Contacts of the helix formed by residues 29 - 37 (chain F) 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 LYS 29 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25F GLY 3.2 1.4 + - - -
26F GLY* 3.7 15.3 - - - +
27F LYS 3.4 7.2 + - - +
28F GLY* 1.3 79.7 - - - +
30F ALA* 1.3 66.3 + - - +
31F LEU 3.2 2.2 - - - -
32F GLN* 2.8 46.3 + - + +
33F LEU* 2.9 32.7 + - + -
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Residues in contact with ALA 30 (chain F).
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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21F LEU* 3.8 11.1 - - + +
22F ASN 3.3 24.5 - - - +
23F PRO* 3.8 7.9 - - + +
25F GLY* 2.8 26.5 + - - +
28F GLY 3.5 1.2 - - - -
29F LYS* 1.3 70.6 - - - +
31F LEU* 1.3 56.0 + - - +
33F LEU* 3.5 11.5 - - - +
34F PHE* 3.0 23.0 + - - +
78F MET* 3.5 12.4 - - - +
110F ALA* 4.1 13.2 - - + -
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Residues in contact with LEU 31 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E PRO* 6.0 1.1 - - + -
31E LEU* 3.7 30.1 - - + -
53E LEU* 4.2 12.8 - - + -
21F LEU* 4.1 15.3 - - + -
23F PRO* 4.9 8.4 + - + -
28F GLY 4.8 2.5 + - - +
29F LYS 2.8 2.8 + - - -
30F ALA* 1.3 74.4 - - - +
32F GLN* 1.3 65.9 + - - +
34F PHE* 3.3 5.2 + - + +
35F ARG* 3.0 47.1 + - - +
51F LEU* 3.7 29.4 - - + -
53F LEU* 5.0 5.8 - - + -
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Residues in contact with GLN 32 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28F GLY 5.5 0.8 + - - +
29F LYS* 2.8 41.4 + - + +
31F LEU* 1.3 77.2 - - - +
33F LEU* 1.3 54.1 + - + +
35F ARG* 3.1 7.2 + - - +
36F SER* 2.8 40.1 + - - +
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Residues in contact with LEU 33 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26F GLY* 4.9 3.6 - - - -
29F LYS* 2.9 38.7 + - + +
30F ALA* 3.5 14.1 - - - +
32F GLN* 1.3 76.0 - - + +
34F PHE* 1.3 53.4 + - - +
36F SER* 3.4 5.8 - - - +
37F HIS* 2.7 59.8 + - + +
38F VAL 3.6 0.2 + - - -
78F MET* 4.1 3.6 - - + -
110F ALA* 4.3 24.5 - - - +
132F GLU* 4.0 13.7 - - + +
135F LEU* 3.7 16.6 - - + +
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Residues in contact with PHE 34 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19F VAL* 3.9 24.9 - - + -
21F LEU* 3.8 16.4 - - + -
30F ALA 3.0 14.4 + - - +
31F LEU* 3.4 9.2 - - + +
32F GLN 3.2 0.4 - - - -
33F LEU* 1.3 75.7 - - - +
35F ARG* 1.3 67.1 + - - +
38F VAL* 3.0 31.3 + - + -
39F GLN* 2.7 45.1 + - + -
42F LEU* 4.3 9.2 - - + -
49F PHE* 3.6 44.4 - + - -
51F LEU* 3.7 19.7 - - + -
78F MET* 3.7 21.2 - - + +
108F LEU* 5.2 1.3 - - + -
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Residues in contact with ARG 35 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E PRO* 3.5 20.0 - - - +
53E LEU* 3.9 15.4 - - - +
55E GLU* 2.7 36.1 + - - +
31F LEU* 3.0 35.7 + - - +
32F GLN* 3.7 6.1 - - + +
34F PHE* 1.3 85.7 - - - +
36F SER* 1.3 59.3 + - - +
39F GLN* 3.0 41.3 + - - +
40F PRO* 3.5 13.3 - - - +
49F PHE* 4.2 9.1 - - - -
51F LEU* 3.9 16.3 - - - +
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Residues in contact with SER 36 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32F GLN* 2.8 27.2 + - - +
33F LEU* 3.2 11.8 + - - +
35F ARG* 1.3 76.9 - - - +
37F HIS* 1.3 80.9 + - - +
40F PRO* 3.1 19.6 - - - +
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Residues in contact with HIS 37 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33F LEU* 2.7 31.5 + - + +
36F SER* 1.3 85.5 + - - +
38F VAL* 1.3 66.2 + - - +
40F PRO* 3.5 9.2 - - - +
41F LEU* 3.5 21.0 - - + +
132F GLU* 3.3 42.5 + - + +
135F LEU* 3.5 31.4 - - + +
136F THR* 4.7 15.9 - - - +
139F THR* 5.1 0.9 - - - -
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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