Contacts of the helix formed by residues 71 - 79 (chain E) in PDB entry 1VLH
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 LEU 71 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133C VAL* 4.1 20.2 - - + +
136C TYR* 3.6 30.5 + - + +
137C GLY 5.0 0.4 - - - -
138C GLY* 3.9 21.8 - - - +
68E HIS* 2.7 19.7 + - - -
70E GLY* 1.3 68.5 - - - -
72E LEU* 1.3 63.9 + - - +
73E VAL* 3.6 27.1 - - + -
74E ASP* 3.0 37.0 + - - +
77E LYS* 6.3 0.2 - - - +
104E ASN* 6.1 0.2 - - - +
107E LEU* 4.3 20.0 - - + -
200E PNS 3.5 17.0 - - - +
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Residues in contact with LEU 72 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E PRO* 3.7 33.9 - - + -
33E LEU* 3.5 31.4 - - + -
35E THR* 4.3 6.3 - - + +
68E HIS* 3.9 6.3 - - + -
70E GLY 3.3 2.4 + - - -
71E LEU* 1.3 71.4 - - - +
73E VAL* 1.3 64.5 + - + +
75E TYR* 3.0 12.3 + - - +
76E LEU* 3.3 16.9 + - + +
84E LEU* 3.7 24.7 - - + -
104E ASN* 4.4 9.4 - - - +
200E PNS 2.7 44.1 + - - +
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Residues in contact with VAL 73 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71E LEU* 3.6 26.4 - - + +
72E LEU* 1.3 79.3 - - + +
74E ASP* 1.3 59.4 + - - +
76E LEU* 3.2 9.9 + - + +
77E LYS* 2.9 42.7 + - - +
84E LEU* 5.7 0.2 - - + -
104E ASN* 3.7 36.5 + - + +
107E LEU* 3.8 19.3 - - + -
108E TYR* 3.7 31.4 - - + -
111E LEU* 4.1 4.5 - - + -
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Residues in contact with ASP 74 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C TYR 4.6 5.2 - - - +
137C GLY 5.7 0.9 - - - +
68E HIS* 4.5 6.5 - - + +
71E LEU* 3.0 40.6 + - + +
73E VAL* 1.3 78.4 - - - +
75E TYR* 1.3 65.2 + - - +
77E LYS* 3.9 15.9 + - - +
78E LYS* 3.0 27.1 + - - +
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Residues in contact with TYR 75 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E VAL* 4.1 15.7 - - + -
31E VAL* 3.6 12.3 - - + +
33E LEU* 3.6 31.2 - - + -
66E ASP* 2.7 34.3 + - - +
67E VAL 4.6 3.6 - - - -
68E HIS* 3.7 38.0 + + + -
71E LEU 3.6 2.0 + - - -
72E LEU 3.0 11.6 + - - +
74E ASP* 1.3 80.7 - - - +
76E LEU* 1.3 74.4 + - + +
78E LYS* 3.6 10.6 + - - +
79E HIS* 3.2 66.8 + + - +
81E ILE* 4.6 4.3 - - + -
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Residues in contact with LEU 76 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E VAL* 3.7 25.1 - - + -
72E LEU* 3.3 16.4 + - + +
73E VAL* 3.2 10.4 + - - +
75E TYR* 1.3 88.3 - - + +
77E LYS* 1.3 56.4 + - - +
79E HIS 3.3 0.7 + - - -
80E GLY 2.9 8.7 + - - -
81E ILE* 2.8 55.9 + - + +
83E VAL 4.5 4.0 - - - +
84E LEU* 3.4 27.6 - - + -
108E TYR* 3.7 7.0 - - + -
111E LEU* 3.3 35.7 - - + -
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Residues in contact with LYS 77 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71E LEU* 6.3 0.2 - - - +
73E VAL* 2.9 29.9 + - - +
74E ASP* 3.9 15.3 + - - +
76E LEU* 1.3 71.2 - - - +
78E LYS* 1.3 63.8 + - - +
80E GLY* 3.3 11.5 + - - +
107E LEU* 2.8 29.9 + - - +
108E TYR* 3.6 43.3 - - + +
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Residues in contact with LYS 78 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68E HIS* 5.2 10.1 + - - -
74E ASP 3.0 19.1 + - - +
75E TYR* 3.6 14.1 - - - +
77E LYS* 1.3 78.2 - - - +
79E HIS* 1.3 83.4 + - + +
80E GLY 3.8 0.5 + - - -
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Residues in contact with HIS 79 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2E LYS* 5.7 7.9 - - - +
66E ASP* 4.6 4.4 + - - -
75E TYR* 3.2 61.0 + + + +
76E LEU 4.2 0.7 - - - +
77E LYS 3.2 0.2 - - - -
78E LYS* 1.3 101.4 - - + +
80E GLY* 1.3 63.3 + - - +
81E ILE* 3.3 25.4 + - + +
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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