Contacts of the helix formed by residues 77 - 87 (chain N) in PDB entry 1VYH
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 77 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75N GLY 4.0 5.6 - - - +
76N ASP* 1.3 78.1 - - - +
78N THR* 1.3 66.8 + - - +
79N ARG* 3.4 18.5 + - - +
80N HIS* 2.9 29.9 + - + +
81N VAL* 3.0 21.8 + - - +
102N VAL* 3.7 6.3 - - - -
105N ASN 3.9 21.1 - - - +
106N ASN* 3.5 22.6 + - - +
109N ASN* 6.0 0.2 - - - +
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Residues in contact with THR 78 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9N ALA* 2.8 30.2 + - - +
77N THR* 1.3 71.9 - - - +
79N ARG* 1.3 65.1 + - - +
80N HIS 3.2 0.3 + - - -
81N VAL* 3.2 1.9 + - - +
82N LEU* 2.9 28.2 + - - +
102N VAL* 3.7 15.0 - - + +
103N GLY* 4.5 4.0 - - - -
106N ASN* 3.0 28.5 + - - +
114N VAL* 4.3 8.3 - - + +
117N GLY* 4.1 10.1 - - - -
118N ILE* 4.1 25.4 - - + +
121N ILE* 4.1 12.6 - - + +
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Residues in contact with ARG 79 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8N PRO* 2.7 39.5 + - - +
9N ALA* 3.6 14.4 - - - +
11N ILE* 3.0 20.4 + - - +
12N PRO* 3.6 2.4 - - - +
13N HIS* 3.0 69.5 + - + +
77N THR* 3.2 11.3 + - - +
78N THR* 1.3 82.8 + - - +
80N HIS* 1.3 62.3 + - - +
82N LEU* 3.6 3.0 - - - +
83N TRP 3.2 15.9 + - - -
106N ASN* 5.3 2.0 - - - +
108N GLU* 4.7 12.5 + - - -
109N ASN* 5.3 8.8 + - - +
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Residues in contact with HIS 80 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13N HIS* 3.4 34.2 + - - -
15N ALA* 3.2 36.1 - - + +
24N TRP* 4.5 5.3 - + + -
75N GLY 4.2 7.6 - - - -
76N ASP* 3.3 28.3 + - - +
77N THR* 2.9 41.6 + - + +
79N ARG* 1.3 73.2 - - - +
81N VAL* 1.3 66.3 + - - +
83N TRP* 3.1 6.5 + - - +
84N ARG* 2.9 27.0 + - - +
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Residues in contact with VAL 81 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45N VAL* 4.8 11.4 - - + -
46N GLY* 4.0 9.9 - - - +
76N ASP* 4.5 4.5 - - + -
77N THR 3.0 11.7 + - - +
78N THR 3.8 5.4 - - - +
80N HIS* 1.3 78.2 - - - +
82N LEU* 1.3 68.4 + - - +
84N ARG* 3.3 30.9 + - - +
85N LEU* 2.9 36.7 + - + +
100N VAL* 5.8 0.2 - - + -
102N VAL* 3.7 28.3 - - + -
121N ILE* 3.8 23.6 - - + -
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Residues in contact with LEU 82 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9N ALA 4.8 1.6 - - - +
10N ALA* 3.3 40.6 - - - +
11N ILE 4.6 0.4 - - - -
12N PRO* 4.1 16.6 - - + -
78N THR 2.9 15.4 + - - +
79N ARG* 3.6 5.2 - - - +
81N VAL* 1.3 77.2 - - - +
83N TRP* 1.3 54.3 + - - +
85N LEU* 2.8 8.8 + - + +
86N LYS* 2.7 36.5 + - + +
117N GLY 5.0 0.9 - - - +
120N ALA* 4.1 14.6 - - + +
121N ILE* 3.6 40.8 - - + +
124N LEU* 4.4 17.0 - - + +
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Residues in contact with TRP 83 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12N PRO* 3.8 13.6 - - + +
13N HIS* 3.5 25.6 - - - +
14N ALA* 3.3 37.7 - - + +
24N TRP* 3.6 27.6 - + + -
25N MET* 4.8 15.7 - - + -
28N HIS* 4.0 21.5 - + - -
79N ARG 3.2 2.9 + - - +
80N HIS 3.1 9.8 + - - +
82N LEU* 1.3 77.9 - - - +
84N ARG* 1.3 58.1 + - - +
86N LYS* 3.2 2.4 + - - -
87N ASN* 2.7 77.7 + - + +
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Residues in contact with ARG 84 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24N TRP* 3.4 28.0 - - + -
28N HIS* 3.6 14.5 - - - +
31N PHE* 3.8 4.2 - - - -
45N VAL* 5.0 3.2 - - - +
46N GLY 3.1 22.2 + - - +
71N PHE 2.8 29.6 + - - -
73N ILE* 3.3 21.3 - - - +
76N ASP* 2.8 25.3 + - - -
80N HIS 2.9 15.3 + - - +
81N VAL* 3.5 22.3 - - - +
83N TRP* 1.3 82.3 - - - +
85N LEU* 1.3 62.7 + - + +
87N ASN 3.3 9.2 + - - -
88N GLY 3.5 1.4 + - - -
89N GLU* 2.8 63.6 + - - +
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Residues in contact with LEU 85 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45N VAL* 3.7 28.3 - - + -
81N VAL* 2.9 23.4 + - + +
82N LEU* 2.8 12.2 + - - +
84N ARG* 1.3 72.3 - - + +
86N LYS* 1.3 60.9 - - - +
87N ASN 3.4 0.2 + - - -
88N GLY* 3.5 8.0 + - - -
89N GLU* 3.8 19.1 + - + +
90N LEU* 3.6 37.1 + - + +
121N ILE* 4.2 14.8 - - + -
124N LEU* 3.3 21.6 - - + +
125N ILE* 3.7 35.0 - - + -
128N ARG* 4.4 4.0 + - - -
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Residues in contact with LYS 86 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12N PRO* 4.4 24.9 - - + +
82N LEU* 2.7 18.4 + - + +
83N TRP* 3.6 10.5 - - + +
85N LEU* 1.3 73.1 - - - +
87N ASN* 1.3 66.5 + - - +
88N GLY 3.3 3.3 + - - -
124N LEU* 4.0 16.7 - - + +
128N ARG* 2.8 43.0 + - - +
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Residues in contact with ASN 87 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28N HIS* 3.4 17.4 + - - +
32N VAL* 4.1 3.6 - - - +
83N TRP* 2.7 85.5 + - + +
84N ARG 3.3 5.4 + - - +
85N LEU 3.2 0.4 - - - -
86N LYS* 1.3 81.7 - - - +
88N GLY* 1.3 55.9 + - - +
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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