Contacts of the helix formed by residues 81 - 86 (chain A) in PDB entry 4ZIN
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 ASP 81 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A TYR* 5.7 0.2 - - - -
70A LYS 4.9 2.4 - - - +
73A VAL 3.8 0.2 - - - +
75A HIS* 3.2 42.5 + - + +
79A ILE 3.1 3.5 + - - +
80A PRO* 1.3 68.8 - - - +
82A TYR* 1.3 66.0 + - - +
83A LEU* 3.9 5.7 + - - +
84A LYS* 2.9 55.3 + - + +
85A LEU* 3.0 30.2 + - + +
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Residues in contact with TYR 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A HIS* 5.5 0.6 + - - -
80A PRO 3.2 4.0 + - - -
81A ASP* 1.3 73.5 + - - +
83A LEU* 1.3 85.5 + - + +
85A LEU* 3.3 7.6 + - - +
86A SER* 3.2 21.7 + - - -
155A GLY 3.8 14.6 + - - -
157A LEU* 3.9 23.3 - - + +
181A TYR 3.7 18.9 + - - -
182A LYS* 3.7 5.7 - - - +
183A ALA* 2.8 33.2 + - + +
186A PRO* 5.8 1.0 - - + +
187A VAL* 3.5 36.9 - - + +
188A GLN 3.4 26.0 - - - +
189A LEU* 3.6 20.9 - - + -
190A PRO* 3.9 14.8 - - + -
193A TYR* 5.8 0.4 + - - -
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Residues in contact with LEU 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LYS* 3.3 44.0 - - + +
71A ALA* 5.1 1.6 - - - -
75A HIS* 6.4 0.2 - - + -
81A ASP* 3.2 3.9 + - - +
82A TYR* 1.3 103.9 - - + +
84A LYS* 1.3 62.0 + - - +
86A SER* 2.7 23.1 + - - -
87A PHE* 3.2 12.9 - - - -
91A PHE* 3.7 37.9 - - + -
157A LEU* 4.7 9.6 - - + -
181A TYR* 4.0 28.7 - - + -
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Residues in contact with LYS 84 (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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7A ILE* 5.9 0.3 - - - +
8A ILE* 4.5 16.7 - - + +
37A PRO* 2.9 33.3 + - - -
38A TYR* 3.9 32.8 - - + +
71A ALA* 2.9 32.0 + - + +
73A VAL 2.9 28.1 + - - -
74A LYS* 5.0 0.2 - - - +
75A HIS 5.2 0.4 - - - +
81A ASP* 2.9 34.7 + - + +
83A LEU* 1.3 78.5 - - - +
85A LEU* 1.3 62.5 + - + +
86A SER 3.1 1.4 + - - -
87A PHE* 3.2 25.4 + - - +
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Residues in contact with LEU 85 (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* 4.6 4.3 - - + -
81A ASP* 3.0 34.0 + - + +
82A TYR 3.3 6.9 + - - +
84A LYS* 1.3 74.0 - - + +
86A SER* 1.3 59.7 + - - +
87A PHE 3.1 9.9 + - - +
185A LYS* 3.7 4.3 + - - -
187A VAL* 3.6 24.7 - - + +
188A GLN* 4.1 33.9 - - + +
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Residues in contact with SER 86 (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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82A TYR 3.2 9.2 + - - -
83A LEU* 2.7 22.2 + - - -
84A LYS 3.1 0.6 + - - -
85A LEU* 1.3 74.7 - - - +
87A PHE* 1.3 60.7 + - - +
89A GLU* 3.5 9.2 - - - +
90A GLY* 2.8 48.3 + - - +
91A PHE* 3.5 9.4 - - - -
183A ALA* 3.6 22.0 - - - -
185A LYS* 3.8 10.0 - - - +
187A VAL* 4.1 7.4 - - - -
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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