Contacts of the helix formed by residues 38 - 45 (chain C) in PDB entry 3VZC
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 VAL 38 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33C LEU 4.0 1.8 - - - +
34C PHE* 3.1 46.0 + - + +
37C HIS* 1.3 78.1 - - - +
39C GLN* 1.3 64.8 + - - +
40C PRO 3.4 0.2 - - - -
41C LEU* 3.2 9.0 + - - +
42C LEU* 3.2 30.8 + - + +
78C MET* 3.8 21.3 - - + -
108C LEU* 3.7 17.5 - - + -
135C LEU* 4.0 9.2 - - + -
139C THR* 3.8 26.8 - - + +
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Residues in contact with GLN 39 (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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55B GLU* 5.5 2.6 + - - -
34C PHE* 2.8 29.8 + - + +
35C ARG* 2.7 48.7 + - - +
38C VAL* 1.3 73.3 - - - +
40C PRO* 1.4 70.7 - - + +
42C LEU* 3.1 19.4 + - - +
43C ALA* 3.2 15.8 + - + +
49C PHE* 3.7 25.3 - - + -
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Residues in contact with PRO 40 (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 ARG 3.4 20.6 - - - +
36C SER* 3.8 18.8 - - - +
37C HIS 4.2 1.8 - - - -
38C VAL 3.5 4.9 - - - +
39C GLN* 1.4 91.1 - - + +
41C LEU* 1.3 67.5 + - + +
43C ALA* 3.6 5.0 + - + +
44C GLU* 3.3 22.2 + - - +
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Residues in contact with LEU 41 (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 HIS 3.6 20.4 - - - +
38C VAL 3.2 7.8 + - - +
39C GLN 3.2 0.4 - - - -
40C PRO* 1.3 86.9 - - + +
42C LEU* 1.3 57.4 + - - +
44C GLU* 3.4 12.6 + - + +
45C ALA* 3.0 28.6 + - - +
136C THR* 4.3 20.0 - - + -
139C THR* 3.8 19.3 - - + -
140C LEU* 4.4 20.6 - - + +
143C CYS* 3.7 17.1 - - - -
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Residues in contact with LEU 42 (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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17C VAL* 5.3 1.8 - - + -
19C VAL* 5.2 2.9 - - + -
34C PHE* 4.0 11.7 - - + -
38C VAL* 3.2 35.5 + - + +
39C GLN* 3.1 8.1 + - - +
41C LEU* 1.3 77.5 - - - +
43C ALA* 1.3 56.1 + - - +
45C ALA* 3.1 4.9 + - - +
46C GLU 3.0 8.5 + - - -
47C ILE* 2.9 55.1 + - + +
49C PHE* 3.7 33.2 - - + -
139C THR* 4.4 2.9 - - + -
142C LEU* 4.2 21.8 - - + -
143C CYS* 4.2 14.6 - - - -
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Residues in contact with ALA 43 (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 GLN* 3.2 16.0 + - + +
40C PRO* 4.0 5.8 - - + +
42C LEU* 1.3 73.9 - - - +
44C GLU* 1.3 65.0 + - - +
46C GLU* 3.1 17.2 + - - +
47C ILE 4.8 2.5 - - - -
49C PHE* 6.0 2.0 - - + -
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Residues in contact with GLU 44 (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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13C ARG* 4.8 4.5 + - - -
40C PRO 3.3 12.2 + - - +
41C LEU* 3.4 15.5 - - + +
43C ALA* 1.3 80.7 - - - +
45C ALA* 1.3 59.8 + - + +
46C GLU* 3.3 6.1 + - - +
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Residues in contact with ALA 45 (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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13C ARG* 3.5 13.7 + - - +
41C LEU 3.0 17.0 + - - +
42C LEU 3.1 4.7 + - - +
44C GLU* 1.3 76.6 - - + +
46C GLU* 1.3 67.1 + - - +
47C ILE* 3.9 12.6 - - + -
143C CYS* 3.9 33.0 - - + +
145C ARG* 2.9 26.1 + - - +
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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