Contacts of the helix formed by residues 66 - 77 (chain D) in PDB entry 1VLP
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 66 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64D ARG* 3.9 8.3 - - + +
65D PHE* 1.3 73.8 - - - +
67D GLU* 1.3 63.8 + - - +
68D GLU* 3.6 9.1 + - - +
69D GLU* 3.1 41.5 + - - +
70D ILE* 3.0 26.0 + - - +
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Residues in contact with GLU 67 (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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66D THR* 1.3 72.5 - - - +
68D GLU* 1.3 57.6 + - - +
70D ILE* 3.3 8.1 + - + +
71D GLU* 2.9 46.6 + - + +
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Residues in contact with GLU 68 (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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66D THR* 3.2 8.6 + - - +
67D GLU* 1.3 78.3 - - - +
69D GLU* 1.3 57.5 + - + +
71D GLU* 3.4 7.3 + - - +
72D TYR* 3.0 26.9 + - - +
220D LYS* 2.5 35.4 + - - +
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Residues in contact with GLU 69 (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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7D LYS 5.0 0.7 - - - +
8D SER* 2.5 35.3 + - - -
9D LEU 4.8 1.9 + - - -
10D LEU* 3.6 30.7 - - + +
64D ARG 3.7 5.2 - - - +
65D PHE* 3.4 17.9 - - + -
66D THR* 3.1 41.9 + - - +
68D GLU* 1.3 71.6 - - + +
70D ILE* 1.3 65.7 + - - +
72D TYR* 3.2 5.9 + - - +
73D LEU* 3.0 27.3 + - - +
217D LEU* 5.2 2.8 - - + +
220D LYS* 5.0 6.5 - - + +
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Residues in contact with ILE 70 (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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65D PHE* 3.9 23.3 - - + +
66D THR 3.0 20.3 + - - +
67D GLU* 3.6 9.9 - - + +
69D GLU* 1.3 73.5 - - - +
71D GLU* 1.3 62.8 + - - +
73D LEU* 3.2 8.4 + - + +
74D LYS* 3.0 44.6 + - + +
85D ILE* 4.0 9.9 - - + -
88D ILE* 3.7 35.4 - - + +
89D SER* 3.6 28.7 - - - +
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Residues in contact with GLU 71 (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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67D GLU* 2.9 32.9 + - + +
68D GLU* 3.7 7.4 - - - +
69D GLU 3.2 0.2 - - - -
70D ILE* 1.3 78.8 - - - +
72D TYR* 1.3 58.3 + - - +
74D LYS* 3.3 36.0 + - - +
75D GLN* 2.9 30.5 + - - +
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Residues in contact with TYR 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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10D LEU* 4.3 4.3 - - + -
68D GLU 3.0 14.0 + - - +
69D GLU* 3.2 9.6 + - - +
71D GLU* 1.3 74.5 - - - +
73D LEU* 1.3 62.5 + - + +
75D GLN* 3.9 19.5 - - - -
76D GLU* 2.9 53.7 + - + +
216D ILE* 3.7 32.5 - - + -
219D ALA* 3.5 13.7 + - - +
220D LYS* 3.4 60.7 + - + -
224D VAL 3.5 8.5 + - - -
226D PRO* 3.6 11.1 - - + +
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Residues in contact with LEU 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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10D LEU* 3.8 28.5 - - + -
17D ILE* 4.5 14.4 - - + -
65D PHE* 4.1 12.1 - - + -
69D GLU 3.0 15.0 + - - +
70D ILE* 3.2 10.3 + - - +
72D TYR* 1.3 77.1 - - + +
74D LYS* 1.3 55.3 + - - +
77D ILE* 2.7 62.9 + - + +
80D LEU* 4.2 13.0 - - + -
85D ILE* 4.9 3.6 - - + -
88D ILE* 4.0 26.9 - - + -
216D ILE* 4.2 19.7 - - + -
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Residues in contact with LYS 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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70D ILE* 3.0 30.3 + - + +
71D GLU* 3.3 37.5 + - - +
72D TYR 3.3 0.2 - - - -
73D LEU* 1.3 75.0 - - - +
75D GLN* 1.3 62.0 + - - +
77D ILE 4.5 3.8 - - - -
78D PRO* 3.3 25.7 - - - +
85D ILE* 4.1 32.5 - - + +
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Residues in contact with GLN 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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71D GLU 2.9 17.6 + - - +
72D TYR* 3.7 19.0 - - - +
74D LYS* 1.3 79.9 - - - +
76D GLU* 1.3 90.1 + - - +
77D ILE 3.8 0.2 + - - -
78D PRO* 3.8 9.5 - - - +
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Residues in contact with GLU 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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14D MSE 5.4 2.1 - - - +
72D TYR* 2.9 51.1 + - + +
75D GLN* 1.3 106.4 + - - +
77D ILE* 1.3 64.8 + - + +
78D PRO* 3.4 7.1 - - - +
79D TYR* 5.0 3.3 + - - -
224D VAL 5.4 1.6 - - - -
225D LYS* 4.7 9.4 - - - +
226D PRO* 3.7 31.2 - - + +
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Residues in contact with ILE 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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14D MSE 4.0 34.5 - - + -
17D ILE* 4.7 8.3 - - + -
18D THR* 4.1 6.3 - - + -
73D LEU* 2.7 48.6 + - + +
74D LYS* 4.2 1.6 - - - +
76D GLU* 1.3 84.5 - - + +
78D PRO* 1.4 65.1 - - - +
79D TYR* 3.1 36.8 + - + +
80D LEU* 3.2 40.8 + - + +
216D ILE* 5.0 2.7 - - + -
226D PRO* 4.9 3.1 - - + -
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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