Contacts of the strand formed by residues 89 - 95 (chain L) in PDB entry 1VPO
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 GLY 89 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42L LEU* 4.0 6.5 - - - -
43L GLN 3.6 9.2 - - - -
45L PRO* 4.1 4.5 - - - -
87L ASP 3.5 0.8 + - - -
88L LEU* 1.3 83.9 - - - +
90L VAL* 1.3 64.4 + - - -
91L TYR* 3.9 0.3 - - - -
107L THR 3.7 0.3 - - - +
108L LYS* 3.6 18.1 - - - -
109L LEU* 2.8 31.8 + - - +
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Residues in contact with VAL 90 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43H LYS* 5.8 7.0 - - + -
42L LEU* 3.5 1.2 - - - +
43L GLN* 2.8 44.6 + - + +
89L GLY* 1.3 71.8 - - - -
91L TYR* 1.3 69.3 + - - +
92L TYR* 3.5 39.1 - - + +
106L GLY* 4.2 2.7 - - - -
107L THR 3.5 16.4 - - - +
108L LYS* 3.3 33.2 - - + +
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Residues in contact with TYR 91 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6L GLN* 3.0 7.2 + - - +
21L ILE* 3.7 27.6 - - + -
40L TRP* 5.0 1.6 - - + -
41L TYR 3.1 7.6 - - - +
42L LEU* 3.6 15.8 - - + +
52L LEU* 3.5 29.4 - - + -
67L PHE* 3.5 17.3 - + - -
78L LEU* 3.4 26.0 - - + -
80L ILE* 3.6 9.3 - - + +
87L ASP* 2.8 43.6 + - - +
89L GLY 3.9 3.6 - - - -
90L VAL* 1.3 76.5 - - - +
92L TYR* 1.3 62.2 + - - +
106L GLY* 3.1 5.0 - - - -
107L THR 2.8 38.1 + - - +
109L LEU* 3.6 21.8 - - + -
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Residues in contact with TYR 92 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39H GLN* 3.3 8.7 + - - -
43H LYS* 2.5 35.2 + - - +
44H ARG* 4.7 0.2 - - - -
45H LEU* 3.7 34.5 - - + -
6L GLN* 3.7 4.0 - - - +
40L TRP* 3.2 7.9 - - - -
41L TYR* 2.7 52.3 + - + +
43L GLN* 3.9 17.3 + - + -
49L PRO* 5.5 0.7 - - + -
90L VAL* 3.5 35.6 - - + +
91L TYR* 1.3 75.8 - - - +
93L CYS* 1.3 64.8 + - - +
103L PHE* 4.3 11.9 - - + -
104L GLY 3.6 19.5 - - - -
105L GLY 4.3 4.5 - - - -
106L GLY* 3.6 17.3 - - - -
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Residues in contact with CYS 93 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4L VAL* 3.3 21.8 - - - -
6L GLN* 3.3 4.8 + - - -
23L CYS* 2.0 50.5 - - + -
38L ILE* 5.7 5.2 - - + -
39L GLU 3.2 6.7 - - - +
40L TRP* 3.4 24.2 - - + -
92L TYR* 1.3 75.4 - - - +
94L PHE* 1.3 62.9 + - - +
95L ASP* 6.1 0.2 - - - -
103L PHE* 3.5 6.2 - - - -
104L GLY* 3.0 27.4 + - - -
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Residues in contact with PHE 94 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47H TRP* 5.1 3.6 - + + -
105H LEU* 4.0 12.6 - - + -
1010H TES 3.5 28.3 - - + -
37L PRO 3.4 5.6 - - - +
38L ILE* 3.4 5.9 - - - +
39L GLU* 2.5 67.0 + - + +
41L TYR* 3.6 17.5 - + + -
93L CYS* 1.3 78.4 - - - +
95L ASP* 1.3 59.3 + - - +
96L GLY* 4.4 6.7 - - - -
101L PRO* 3.3 35.0 - - + -
102L LYS 3.4 15.3 - - - -
103L PHE* 3.4 38.8 - + + -
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Residues in contact with ASP 95 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2L VAL* 4.6 8.4 - - - +
4L VAL* 3.5 24.5 - - + +
25L SER* 3.0 32.9 + - - -
29L ILE* 3.7 8.2 - - - +
37L PRO 3.7 4.1 - - - +
38L ILE* 4.2 14.4 - - + +
94L PHE* 1.3 72.0 - - - +
96L GLY* 1.3 59.3 + - - +
97L SER* 2.8 33.3 + - - -
98L THR 4.9 0.7 + - - +
100L PRO 4.8 0.3 - - - +
101L PRO* 3.5 2.4 - - - +
102L LYS* 2.8 30.8 + - + +
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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