Contacts of the helix formed by residues 75 - 89 (chain A) in PDB entry 5WZF
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 THR 75 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A GLU* 6.1 0.9 - - - +
73A HIS* 3.9 14.6 - - + +
74A VAL* 1.3 78.6 - - - +
76A ALA* 1.3 65.1 + - - +
77A ASP* 3.6 9.6 + - - +
78A LEU* 3.2 29.9 + - + +
79A GLU* 3.0 21.3 + - - +
107A LYS* 5.7 2.9 + - - +
73B HIS* 4.0 3.8 - - - -
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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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75A THR* 1.3 74.2 - - - +
77A ASP* 1.3 61.6 + - - +
79A GLU* 3.3 8.0 + - - +
80A GLU* 2.9 27.8 + - - +
73B HIS* 3.7 30.7 + - + +
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Residues in contact with ASP 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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75A THR* 3.2 8.9 + - - +
76A ALA* 1.3 78.6 - - - +
78A LEU* 1.3 60.7 + - - +
80A GLU* 3.2 9.2 + - - +
81A GLN* 3.0 38.4 + - - +
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Residues in contact with LEU 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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72A GLU* 5.7 4.7 - - + -
74A VAL* 3.8 14.4 - - + -
75A THR* 3.2 24.9 + - + +
77A ASP* 1.3 76.0 - - + +
79A GLU* 1.3 61.0 + - - +
81A GLN* 3.3 31.2 + - - +
82A ALA* 2.9 27.0 + - - +
103A ALA* 3.8 29.3 - - + +
104A VAL* 3.8 34.1 - - + -
107A LYS* 4.3 28.5 - - + +
108A LYS* 6.5 0.9 - - - -
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Residues in contact with GLU 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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39A HIS* 2.8 27.0 + - - +
74A VAL* 3.6 14.2 - - + +
75A THR 3.0 13.6 + - - +
76A ALA* 3.5 9.6 - - - +
78A LEU* 1.3 76.6 - - - +
80A GLU* 1.3 55.5 + - - +
82A ALA* 3.1 9.6 + - - +
83A TRP* 2.8 41.8 + - + -
96A PHE* 4.1 20.4 - - + -
100A THR* 4.4 1.1 - - + -
38B ASN* 2.8 39.5 + - - +
73B HIS* 3.6 18.6 + - - -
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Residues in contact with GLU 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 2.9 13.1 + - - +
77A ASP* 3.2 14.3 + - - +
79A GLU* 1.3 77.4 - - - +
81A GLN* 1.3 61.3 + - + +
83A TRP* 3.3 5.0 + - - +
84A GLU* 3.0 52.5 + - - +
64B ARG* 2.9 46.2 + - - +
65B LEU* 4.9 5.2 - - - +
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Residues in contact with GLN 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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77A ASP* 3.0 24.3 + - - +
78A LEU* 3.6 32.3 - - - +
79A GLU 3.3 0.4 - - - -
80A GLU* 1.3 76.9 - - + +
82A ALA* 1.3 57.5 + - - +
84A GLU* 3.4 10.1 + - - +
85A TRP* 2.9 29.2 + - - +
88A ARG* 5.2 0.5 + - - -
103A ALA* 4.7 6.7 - - + +
106A ARG* 4.6 14.9 + - - +
107A LYS* 5.6 5.6 - - - +
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Residues in contact with ALA 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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78A LEU 2.9 13.9 + - - +
79A GLU 3.4 8.1 - - - +
81A GLN* 1.3 75.1 - - - +
83A TRP* 1.3 59.2 + - - +
85A TRP* 3.3 7.0 + - - +
86A LEU* 2.8 35.3 + - - +
96A PHE* 4.8 3.6 - - + -
99A ALA* 3.6 35.4 - - + +
100A THR* 3.8 16.6 - - + +
103A ALA* 4.5 2.4 - - + +
106A ARG* 5.2 0.2 - - - +
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Residues in contact with TRP 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 GLU* 2.8 38.9 + - + +
80A GLU* 3.3 8.0 + - - +
82A ALA* 1.3 74.0 - - - +
84A GLU* 1.3 62.2 + - - +
86A LEU* 3.2 12.6 + - + +
87A VAL* 3.0 30.2 + - - +
96A PHE* 3.5 31.9 - + - -
38B ASN* 5.0 3.2 - - - +
41B LEU* 3.5 44.4 - - + +
42B GLY 4.0 2.7 - - - -
45B TRP* 3.7 27.6 - + + -
60B ALA 5.1 0.2 - - - -
61B ALA* 3.6 36.6 - - + -
64B ARG* 3.3 46.2 - - + +
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Residues in contact with GLU 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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80A GLU* 3.0 46.1 + - - +
81A GLN* 3.8 8.0 - - - +
83A TRP* 1.3 75.0 - - - +
85A TRP* 1.3 61.8 + - - +
87A VAL* 3.4 7.9 + - - +
88A ARG* 3.2 38.6 + - + +
64B ARG* 4.0 7.6 + - - +
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Residues in contact with TRP 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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81A GLN 2.9 18.0 + - - +
82A ALA* 3.4 8.3 - - - +
84A GLU* 1.3 76.7 - - - +
86A LEU* 1.3 71.7 + - + +
88A ARG* 3.2 33.5 + - - +
89A HIS* 3.0 60.1 + + + +
94A TYR* 3.5 51.1 - + + -
99A ALA* 4.1 14.6 - - + -
102A PHE* 3.7 27.6 - + + -
106A ARG* 3.7 35.0 - - - +
123A ALA* 4.1 14.1 + - + -
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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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82A ALA 2.8 23.3 + - - +
83A TRP* 3.2 16.8 + - + +
85A TRP* 1.3 77.3 - - + +
87A VAL* 1.3 53.0 + - - +
88A ARG 3.4 0.2 + - - -
89A HIS* 3.5 10.0 + - - +
94A TYR* 3.8 22.7 - - + +
95A SER 3.8 4.3 - - - +
96A PHE* 3.9 25.8 - - + -
99A ALA* 3.5 27.1 - - + -
45B TRP* 3.6 47.5 - - + +
54B HIS* 2.7 30.5 + - - -
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Residues in contact with VAL 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 TRP 3.0 19.0 + - - +
84A GLU* 3.8 8.1 - - - +
86A LEU* 1.3 75.7 - - - +
88A ARG* 1.3 63.6 + - + +
90A ASP* 4.9 0.5 - - - +
45B TRP* 4.7 2.0 - - + -
54B HIS* 3.0 25.8 - - - -
58B VAL* 4.5 25.6 - - + -
61B ALA* 4.3 22.2 - - + -
64B ARG* 5.0 6.7 - - - +
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Residues in contact with ARG 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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81A GLN 5.2 0.6 + - - -
84A GLU* 3.2 31.7 + - + +
85A TRP* 3.2 41.0 + - - +
87A VAL* 1.3 81.8 - - + +
89A HIS* 1.3 72.0 + - + +
90A ASP* 3.1 17.5 + - - +
91A GLU* 4.4 1.0 - - - +
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Residues in contact with HIS 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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85A TRP* 3.0 83.1 + + + +
86A LEU* 3.5 11.1 + - - +
87A VAL 3.5 0.6 - - - -
88A ARG* 1.3 90.6 + - + +
90A ASP* 1.3 57.7 + - - +
91A GLU* 2.9 35.6 + - - +
92A ARG 3.5 14.7 - - - +
94A TYR* 4.2 5.3 + - + +
123A ALA* 6.5 0.2 - - - -
54B HIS* 3.9 2.8 - - - -
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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