Contacts of the strand formed by residues 141 - 146 (chain E) in PDB entry 4ZZ7
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 VAL 141 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46E ILE* 4.4 10.3 - - + +
49E ALA* 3.8 32.8 - - + +
50E GLN* 3.3 36.0 + - + +
53E PHE* 5.5 0.9 - - + -
140E GLY* 1.3 72.6 - - - -
142E VAL* 1.3 70.3 + - - +
168E CYS* 3.5 4.3 - - + +
170E VAL* 4.2 11.9 - - + -
216E ARG 3.4 18.2 + - - +
217E VAL* 3.6 18.9 - - + -
218E LYS* 2.8 31.0 + - - +
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Residues in contact with VAL 142 (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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139E MET* 4.3 7.0 - - + -
141E VAL* 1.3 82.1 - - - +
143E ALA* 1.3 70.4 + - - +
162E ALA* 4.7 0.7 - - + -
167E ASN* 3.8 31.2 - - + +
168E CYS 2.9 11.4 + - - +
169E PHE* 3.4 22.8 - - + -
170E VAL* 2.9 25.3 + - - +
219E ALA* 3.7 22.9 - - + +
221E SER 5.3 0.2 - - - +
471E TYR* 3.7 34.8 - - + -
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Residues in contact with ALA 143 (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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142E VAL* 1.3 81.8 - - - +
144E GLY* 1.3 58.7 + - - +
145E ILE* 5.5 1.3 - - + -
169E PHE* 4.1 0.7 - - - -
170E VAL* 3.4 5.2 - - - +
211E LEU* 4.0 29.8 - - + -
217E VAL* 3.8 18.4 - - + +
219E ALA 2.9 15.0 + - - +
220E VAL* 3.5 12.1 - - + -
221E SER* 2.9 26.0 + - - -
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Residues in contact with GLY 144 (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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143E ALA* 1.3 75.6 - - - +
145E ILE* 1.3 62.5 + - - +
158E MET* 3.8 6.7 - - - -
169E PHE* 3.6 20.1 - - - -
170E VAL 3.1 9.2 + - - +
171E LEU* 3.4 8.5 - - - +
172E LYS* 2.8 32.4 + - - +
211E LEU* 5.0 0.2 - - - +
221E SER* 3.3 7.4 - - - -
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Residues in contact with ILE 145 (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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143E ALA* 5.6 0.4 - - + -
144E GLY* 1.3 80.4 - - - +
146E THR* 1.3 62.2 + - - +
158E MET* 3.8 3.0 - - - +
172E LYS* 3.5 19.3 - - + +
208E VAL* 3.8 37.7 - - + +
211E LEU* 4.5 12.6 - - + -
212E LEU* 5.0 3.4 - - + -
220E VAL* 4.1 23.3 - - + -
221E SER 2.9 9.8 + - - +
222E PHE* 3.5 22.4 - - + -
223E VAL 3.0 27.2 + - - +
232E ILE* 4.3 8.3 - - + -
501E NAD 3.6 20.9 - - + +
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Residues in contact with THR 146 (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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145E ILE* 1.3 79.5 - - - +
147E PRO* 1.3 71.5 + - - +
151E PRO* 5.6 0.7 - - - +
154E VAL* 4.1 1.1 - - + -
155E PRO* 3.8 33.6 - - + +
158E MET* 3.9 15.0 - - + -
171E LEU* 3.6 24.0 - - + -
172E LYS 3.5 4.8 + - - -
173E PRO* 3.2 23.9 - - - +
174E SER 3.0 9.0 + - - -
223E VAL 3.9 2.2 - - - -
501E NAD 2.7 26.2 + - - -
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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