Contacts of the helix formed by residues 71 - 79 (chain H) in PDB entry 3H2V
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 71 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69H ASP 3.9 6.3 - - - +
70H VAL* 1.3 81.1 - - - +
72H ASN* 1.3 67.2 + - - +
73H GLN* 3.6 10.8 + - - +
74H GLU* 2.9 49.8 + - - +
75H VAL* 3.5 13.2 + - - +
89H VAL* 5.1 1.1 - - - -
91H LYS* 4.6 9.2 - - - +
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Residues in contact with ASN 72 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71H THR* 1.3 72.7 - - - +
73H GLN* 1.3 64.9 + - - +
75H VAL* 2.8 11.1 + - - +
76H HIS* 2.8 37.4 + - + +
87H CYS* 5.0 4.7 - - - +
89H VAL* 3.3 36.1 + - + +
91H LYS* 4.0 18.8 - - - +
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Residues in contact with GLN 73 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71H THR* 3.6 10.0 + - - +
72H ASN* 1.3 77.7 - - - +
74H GLU* 1.3 58.7 + - + +
76H HIS* 3.0 22.0 + - - +
77H ASP* 2.7 60.8 + - - +
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Residues in contact with GLU 74 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69H ASP 3.7 5.5 - - - +
70H VAL* 3.9 11.0 - - + +
71H THR* 2.9 45.2 + - - +
73H GLN* 1.3 77.0 - - + +
75H VAL* 1.3 56.7 + - - +
77H ASP* 3.4 10.3 + - - +
78H LEU* 2.8 27.9 + - - +
118H LEU* 4.7 14.0 - - + +
119H ARG* 2.3 46.8 + - - -
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Residues in contact with VAL 75 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63H ILE* 4.6 6.1 - - + -
66H LEU* 4.6 10.3 - - + -
70H VAL* 4.5 12.6 - - + -
71H THR 3.8 9.4 - - - +
72H ASN 2.8 11.5 + - - +
74H GLU* 1.3 70.4 - - - +
76H HIS* 1.3 67.8 + - + +
78H LEU* 3.1 11.4 + - + +
79H LEU* 3.0 46.9 + - + +
87H CYS* 4.0 17.3 - - - -
89H VAL* 3.4 27.8 - - + -
96H ALA* 4.4 17.0 - - + -
98H VAL* 4.4 1.8 - - + -
118H LEU* 6.1 0.4 - - - -
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Residues in contact with HIS 76 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72H ASN* 2.8 41.1 + - + +
73H GLN* 3.0 22.6 + - - +
75H VAL* 1.3 77.0 - - - +
77H ASP* 1.3 63.4 + - - +
79H LEU 3.2 4.6 - - - +
80H SER* 3.1 22.7 + - - -
84H LEU* 4.1 19.7 - - + +
87H CYS* 3.7 34.7 + - + +
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Residues in contact with ASP 77 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73H GLN* 2.7 47.4 + - - +
74H GLU* 3.5 9.6 - - - +
76H HIS* 1.3 77.3 - - - +
78H LEU* 1.3 60.9 + - - +
80H SER* 2.8 29.3 + - - -
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Residues in contact with LEU 78 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63H ILE* 4.3 14.1 - - + -
66H LEU* 5.1 4.0 - - + -
74H GLU 2.8 15.0 + - - +
75H VAL* 3.2 14.4 - - + +
77H ASP* 1.3 79.9 - - - +
79H LEU* 1.3 75.9 + - + +
80H SER* 3.2 4.5 + - - -
81H ASP 4.9 0.2 + - - -
113H PHE* 2.5 56.9 - - + -
116H SER* 5.3 0.9 - - - +
118H LEU* 4.6 22.4 - - + -
123H LEU* 4.0 27.1 - - + -
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Residues in contact with LEU 79 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61H ILE* 5.0 9.0 - - + -
63H ILE* 4.3 9.9 - - + -
75H VAL* 3.0 35.0 + - + +
76H HIS 3.2 6.0 - - - +
78H LEU* 1.3 88.7 - - + +
80H SER* 1.3 59.9 + - - +
81H ASP 3.1 6.2 + - - -
82H TYR* 3.4 30.1 + - + +
84H LEU* 4.1 18.4 - - + +
98H VAL* 4.0 28.3 - - + -
100H LEU* 5.4 2.5 - - + -
109H ALA* 5.4 1.6 - - + -
113H PHE* 3.4 35.0 - - + -
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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