Contacts of the strand formed by residues 67 - 73 (chain B) in PDB entry 1PVI
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 TYR 67 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48B LEU* 4.1 19.5 - - + -
58B ASP* 3.0 27.5 - - - +
59B ALA 2.8 16.9 + - - +
61B ASP* 4.0 18.2 + - + +
65B GLN* 3.0 54.8 + - + -
66B GLU* 1.3 75.9 - - - +
68B GLU* 1.3 60.8 + - - +
69B LEU* 4.0 8.5 - - + -
97B VAL* 4.5 5.2 - - - -
98B PRO* 3.4 35.2 - - + +
100B ILE* 3.3 29.8 - - + -
114B ARG* 4.6 19.8 + - - -
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Residues in contact with GLU 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B GLU 5.2 0.5 - - - +
57B ASN 4.0 11.2 - - - +
58B ASP* 4.6 7.6 - - - +
67B TYR* 1.3 72.5 - - - +
69B LEU* 1.3 59.1 + - - +
70B LYS* 3.8 22.0 - - - -
93B LYS 5.3 3.6 - - - +
94B TYR* 5.7 2.6 - - - +
97B VAL* 4.4 9.3 - - + +
98B PRO 2.9 6.0 + - - +
99B TRP* 3.1 46.4 + - + +
100B ILE 2.7 31.9 + - - +
9C C 3.3 22.0 + - - -
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Residues in contact with LEU 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B LEU* 3.5 31.6 - - + +
42B VAL* 4.1 19.5 - - + -
43B LEU* 4.5 5.2 - - + -
48B LEU* 4.4 10.1 - - + -
50B VAL* 6.2 0.4 - - + -
57B ASN* 3.5 26.7 + - - +
59B ALA* 3.9 33.9 - - + +
67B TYR* 4.0 11.2 - - + -
68B GLU* 1.3 90.8 - - - +
70B LYS* 1.3 72.2 + - - +
100B ILE* 3.5 19.7 - - + +
9C C 5.6 0.3 + - - -
10C T 4.3 7.4 + - - -
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Residues in contact with LYS 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B GLU* 3.8 35.4 + - + +
69B LEU* 1.3 76.6 + - - +
71B SER* 1.3 62.0 + - - +
80B PHE* 3.8 22.4 - - + -
81B SER 4.0 14.8 + - - +
82B THR* 3.9 20.8 + - - +
99B TRP* 4.0 34.0 - - + -
100B ILE* 3.0 8.3 + - - +
101B PHE* 3.7 12.4 - - + -
102B ALA* 2.9 27.7 + - - +
9C C 4.2 12.1 + - - -
10C T 3.6 24.2 + - - +
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Residues in contact with SER 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B ASN* 3.5 29.4 - - - -
38B LYS* 3.9 11.6 - - - +
42B VAL* 5.7 0.3 - - - +
70B LYS* 1.3 76.0 - - - +
72B ILE* 1.3 63.3 + - - +
80B PHE* 4.0 6.2 - - - -
81B SER 5.8 1.0 + - - -
102B ALA* 3.7 6.1 - - - +
104B TYR* 3.0 31.5 + - - -
10C T 3.3 18.0 + - - +
11C G 4.3 8.0 + - - -
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Residues in contact with ILE 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B LYS* 5.3 3.5 - - - +
71B SER* 1.3 78.6 + - - +
73B ASN* 1.3 69.7 + - - +
74B ILE* 3.4 5.4 + - + +
77B THR* 3.7 19.3 - - - +
79B GLY 3.6 44.0 - - - +
80B PHE* 3.2 33.7 - - + +
102B ALA 3.3 9.8 + - - +
103B ILE* 3.9 11.9 - - + -
104B TYR* 2.9 32.1 + - - +
146B VAL* 4.0 13.0 - - + -
11C G 4.5 9.9 - - - +
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Residues in contact with ASN 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ASN 5.4 4.8 + - - -
30A ASP* 5.5 6.6 + - - +
38B LYS* 4.8 4.9 - - - +
72B ILE* 1.3 78.4 - - - +
74B ILE* 1.3 52.8 + - - +
75B ASP* 2.6 31.6 + - - +
76B LEU* 2.9 46.5 + - + +
77B THR* 3.5 10.3 + - - +
104B TYR* 3.5 4.9 - - - -
106B GLY* 2.9 40.8 + - - +
11C G 4.4 12.4 + - - +
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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