Contacts of the helix formed by residues 91 - 96 (chain A) in PDB entry 1Z29
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 SER 91 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A ALA* 6.3 0.2 - - - -
84A PHE* 3.8 7.2 - - - -
85A LYS* 3.5 28.6 - - - +
89A ILE 3.5 2.6 + - - -
90A PRO* 1.3 75.9 - - - +
92A GLY* 1.3 61.1 + - - +
93A MET* 3.1 10.0 + - - +
94A GLU* 2.7 57.9 + - - +
95A THR* 3.0 13.3 + - - -
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Residues in contact with GLY 92 (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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80A PRO* 3.9 8.0 - - - +
81A PHE 3.2 29.8 - - - -
82A LEU* 4.1 5.5 - - - -
84A PHE* 2.9 25.1 + - - -
90A PRO 3.7 0.6 + - - -
91A SER* 1.3 72.6 + - - +
93A MET* 1.3 61.0 + - - +
95A THR* 3.7 7.0 + - - -
96A LEU* 3.3 19.9 + - - +
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Residues in contact with MET 93 (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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30A PRO* 2.6 37.7 - - + +
31A LEU* 3.4 24.2 - - + -
33A SER* 4.1 2.7 - - - -
34A PHE* 3.2 55.2 - - + +
82A LEU* 4.2 6.7 + - + +
91A SER* 3.1 7.6 + - - +
92A GLY* 1.3 75.3 - - - +
94A GLU* 1.3 65.3 + - - +
96A LEU* 3.3 15.9 + - + +
97A LYS* 3.4 11.6 + - - +
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Residues in contact with GLU 94 (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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85A LYS* 3.6 11.3 + - - -
90A PRO* 3.6 19.3 - - + +
91A SER* 2.7 51.4 + - - +
93A MET* 1.3 72.9 - - - +
95A THR* 1.3 57.3 + - - +
96A LEU 2.9 3.8 - - - -
97A LYS* 2.8 38.3 + - - +
98A ASN* 3.9 2.4 + - - +
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Residues in contact with THR 95 (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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76A PHE 4.4 5.2 + - - +
77A MET* 3.7 52.1 - - + +
80A PRO* 3.9 12.3 - - + -
84A PHE* 5.7 0.5 - - - -
90A PRO* 4.0 14.8 + - - +
91A SER 3.0 12.3 + - - -
92A GLY* 3.9 7.5 - - - -
94A GLU* 1.3 78.1 - - - +
96A LEU* 1.3 56.9 + - - +
97A LYS 3.5 0.5 + - - -
98A ASN* 3.9 11.5 + - - +
99A THR* 2.9 14.2 + - - -
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Residues in contact with LEU 96 (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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34A PHE* 3.2 27.8 - - + -
80A PRO* 3.6 22.2 - - + +
82A LEU* 5.3 2.5 - - + -
92A GLY 3.3 11.1 + - - +
93A MET* 3.3 17.0 + - + +
94A GLU 2.8 1.2 + - - -
95A THR* 1.3 79.1 - - - +
97A LYS* 1.3 59.8 + - - +
99A THR* 3.1 24.2 - - + +
103A ARG* 3.0 40.2 + - + +
105A LEU* 3.2 31.0 - - + -
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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