Contacts of the helix formed by residues 78 - 91 (chain A) in PDB entry 5A19
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 78 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A ALA 4.2 1.2 + - - -
77A VAL* 1.3 72.1 - - - +
79A TYR* 1.3 58.4 + - - +
80A GLN* 3.5 12.0 + - - +
81A LYS* 3.2 45.4 + - + +
82A VAL* 3.0 29.7 + - - +
400A PEG 3.7 39.6 - - - +
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Residues in contact with TYR 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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41A VAL* 3.8 23.8 - - + -
45A HIS* 2.8 28.4 + - - -
67A LEU* 3.8 21.8 - - + -
71A ILE* 3.7 3.6 - - - +
77A VAL* 3.2 31.2 + - + -
78A ASP* 1.3 72.5 + - - +
80A GLN* 1.3 62.3 + - + +
82A VAL* 4.5 3.1 - - + +
83A VAL* 3.1 32.2 + - + +
106A VAL* 4.9 1.8 - - - -
108A VAL* 3.8 34.5 - - + -
110A LEU* 3.4 29.4 - - + +
112A GLN* 3.8 10.6 + - - +
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Residues in contact with GLN 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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78A ASP* 3.3 9.5 + - - +
79A TYR* 1.3 77.9 - - + +
81A LYS* 1.3 62.6 + - - +
84A ARG* 3.0 70.7 + - - +
106A VAL* 3.2 37.8 + - - +
108A VAL* 5.1 6.0 - - + +
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Residues in contact with LYS 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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78A ASP* 3.2 36.6 + - - +
80A GLN* 1.3 77.2 - - - +
82A VAL* 1.3 73.7 + - - +
84A ARG* 4.3 2.0 - - - +
85A GLU* 3.1 30.0 + - + +
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Residues in contact with VAL 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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40A ALA* 3.7 39.3 - - + +
41A VAL* 4.0 14.1 - - + +
44A ALA* 4.0 10.3 - - + -
77A VAL* 3.9 19.1 - - + -
78A ASP 3.0 21.7 + - - +
79A TYR* 4.1 5.4 - - - +
81A LYS* 1.3 83.8 - - - +
83A VAL* 1.3 67.1 + - + +
85A GLU* 4.0 3.0 - - - +
86A ALA* 3.1 22.7 + - - +
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Residues in contact with VAL 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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37A ILE* 3.9 19.7 - - + +
41A VAL* 4.9 4.5 - - + -
65A ILE* 3.6 38.8 - - + -
67A LEU* 3.8 28.9 - - + -
79A TYR* 3.1 18.9 + - - +
80A GLN 4.3 1.6 - - - +
82A VAL* 1.3 75.4 - - + +
84A ARG* 1.3 60.1 + - + +
86A ALA* 3.2 7.9 + - - +
87A VAL* 3.0 28.1 + - - +
104A CYS* 5.7 0.2 - - - -
106A VAL* 4.0 21.5 - - + -
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Residues in contact with ARG 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 GLN* 3.0 49.6 + - - +
81A LYS* 4.3 2.2 - - - +
83A VAL* 1.3 78.2 - - - +
85A GLU* 1.3 57.3 + - - +
87A VAL* 3.3 2.7 + - - -
88A LYS* 3.0 25.5 + - - +
101A TYR* 2.8 63.9 + - + +
102A LYS* 3.8 12.7 + - - +
104A CYS* 2.8 42.0 + - - +
105A ASN* 4.6 0.4 - - - +
106A VAL* 3.6 21.5 - - + +
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Residues in contact with GLU 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 LYS* 3.1 22.8 + - + +
82A VAL* 4.0 4.3 - - - +
84A ARG* 1.3 73.2 - - - +
86A ALA* 1.3 61.1 + - - +
88A LYS* 3.4 31.4 + - - +
89A HIS* 2.9 30.5 + - + +
101A TYR* 5.5 0.2 - - - -
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Residues in contact with ALA 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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36A GLN* 4.1 2.8 - - - +
37A ILE* 4.1 20.9 - - + +
40A ALA* 4.2 9.4 - - + -
82A VAL 3.1 14.5 + - - +
83A VAL* 3.2 9.8 + - - +
85A GLU* 1.3 77.4 - - - +
87A VAL* 1.3 60.5 + - - +
89A HIS* 3.5 3.9 + - - +
90A ILE* 3.2 31.0 + - + +
372A GLN* 4.0 24.0 - - - +
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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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33A ILE* 4.8 7.4 - - + -
37A ILE* 4.1 10.3 - - + -
65A ILE* 3.4 33.0 - - + -
83A VAL* 3.0 13.4 + - + +
84A ARG* 3.3 7.4 + - - +
86A ALA* 1.3 73.9 - - - +
88A LYS* 1.3 64.7 + - - +
90A ILE* 3.5 8.2 + - + +
91A GLY 3.2 16.6 + - - -
92A TYR* 3.3 38.1 + - + +
99A PHE* 3.8 17.7 - - + -
101A TYR* 3.8 11.2 - - + -
104A CYS* 5.4 0.9 - - - -
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Residues in contact with LYS 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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84A ARG 3.0 13.4 + - - +
85A GLU* 3.5 31.8 + - - +
87A VAL* 1.3 73.6 - - - +
89A HIS* 1.3 66.0 + - - +
91A GLY* 3.1 14.7 + - - -
92A TYR 4.7 1.3 - - - +
93A ASP* 5.5 3.9 - - + +
101A TYR* 3.7 48.9 + - + +
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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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27A GLU* 3.6 18.3 + - - -
36A GLN* 3.5 22.9 - - - +
85A GLU* 2.9 24.2 + - - +
86A ALA* 3.7 7.4 - - - +
87A VAL 3.4 0.2 - - - -
88A LYS* 1.3 76.4 - - - +
90A ILE* 1.3 60.5 - - - +
91A GLY* 3.4 1.0 + - - -
169A ARG* 2.9 35.6 + - - -
372A GLN* 5.2 2.5 - - - +
407A PG4 3.4 27.2 + - - -
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Residues in contact with ILE 90 (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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27A GLU* 3.8 15.4 - - + +
28A GLY* 3.7 29.8 - - - +
33A ILE* 4.1 28.3 - - + +
36A GLN* 3.5 35.4 - - + +
37A ILE* 5.4 1.1 - - + -
86A ALA* 3.2 20.3 + - + +
87A VAL* 3.6 10.1 - - + +
88A LYS 3.3 0.2 - - - -
89A HIS* 1.3 75.7 - - - +
91A GLY* 1.3 57.1 + - - +
92A TYR* 3.8 18.2 - - + -
168A ARG* 3.1 27.9 + - - -
169A ARG* 3.6 5.3 + - - +
178A PRO* 3.7 2.5 - - + +
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Residues in contact with GLY 91 (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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87A VAL 3.2 1.0 + - - -
88A LYS 3.1 15.4 + - - -
89A HIS 4.3 1.1 - - - -
90A ILE* 1.3 78.3 - - - +
92A TYR* 1.3 61.4 + - - +
93A ASP* 3.3 19.9 + - - +
97A LYS* 3.6 16.5 + - - +
168A ARG* 4.0 13.0 + - - -
178A PRO* 3.9 10.0 - - - +
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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