Contacts of the strand formed by residues 145 - 149 (chain A) in PDB entry 2Z1Z
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 145 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A GLN* 4.5 1.3 - - - +
143A VAL* 4.2 4.5 - - + -
144A THR* 1.3 83.4 - - - +
146A ALA* 1.3 58.4 + - - +
147A VAL* 3.6 29.4 - - + -
155A TYR 4.2 7.6 - - - +
156A VAL* 4.8 0.4 - - - -
159A SER* 3.5 28.5 - - - +
164A GLN* 3.4 23.3 - - + +
177A ASN 4.3 2.3 + - - +
178A ILE* 3.6 23.6 - - + -
179A GLU 3.0 21.0 + - - -
199A THR* 3.7 7.6 - - - +
201A ILE* 3.2 26.0 - - + +
203A PHE* 4.0 21.3 - - + -
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Residues in contact with ALA 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A ILE* 1.3 74.8 - - - +
147A VAL* 1.3 68.1 + - - +
179A GLU* 3.1 27.1 - - + +
181A MET* 4.2 17.5 - - - -
196A VAL* 5.0 2.5 - - + -
199A THR* 3.8 14.8 - - + +
201A ILE 2.8 7.6 + - - +
202A ILE* 4.3 10.1 - - + -
203A PHE* 3.0 26.3 + - - +
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Residues in contact with VAL 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A ILE* 3.6 22.9 - - + -
146A ALA* 1.3 79.7 - - - +
148A GLN* 1.3 66.3 + - - +
151A SER* 4.7 7.2 - - - -
155A TYR* 4.0 24.0 - - + -
156A VAL* 3.8 23.8 - - + -
178A ILE* 4.1 11.6 - - + +
179A GLU 2.9 6.1 + - - +
180A TYR* 4.2 11.9 - - + -
181A MET* 2.8 39.7 + - - +
203A PHE* 4.0 11.7 - - + +
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Residues in contact with GLN 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A VAL* 1.3 85.2 - - - +
149A ASP* 1.3 58.6 + - - +
150A PRO 3.5 13.0 - - - +
151A SER* 3.1 27.5 + - - +
155A TYR* 5.2 1.2 - - - -
181A MET* 3.6 13.4 - - + +
183A CYS* 3.9 18.6 - - - -
189A PHE 5.2 2.6 - - - +
191A PRO* 5.5 0.2 - - + -
203A PHE 4.2 4.4 + - - +
204A PHE* 3.6 36.1 - - + +
205A CYS* 2.7 48.9 - - - +
208A ASN* 3.2 24.0 + - - +
213A ALA 5.6 0.2 - - - +
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Residues in contact with ASP 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A GLN* 1.3 73.8 - - - +
150A PRO* 1.3 63.5 - - - +
151A SER 3.9 0.9 - - - +
174A LYS* 4.8 3.8 + - - -
180A TYR* 3.8 31.1 - - + +
181A MET 3.0 12.0 + - - +
182A ARG* 3.5 17.8 + - - +
183A CYS* 2.9 27.0 + - - +
396A GLY* 3.5 4.0 - - - -
397A PRO* 3.3 26.5 - - - +
398A GLY* 2.5 37.0 + - - -
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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