Contacts of the strand formed by residues 45 - 52 (chain C) in PDB entry 3VTW
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 LYS 45 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C ARG* 2.9 20.3 + - - -
42C HIS* 3.1 45.8 + - + +
44C THR* 1.3 86.8 + - - +
46C ILE* 1.3 63.5 + - - +
47C PRO* 3.6 5.4 - - - +
68C LEU* 3.8 32.8 - - + +
69C VAL 3.4 6.5 - - - +
70C PRO* 3.8 35.2 - - + -
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Residues in contact with ILE 46 (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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39C ARG* 4.2 7.9 - - - +
44C THR 5.2 0.4 - - - +
45C LYS* 1.3 77.9 - - - +
47C PRO* 1.3 69.7 - - + +
48C VAL* 3.4 13.5 - - + +
67C PHE 3.2 4.7 - - - +
68C LEU* 4.1 2.2 - - - -
69C VAL 2.6 44.3 + - - +
71C ASP* 4.1 10.5 - - + -
110C ILE* 3.8 27.8 - - + -
111C SER* 3.8 26.0 - - - +
114C TYR* 3.4 47.8 - - + -
124C LEU* 4.5 1.6 - - + -
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Residues in contact with PRO 47 (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* 4.6 5.2 - - + -
38C ILE* 4.3 20.4 - - + -
39C ARG* 4.2 18.4 - - - +
45C LYS 3.6 8.5 - - - +
46C ILE* 1.3 87.1 - - + +
48C VAL* 1.3 65.8 + - - +
67C PHE 3.3 6.1 - - - +
68C LEU* 4.2 6.3 - - + -
114C TYR* 4.2 7.8 - - + +
122C GLY 3.8 19.1 - - - +
123C PHE* 4.0 23.1 - - + -
124C LEU* 3.2 23.2 + - - +
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Residues in contact with VAL 48 (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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46C ILE* 3.4 17.7 - - + +
47C PRO* 1.3 80.5 - - - +
49C ILE* 1.3 67.7 + - - +
50C ILE* 3.8 21.8 - - + -
65C THR 3.6 1.0 - - - +
66C LYS* 3.4 3.3 - - - -
67C PHE* 2.6 49.0 + - + +
69C VAL* 3.8 7.6 - - + -
78C LEU* 5.0 1.6 - - + -
110C ILE* 3.7 25.6 - - + -
123C PHE* 4.3 1.2 - - - -
124C LEU* 3.2 13.2 - - + +
126C MET* 3.6 26.7 - - + -
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Residues in contact with ILE 49 (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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22C PHE* 3.4 40.4 - - + -
48C VAL* 1.3 74.1 - - - +
50C ILE* 1.3 63.4 + - - +
51C GLU* 3.7 32.8 - - + +
65C THR* 3.4 9.4 - - + +
66C LYS* 3.6 21.3 - - + -
123C PHE* 3.5 32.1 - - + -
124C LEU 2.8 8.1 + - - +
125C TYR* 3.7 24.5 - - + -
126C MET* 2.9 26.9 + - - +
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Residues in contact with ILE 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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48C VAL* 3.8 18.4 - - + -
49C ILE* 1.3 78.3 - - - +
51C GLU* 1.3 67.4 + - - +
62C LEU* 3.9 20.1 - - + +
64C LYS 4.1 5.4 - - - +
65C THR* 3.0 23.7 + - - +
67C PHE* 3.8 28.5 - - + -
78C LEU* 4.4 11.0 - - + -
82C ILE* 3.6 36.6 - - + -
96C LEU* 4.7 7.9 - - + -
126C MET* 3.5 15.5 - - + +
128C TYR* 4.0 16.2 - - + -
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Residues in contact with GLU 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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21C THR* 3.5 19.8 - - + +
22C PHE* 2.8 33.4 + - - +
23C LYS 5.3 0.2 + - - -
25C ARG* 4.6 3.5 + - - -
49C ILE* 3.7 24.2 - - + +
50C ILE* 1.3 81.5 - - - +
52C ARG* 1.3 65.9 + - - +
62C LEU* 6.1 0.2 - - - -
65C THR* 4.0 7.7 - - + +
125C TYR* 4.5 8.0 - - - -
126C MET 3.0 10.9 + - - +
127C VAL* 3.1 14.4 - - + +
128C TYR* 2.9 31.3 + - - -
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Residues in contact with ARG 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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19C GLU* 2.9 39.0 + - - +
51C GLU* 1.3 78.9 - - - +
53C TYR* 1.3 69.4 + - - +
54C LYS* 3.5 3.1 + - - -
56C GLU* 3.5 37.0 + - + +
57C LYS 6.3 0.2 - - - -
59C LEU 3.1 28.7 + - - -
60C PRO* 3.9 7.7 - - - +
61C VAL* 3.8 33.0 - - + +
127C VAL* 4.4 0.8 - - - +
128C TYR* 3.4 30.2 + - + +
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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