Contacts of the helix formed by residues 79 - 90 (chain A) in PDB entry 4H7Y
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 ALA 79 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A LYS* 3.7 9.6 - - + -
72A ALA* 3.6 38.1 - - + +
75A GLU 3.2 4.7 + - - +
76A PRO 3.5 3.4 + - - +
77A ASP 3.7 0.2 - - - -
78A ASP* 1.3 76.0 - - - +
80A ARG* 1.3 67.0 + - - +
81A ASP 3.2 3.1 - - - -
82A TYR* 3.0 24.5 + - - +
83A PHE* 3.3 15.7 - - + -
103A PHE* 4.1 13.5 - - + -
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Residues in contact with ARG 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 PRO 4.8 0.2 + - - -
77A ASP 5.5 5.6 + - - +
78A ASP 3.4 2.1 - - - -
79A ALA* 1.3 76.7 - - - +
81A ASP* 1.3 65.4 + - - +
83A PHE* 3.1 9.1 + - - +
84A GLN* 3.1 42.2 + - - +
100A PHE* 4.1 6.1 - - + -
103A PHE* 3.8 27.6 - - + -
104A GLU* 2.5 41.8 + - - +
107A GLN* 4.8 4.6 - - - +
109A ASN* 3.3 14.8 - - - +
112A LYS* 6.5 0.7 - - - +
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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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78A ASP 4.3 7.0 + - - +
79A ALA 3.2 1.2 - - - -
80A ARG* 1.3 79.1 - - - +
82A TYR* 1.3 61.1 + - + +
84A GLN* 2.9 26.1 + - - +
85A MET* 2.9 26.7 + - - +
84D GLN* 4.0 16.7 + - - +
87D ARG* 2.5 36.6 + - - +
112D LYS* 3.3 27.1 + - - -
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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
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64A GLN 4.7 0.7 - - - +
67A PHE* 3.6 26.2 - + + -
68A ALA* 3.8 23.1 - - + +
71A LYS* 3.8 28.9 - - + -
78A ASP* 3.4 21.0 - - + +
79A ALA* 3.0 20.9 + - - +
81A ASP* 1.3 78.1 - - + +
83A PHE* 1.3 59.3 + - - +
85A MET* 3.3 13.9 + - + +
86A ALA* 3.0 26.3 + - - +
84D GLN* 4.0 29.1 + - + -
85D MET* 4.5 6.3 - - + -
87D ARG* 4.5 13.0 + - - +
88D ALA* 3.2 31.1 + - + +
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Residues in contact with PHE 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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65A VAL* 5.9 2.0 - - + -
68A ALA* 3.5 41.7 - - + -
69A GLU* 3.9 10.8 - - + -
72A ALA* 4.1 7.2 - - + -
79A ALA* 3.3 23.3 - - + -
80A ARG 3.1 4.3 + - - +
82A TYR* 1.3 74.4 - - - +
84A GLN* 1.3 66.1 + - - +
86A ALA* 3.3 5.1 + - + +
87A ARG* 3.0 24.9 + - - +
96A VAL* 5.0 1.5 - - - +
99A SER* 3.2 32.8 - - - -
100A PHE* 3.4 43.0 - + + +
103A PHE* 3.5 39.3 - + + -
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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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80A ARG* 3.1 32.7 + - - +
81A ASP* 2.9 31.4 + - - +
82A TYR 3.3 0.2 - - - -
83A PHE* 1.3 77.2 - - - +
85A MET* 1.3 55.4 + - - +
87A ARG* 3.4 12.6 + - - +
88A ALA* 2.9 31.8 + - - +
100A PHE* 3.4 29.4 - - + -
112D LYS* 4.9 4.7 + - - -
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Residues in contact with MET 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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46A ILE* 4.0 9.9 - - + -
64A GLN* 3.8 26.2 - - + +
67A PHE* 4.5 8.7 - - + -
81A ASP 2.9 17.1 + - - +
82A TYR* 3.4 17.7 - - + +
83A PHE 3.2 0.2 - - - -
84A GLN* 1.3 76.7 - - - +
86A ALA* 1.3 62.5 + - - +
88A ALA* 3.3 6.0 + - - +
89A ASN* 3.0 29.2 + - - +
81D ASP* 3.6 31.4 - - - +
84D GLN* 4.0 31.6 - - - +
85D MET* 3.9 25.8 - - + -
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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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61A ALA 5.1 0.4 - - - +
64A GLN* 3.6 35.0 + - + +
65A VAL* 4.1 14.6 - - + -
68A ALA* 5.5 0.4 - - + -
82A TYR 3.0 15.5 + - - +
83A PHE* 3.3 7.2 + - + +
85A MET* 1.3 76.2 - - - +
87A ARG* 1.3 57.2 + - - +
89A ASN 3.3 0.5 + - - -
90A CYS* 2.9 34.3 + - + +
96A VAL* 3.7 16.0 - - + +
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Residues in contact with ARG 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 PHE 3.0 17.8 + - - +
84A GLN* 3.9 10.7 + - - +
86A ALA* 1.3 76.7 - - - +
88A ALA* 1.3 63.3 + - - +
89A ASN 3.4 0.2 + - - -
90A CYS 4.9 0.4 - - - -
91A LYS* 3.4 24.9 - - + +
96A VAL* 3.6 14.9 - - + +
97A HIS* 3.6 38.5 + - + +
100A PHE* 3.9 25.5 - - + -
112A LYS* 5.6 3.4 - - - +
116A LEU* 3.3 29.0 - - - +
119A LYS* 4.7 15.2 - - - +
123A ARG* 4.1 22.2 - - - +
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Residues in contact with ALA 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 GLN 2.9 18.6 + - - +
85A MET* 3.7 7.2 - - - +
87A ARG* 1.3 80.0 - - - +
89A ASN* 1.3 66.2 + - - +
91A LYS* 4.8 7.0 + - - +
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Residues in contact with ASN 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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51A PRO* 3.8 21.1 - - + +
55A GLY* 3.3 24.8 - - - +
60A PHE* 4.2 6.5 - - + -
64A GLN* 2.9 27.2 + - - +
85A MET* 3.0 17.7 + - - +
86A ALA 4.1 0.2 - - - +
88A ALA* 1.3 86.2 - - - +
90A CYS* 1.3 66.0 + - - +
91A LYS* 3.7 1.5 + - - -
81D ASP* 3.0 33.3 + - - +
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Residues in contact with CYS 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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54A TYR 4.3 2.2 - - - -
55A GLY 3.6 13.9 - - - +
57A ASN 4.8 0.7 - - - -
60A PHE* 3.5 33.0 - - - -
61A ALA* 3.7 35.9 - - + -
64A GLN* 5.0 3.6 - - - -
86A ALA* 2.9 15.2 + - + +
87A ARG* 4.7 0.4 - - - -
89A ASN* 1.3 88.2 - - - +
91A LYS* 1.3 63.1 + - - +
92A LYS 3.1 4.8 + - - -
93A PHE* 3.4 15.9 + - + -
96A VAL* 3.9 13.8 - - + +
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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