Contacts of the helix formed by residues 75 - 89 (chain A) in PDB entry 2Z9O
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 75 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A VAL* 3.5 27.4 - - - +
65A ALA* 4.3 8.7 - - - +
68A ALA* 4.1 8.9 - - - +
73A LEU 3.7 0.4 + - - -
74A THR* 1.3 72.2 - - - +
76A ALA* 1.3 58.2 + - - +
78A ALA* 3.9 0.7 - - - -
79A SER* 2.6 36.1 + - - -
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Residues in contact with ALA 76 (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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74A THR* 3.5 12.5 - - - +
75A SER* 1.3 82.8 - - - +
77A GLU* 1.3 62.3 + - + +
79A SER* 3.2 14.3 - - - -
80A LYS* 3.3 8.7 + - - +
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Residues in contact with GLU 77 (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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73A LEU* 2.6 40.9 - - + +
74A THR* 2.8 26.1 + - - +
76A ALA* 1.3 75.6 - - + +
78A ALA* 1.3 68.0 - - - +
79A SER 2.9 1.1 - - - -
80A LYS* 3.0 13.8 + - + +
81A ASP* 2.9 29.9 + - - +
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Residues in contact with ALA 78 (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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64A VAL* 3.6 21.1 - - + -
67A TYR* 3.4 33.9 - - + -
68A ALA* 3.7 11.7 - - + -
73A LEU* 4.4 4.6 - - + +
74A THR 2.9 22.3 + - - +
77A GLU* 1.3 71.9 - - - +
79A SER* 1.3 68.5 + - - +
81A ASP* 3.7 1.6 - - - +
82A ILE* 2.9 27.0 + - - +
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Residues in contact with SER 79 (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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64A VAL* 4.1 17.0 - - - +
75A SER 2.6 24.5 + - - -
76A ALA* 3.2 7.6 - - - -
77A GLU 2.9 0.2 - - - -
78A ALA* 1.3 80.1 - - - +
80A LYS* 1.3 65.9 + - - -
82A ILE* 3.0 2.8 + - - +
83A ARG* 3.0 22.3 + - - -
127A TYR* 3.1 21.0 + - - -
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Residues in contact with LYS 80 (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 ALA 3.3 8.6 + - - +
77A GLU* 3.0 16.4 + - + +
79A SER* 1.3 77.9 + - - +
81A ASP* 1.3 80.2 + - - +
83A ARG* 3.0 29.5 + - - +
84A GLN* 3.0 16.5 + - + +
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Residues in contact with ASP 81 (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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33A ARG* 5.0 3.1 + - - -
34A ASP* 2.6 36.0 - - - +
37A ARG* 5.5 0.5 + - - -
67A TYR* 3.7 19.4 + - + +
73A LEU* 4.5 12.6 - - - +
77A GLU* 2.9 18.2 + - - +
78A ALA* 3.7 6.3 - - - +
80A LYS* 1.3 81.2 - - - +
82A ILE* 1.3 69.5 + - - +
84A GLN* 2.6 21.8 + - - +
85A ALA* 3.0 12.4 + - - -
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Residues in contact with ILE 82 (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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38A MET* 3.3 21.4 - - + +
62A ILE* 3.2 36.8 - - + -
64A VAL* 4.6 8.3 - - + -
67A TYR* 3.6 37.6 + - + -
78A ALA 2.9 27.2 + - - +
79A SER* 3.2 8.1 - - - +
81A ASP* 1.3 74.7 - - - +
83A ARG* 1.3 63.8 + - - +
85A ALA* 3.3 1.3 + - - -
86A LEU* 2.9 24.1 + - + +
127A TYR* 3.7 31.6 - - + -
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Residues in contact with ARG 83 (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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79A SER* 3.0 6.4 + - - +
80A LYS* 3.2 30.2 - - - +
81A ASP 2.7 3.2 + - - -
82A ILE* 1.3 77.9 - - - +
84A GLN* 1.3 62.5 + - - +
86A LEU* 3.6 3.7 + - - +
87A LYS* 3.1 22.3 + - + +
120A HIS* 3.7 15.0 - - + -
127A TYR* 3.1 35.1 + - + +
105B ASP* 4.3 13.5 + - - -
106B GLU* 3.5 46.3 + - - +
109B TYR* 4.6 5.9 + - + +
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Residues in contact with GLN 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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34A ASP* 6.5 0.2 - - + -
80A LYS* 3.0 13.6 + - + +
81A ASP* 2.6 15.7 + - - +
83A ARG* 1.3 70.5 - - - +
85A ALA* 1.3 66.5 + - - +
87A LYS* 3.0 29.1 + - + +
88A SER* 2.7 39.1 + - - -
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Residues in contact with ALA 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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32A SER* 4.9 1.3 - - - -
34A ASP* 4.1 13.4 - - + +
35A GLN* 3.3 37.1 - - + +
38A MET* 3.4 21.5 - - + -
81A ASP 3.0 8.7 + - - +
82A ILE* 3.5 4.3 - - - +
84A GLN* 1.3 77.9 - - - +
86A LEU* 1.3 65.4 + - - +
88A SER* 2.9 5.3 + - - -
89A PHE* 2.7 23.5 + - - +
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Residues in contact with LEU 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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38A MET* 3.5 17.1 - - + +
62A ILE* 4.6 1.8 - - + -
82A ILE 2.9 20.8 + - - +
83A ARG* 3.7 4.9 - - - +
85A ALA* 1.3 71.5 - - - +
87A LYS* 1.3 64.5 + - - +
89A PHE* 2.8 23.1 + - - +
115A PHE* 5.0 7.9 - - + -
118A ARG* 3.4 28.7 + - + +
119A ALA 4.2 20.0 - - - +
127A TYR* 4.4 22.0 - - + -
128A SER 4.3 1.6 - - - +
129A VAL* 3.4 34.3 - - + -
109B TYR* 3.5 18.4 - - - +
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Residues in contact with LYS 87 (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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83A ARG* 3.1 11.2 + - + +
84A GLN* 3.0 32.6 + - - +
86A LEU* 1.3 77.7 - - - +
88A SER* 1.3 57.7 + - - +
90A ALA* 2.8 30.5 + - - +
118A ARG* 3.7 9.6 - - - +
109B TYR* 4.0 12.0 + - + +
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Residues in contact with SER 88 (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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32A SER* 5.1 5.3 - - - -
35A GLN* 3.0 20.4 - - - +
84A GLN* 2.7 29.6 + - - -
85A ALA* 3.3 7.9 - - - -
87A LYS* 1.3 69.2 - - - +
89A PHE* 1.3 55.8 + - - +
90A ALA* 2.9 17.0 + - - +
92A LYS* 3.6 16.8 - - - -
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Residues in contact with PHE 89 (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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31A LEU* 3.9 20.2 - - + -
35A GLN* 3.2 39.4 + - + -
38A MET* 4.4 12.8 - - - -
39A LEU* 3.5 28.7 - - + -
85A ALA 2.7 12.9 + - - -
86A LEU* 2.8 15.4 + - - +
88A SER* 1.3 72.7 - - - +
90A ALA* 1.3 67.8 + - - +
92A LYS* 3.6 15.8 + - + +
114A TRP* 3.4 41.7 - + + +
115A PHE* 3.7 26.2 - + + -
118A ARG* 4.3 9.9 + - - +
93B GLU* 4.4 2.9 - - - +
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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