - + +
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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