Contacts of the helix formed by residues 76 - 88 (chain A) in PDB entry 3UVH
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 76 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A GLN* 5.7 0.8 - - - +
65A PRO 4.7 3.2 + - - -
75A THR* 1.3 82.1 - - - +
77A THR* 1.3 54.6 + - - +
78A ASN* 3.2 20.4 + - - +
79A LYS* 2.9 42.2 + - + +
80A ILE* 2.7 36.3 + - - +
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Residues in contact with THR 77 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A PHE* 3.4 35.6 - - + +
29A ARG* 3.8 34.5 - - - +
30A LEU* 3.8 17.6 - - + +
65A PRO* 3.5 16.2 + - - +
76A ASP* 1.3 72.8 + - - +
78A ASN* 1.3 59.2 + - - +
80A ILE* 3.6 10.9 - - - +
81A MET* 2.8 28.9 + - - +
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Residues in contact with ASN 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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29A ARG* 2.9 33.3 + - - +
76A ASP* 3.2 10.3 + - - +
77A THR* 1.3 79.8 - - - +
79A LYS* 1.3 60.7 + - + +
81A MET* 3.3 10.2 + - - +
82A GLU* 2.9 54.4 + - - +
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Residues in contact with LYS 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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74A HIS* 5.3 3.4 + - - +
75A THR 4.0 5.6 - - - +
76A ASP* 2.9 37.8 + - + +
78A ASN* 1.3 76.0 - - + +
80A ILE* 1.3 61.5 + - - +
82A GLU* 3.4 18.2 + - - +
83A PHE* 2.9 30.1 + - - +
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Residues in contact with ILE 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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10A LEU* 5.3 0.7 - - + -
30A LEU* 3.8 32.5 - - + -
65A PRO 4.1 4.0 - - - +
66A PHE* 3.9 16.8 - - - -
67A LEU* 4.0 22.2 - - + +
74A HIS* 3.3 37.0 - - + +
75A THR* 3.8 10.8 - - - +
76A ASP 2.7 27.1 + - - +
77A THR* 3.6 3.6 - - - +
79A LYS* 1.3 73.8 - - - +
81A MET* 1.3 58.1 + - - +
83A PHE* 3.2 7.2 + - - +
84A LEU* 2.9 41.1 + - + +
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Residues in contact with MET 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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29A ARG* 3.5 28.0 - - - +
30A LEU* 3.8 12.3 - - + +
33A VAL* 4.4 11.4 - - + +
77A THR 2.8 20.5 + - - +
78A ASN* 3.4 12.8 - - - +
80A ILE* 1.3 73.0 - - - +
82A GLU* 1.3 89.9 + - + +
84A LEU* 3.3 6.8 + - - +
85A GLU* 3.0 24.1 + - + +
175A LEU* 4.0 48.8 - - + +
179A ASN* 6.3 0.4 - - - -
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Residues in contact with GLU 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 ASN* 2.9 36.8 + - - +
79A LYS* 3.6 23.2 - - - +
81A MET* 1.3 88.8 - - + +
83A PHE* 1.3 63.1 + - - +
85A GLU* 3.3 5.1 + - - +
86A ALA* 3.0 24.3 + - - +
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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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67A LEU* 3.8 18.2 - - + -
69A TYR* 3.5 47.8 - + + -
72A GLU* 3.7 8.3 - - - -
74A HIS* 3.3 42.4 - + - +
79A LYS 2.9 17.3 + - - +
80A ILE* 3.3 5.8 - - - +
82A GLU* 1.3 74.3 - - - +
84A LEU* 1.3 63.1 + - + +
86A ALA* 3.1 5.7 + - - -
87A VAL* 2.8 60.1 + - + +
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Residues in contact with LEU 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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8A VAL* 4.9 0.4 - - + -
30A LEU* 4.6 9.2 - - + +
33A VAL* 4.4 21.1 - - + -
34A LEU* 3.7 44.0 - - + -
37A LYS* 4.0 3.1 + - - -
67A LEU* 3.9 26.0 - - + -
69A TYR* 4.8 6.7 - - + -
80A ILE* 2.9 34.9 + - + +
81A MET* 3.7 4.7 - - - +
83A PHE* 1.3 83.4 - - + +
85A GLU* 1.3 62.0 + - - +
87A VAL* 4.2 2.7 - - + -
88A LEU* 3.1 44.6 + - + +
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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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33A VAL* 5.5 0.4 - - - +
37A LYS* 2.5 44.8 + - - +
81A MET* 3.0 17.2 + - + +
82A GLU* 3.8 6.5 - - - +
84A LEU* 1.3 77.5 - - - +
86A ALA* 1.3 63.3 + - - +
88A LEU 3.6 4.5 - - - +
89A CYS* 4.3 4.3 - - - +
95A LYS* 3.4 12.4 - - - +
96A LEU* 3.1 20.4 + - - +
97A ALA* 3.0 33.6 + - + +
175A LEU* 3.8 21.3 - - + +
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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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82A GLU 3.0 17.0 + - - +
83A PHE* 3.1 5.6 + - - +
85A GLU* 1.3 77.5 - - - +
87A VAL* 1.4 65.9 + - + +
89A CYS* 3.5 20.1 - - - +
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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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69A TYR* 3.8 28.5 + - + +
83A PHE* 2.8 66.3 + - + +
84A LEU* 4.2 2.5 - - - +
86A ALA* 1.4 75.5 - - + +
88A LEU* 1.3 72.0 + - + +
89A CYS* 3.3 12.8 + - - -
93A TYR* 5.1 1.2 - - - -
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Residues in contact with LEU 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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5A GLN* 3.8 14.6 - - - +
8A VAL* 5.6 0.9 - - + -
34A LEU* 4.1 2.9 - - + -
37A LYS* 2.7 54.6 + - + +
39A VAL* 3.9 32.8 - - + -
69A TYR* 4.0 18.2 - - + +
84A LEU* 3.1 35.9 + - + +
85A GLU 3.6 1.6 - - - +
87A VAL* 1.3 80.7 - - + +
89A CYS* 1.3 58.0 + - - +
93A TYR* 3.7 36.1 - - + +
94A PRO 4.1 0.2 - - - +
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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