Contacts of the helix formed by residues 106 - 111 (chain A) in PDB entry 1PZY
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 ALA 106 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A VAL* 4.5 6.5 - - + +
32A HIS* 3.7 21.3 - - + -
33A THR* 4.3 14.1 + - - +
104A TRP 3.1 1.8 + - - -
105A LYS* 1.3 77.9 - - - +
107A TYR* 1.3 65.0 + - - +
108A LYS 3.6 0.2 - - - -
109A PRO* 3.9 0.9 - - - -
110A MET* 3.1 26.4 + - + +
111A CYS* 3.8 3.5 + - - -
360B PHE* 3.5 37.9 - - + -
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Residues in contact with TYR 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ILE* 3.9 12.7 - - + +
25A GLU* 2.8 40.5 + - + -
29A VAL* 3.8 29.2 - - + +
101A ILE* 3.6 44.2 - - + +
102A ASP* 4.4 8.3 - - - +
104A TRP* 3.1 16.9 + - + +
106A ALA* 1.3 77.0 - - - +
108A LYS* 1.3 66.1 + - + +
111A CYS* 2.9 49.2 + - + +
112A SER* 3.9 4.2 + - - -
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Residues in contact with LYS 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ASP* 4.9 11.2 + - - +
104A TRP 4.7 0.2 + - - -
105A LYS 4.3 1.9 + - - +
107A TYR* 1.3 86.6 - - + +
109A PRO* 1.3 71.1 - - + +
112A SER* 2.6 30.7 + - - +
364B ALA* 6.1 4.9 - - - -
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Residues in contact with PRO 109 (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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105A LYS 3.2 23.8 - - - +
106A ALA* 3.6 5.8 - - - +
108A LYS* 1.3 98.8 - - + +
110A MET* 1.3 71.5 + - + +
112A SER* 5.1 1.0 + - - -
113A GLU* 6.0 2.3 - - - +
360B PHE* 4.0 13.9 - - + +
363B ILE* 3.6 32.5 - - + +
364B ALA* 4.6 13.5 - - + -
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Residues in contact with MET 110 (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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28A CYS* 3.3 10.4 - - - -
32A HIS* 3.5 42.9 + - + +
106A ALA 3.1 15.8 + - - +
109A PRO* 1.3 92.8 - - + +
111A CYS* 1.3 60.2 + - - +
112A SER 3.7 2.0 + - - -
113A GLU* 4.5 5.0 - - - +
118A TRP* 4.9 1.6 + - - -
286B TYR* 5.6 3.6 - - + -
288B GLN* 4.0 28.3 + - + +
319B ASP* 4.3 24.7 - - + +
323B ASN* 5.7 5.8 - - - +
360B PHE* 4.3 7.9 - - + -
363B ILE* 3.4 29.8 - - + -
405B NAG 4.6 3.4 - - - -
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Residues in contact with CYS 111 (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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25A GLU* 4.4 4.1 - - - +
28A CYS* 2.0 61.9 - - + -
29A VAL* 3.5 11.0 - - - -
32A HIS* 4.4 0.9 - - - -
106A ALA 4.0 9.9 - - - -
107A TYR* 2.9 38.4 + - + +
110A MET* 1.3 82.6 - - - +
112A SER* 1.3 57.7 + - - +
113A GLU 3.4 2.9 - - - +
115A LEU* 3.4 26.1 - - + +
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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