Contacts of the strand formed by residues 49 - 56 (chain C) in PDB entry 3VBI
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 ILE 49 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ASP* 4.1 8.3 - - + +
47A PHE* 3.8 18.8 - - + -
64A ALA* 3.6 29.8 - - + -
65A TYR* 3.4 21.1 - - + +
1500A 0FX 4.3 13.0 - - + -
29C SER* 3.3 10.3 - - - -
31C TYR* 4.3 20.4 - - + -
48C CYS* 1.3 80.4 - - - +
50C LEU* 1.3 67.6 + - - +
51C SER* 4.3 7.6 - - - -
66C THR 2.9 7.9 + - - +
67C ALA* 3.3 6.0 - - + -
68C LEU 2.8 31.5 + - - -
69C TYR* 4.7 9.2 - - + +
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Residues in contact with LEU 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C PHE* 5.5 0.2 - - + -
29C SER 2.9 8.2 + - - +
30C ILE* 3.5 20.5 - - + -
31C TYR* 2.9 27.0 + - - +
36C ILE* 4.1 28.7 - - + +
38C ILE* 4.8 1.8 - - + -
44C ILE* 4.0 38.8 - - + -
48C CYS* 4.4 7.2 - - + -
49C ILE* 1.3 80.2 - - - +
51C SER* 1.3 61.4 + - - +
54C VAL* 4.1 24.7 - - + -
56C ILE* 4.3 5.4 - - + -
62C ILE* 4.8 4.0 - - + -
68C LEU* 3.5 25.6 - - + -
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Residues in contact with SER 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1500A 0FX 2.5 45.1 + - - -
31C TYR* 3.6 17.1 - - - +
49C ILE* 4.3 13.5 - - - -
50C LEU* 1.3 76.7 - - - +
52C GLY* 1.3 64.3 + - - +
54C VAL* 4.2 1.7 - - - +
68C LEU 3.0 10.5 + - - +
69C TYR* 3.7 4.1 - - - -
70C GLY 2.8 28.2 + - - -
71C GLY 3.7 1.8 + - - -
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Residues in contact with GLY 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C TYR* 3.3 11.9 + - - +
32C ASN* 4.5 12.6 - - - +
35C VAL* 4.2 6.5 - - - +
36C ILE* 3.3 20.1 - - - +
51C SER* 1.3 79.5 + - - +
53C LYS* 1.3 63.7 + - - -
54C VAL* 3.3 5.2 + - - +
71C GLY* 3.8 13.9 - - - -
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Residues in contact with LYS 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C LEU* 6.5 0.4 - - + -
35C VAL* 3.5 34.5 - - + +
52C GLY* 1.3 69.8 - - - -
54C VAL* 1.3 65.4 + - - +
55C THR* 4.9 10.4 + - - +
70C GLY* 3.2 5.0 - - - -
71C GLY 3.1 19.6 + - - +
72C GLU 3.8 17.3 - - - +
73C VAL 3.9 11.0 - - - -
74C GLY* 3.0 16.3 - - - -
75C ILE 2.9 22.6 + - - +
117C LYS* 6.0 3.9 - - - +
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Residues in contact with VAL 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C VAL 3.5 4.0 + - - +
36C ILE* 3.3 14.9 - - + +
37C SER 3.2 22.0 + - - +
50C LEU* 4.1 11.4 - - + -
51C SER 4.2 13.5 - - - +
52C GLY 3.3 15.6 + - - +
53C LYS* 1.3 83.0 - - - +
55C THR* 1.3 65.4 + - - +
56C ILE* 3.9 29.4 - - + -
68C LEU* 4.1 32.5 - - + +
70C GLY* 4.3 4.5 - - - +
75C ILE* 3.3 13.0 - - + +
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Residues in contact with THR 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C VAL 5.3 0.5 + - - -
37C SER* 3.4 22.2 + - - +
53C LYS* 4.9 11.3 + - - +
54C VAL* 1.3 76.7 + - - +
56C ILE* 1.3 66.6 + - - +
75C ILE 2.8 12.3 + - - +
76C GLU* 3.2 30.9 + - - +
77C MET* 2.7 33.5 + - - +
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Residues in contact with ILE 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C SER* 2.9 10.1 + - - +
38C ILE* 3.3 19.4 - - + -
39C GLY* 3.0 20.6 + - - -
42C VAL* 4.0 19.5 - - + -
44C ILE* 4.5 4.9 - - + -
50C LEU* 4.3 15.9 - - + -
54C VAL* 3.9 22.9 - - + -
55C THR* 1.3 83.5 - - - +
57C GLY* 1.3 70.7 + - - +
60C SER* 4.0 18.6 - - - +
62C ILE* 4.2 21.8 - - + -
68C LEU* 4.6 1.1 - - + -
77C MET* 3.9 22.9 - - + -
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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