Contacts of the helix formed by residues 71 - 79 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133B VAL* 4.0 27.8 - - + +
136B TYR* 3.7 29.7 + - + +
137B GLY 4.8 0.2 - - - -
138B GLY* 3.7 23.3 - - - +
68D HIS* 2.8 17.0 + - - -
70D GLY* 1.3 69.4 - - - -
72D LEU* 1.3 67.8 + - - +
73D VAL* 3.7 20.2 - - + -
74D ASP* 3.0 46.5 + - - +
104D ASN* 6.0 0.4 - - - +
107D LEU* 4.5 10.8 - - + -
200D PNS 3.4 18.4 - - - +
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Residues in contact with LEU 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D PRO* 3.9 26.2 - - + -
33D LEU* 3.5 31.2 - - + -
35D THR* 4.5 5.4 - - + +
68D HIS* 3.9 7.4 - - + -
70D GLY 3.4 2.4 + - - -
71D LEU* 1.3 65.3 - - - +
73D VAL* 1.3 63.0 + - + +
75D TYR* 3.0 19.5 + - + +
76D LEU* 3.3 12.3 + - + +
84D LEU* 3.6 38.1 - - + -
104D ASN* 4.1 11.4 - - - +
200D PNS 2.4 54.2 + - + +
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Residues in contact with VAL 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D LEU* 3.7 24.7 - - + +
72D LEU* 1.3 75.9 - - + +
74D ASP* 1.3 61.5 + - - +
76D LEU* 3.4 11.8 + - + +
77D LYS* 2.9 37.1 + - - +
104D ASN* 3.6 48.9 - - + +
107D LEU* 3.8 24.2 - - + +
108D TYR* 3.9 17.0 - - + -
111D LEU* 4.6 4.3 - - + -
200D PNS 4.4 0.4 + - - -
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Residues in contact with ASP 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B TYR 4.5 5.4 - - - +
137B GLY 5.5 1.7 - - - +
68D HIS* 4.5 6.5 - - + +
71D LEU* 3.0 43.6 + - + +
73D VAL* 1.3 78.2 - - - +
75D TYR* 1.3 64.8 + - - +
77D LYS* 4.0 11.9 - - - +
78D LYS* 3.0 25.9 + - - +
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Residues in contact with TYR 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D VAL* 4.4 1.3 - - + -
31D VAL* 3.7 16.2 - - + +
33D LEU* 3.7 34.5 - - + -
66D ASP* 2.6 34.5 + - - +
67D VAL 4.5 3.4 - - - -
68D HIS* 3.9 36.5 + + + -
71D LEU 3.6 2.0 + - - -
72D LEU 3.0 11.0 + - - +
74D ASP* 1.3 78.1 - - - +
76D LEU* 1.3 74.7 + - + +
78D LYS* 3.4 7.0 + - + +
79D HIS* 3.1 61.6 + + - -
81D ILE* 4.0 15.5 - - + -
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Residues in contact with LEU 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D VAL* 3.1 44.2 - - + -
72D LEU* 3.3 11.8 + - + +
73D VAL* 3.7 14.8 - - - +
75D TYR* 1.3 83.6 - - + +
77D LYS* 1.3 58.3 + - - +
79D HIS 3.3 0.7 + - - -
80D GLY* 3.0 8.7 + - - -
81D ILE* 2.8 52.0 + - + +
84D LEU* 3.3 29.2 - - + -
108D TYR* 3.6 7.4 - - + -
111D LEU* 3.5 26.9 - - + -
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Residues in contact with LYS 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73D VAL* 2.9 30.6 + - - +
74D ASP* 4.0 12.6 - - - +
76D LEU* 1.3 72.5 - - - +
78D LYS* 1.3 66.1 + - - +
80D GLY* 3.3 11.4 + - - -
107D LEU 2.9 28.2 + - - -
108D TYR* 3.6 44.7 - - + +
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Residues in contact with LYS 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D ASP 3.0 20.0 + - - +
75D TYR* 3.5 8.1 - - + +
77D LYS* 1.3 77.7 - - - +
79D HIS* 1.3 89.8 + - + +
80D GLY 3.7 0.2 + - - -
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Residues in contact with HIS 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D LYS* 5.6 1.6 - - - +
66D ASP* 5.0 1.7 + - - -
75D TYR* 3.1 61.4 + + - +
77D LYS 3.2 0.2 - - - -
78D LYS* 1.3 109.2 + - + +
80D GLY* 1.3 64.5 + - - +
81D ILE* 3.3 25.5 + - + +
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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