Contacts of the helix formed by residues 27 - 42 (chain A) 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 THR 27 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A ARG* 1.3 76.1 - - - +
28A PHE* 1.3 65.9 + - - +
29A GLU* 3.6 12.8 + - - +
30A GLN* 3.1 40.8 + - + +
31A ARG* 3.1 21.8 + - - +
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Residues in contact with PHE 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A THR* 1.3 74.2 - - - +
29A GLU* 1.3 86.5 + - - +
31A ARG* 3.1 18.7 + - - +
32A VAL* 3.0 42.4 + - + +
120A GLU* 3.9 18.4 - - + -
121A ASP* 3.6 28.5 - - + -
201A SO4 3.5 17.3 - - - +
84B ARG* 3.1 35.0 - - - +
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Residues in contact with GLU 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A THR* 3.3 10.4 + - - +
28A PHE* 1.3 102.5 + - - +
30A GLN* 1.3 61.0 + - + +
32A VAL* 3.8 5.6 - - - +
33A GLU* 3.3 24.3 + - - +
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Residues in contact with GLN 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ARG 4.7 1.0 - - - +
26A ARG* 3.3 28.7 + - - +
27A THR* 3.1 45.7 + - + +
29A GLU* 1.3 74.8 - - + +
31A ARG* 1.3 61.3 + - - +
33A GLU* 3.8 5.3 - - - +
34A ASP* 2.8 32.8 + - - +
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Residues in contact with ARG 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A PHE* 3.7 24.5 - - + -
23A LYS* 3.5 26.6 + - - +
26A ARG* 3.0 31.3 + - + -
27A THR* 3.1 5.7 + - - +
28A PHE* 3.1 30.0 + - - +
30A GLN* 1.3 73.5 - - - +
32A VAL* 1.3 66.8 + - - +
34A ASP* 2.9 12.0 - - - +
35A VAL* 2.9 19.9 + - - +
121A ASP* 3.0 41.0 + - + +
123A PHE* 3.4 11.1 - - + -
125A TYR* 3.4 11.2 - - - -
201A SO4 2.4 42.4 + - - -
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Residues in contact with VAL 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A PHE* 3.0 49.1 + - + +
29A GLU* 3.8 6.3 - - - +
31A ARG* 1.3 73.7 - - - +
33A GLU* 1.3 62.0 + - + +
35A VAL* 3.0 7.1 + - - +
36A ARG* 2.9 29.3 + - + +
120A GLU 4.7 1.6 - - - +
121A ASP* 3.5 22.9 + - - +
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Residues in contact with GLU 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A GLU 3.3 14.6 + - - +
30A GLN* 4.1 4.9 - - - +
31A ARG 3.2 0.4 - - - -
32A VAL* 1.3 77.8 - - + +
34A ASP* 1.3 65.1 + - - +
36A ARG* 2.9 46.4 + - - +
37A LEU* 3.1 36.1 + - + +
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Residues in contact with ASP 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A PHE* 4.7 2.9 - - - -
26A ARG* 3.8 22.0 + - - -
30A GLN* 2.8 20.7 + - - +
31A ARG* 2.9 17.3 - - - +
33A GLU* 1.3 77.6 - - - +
35A VAL* 1.3 54.3 - - - +
37A LEU* 3.8 4.3 - - - +
38A ILE* 3.1 36.1 + - + +
66A LYS* 3.7 24.8 + - - -
123A PHE* 3.7 19.3 - - + -
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Residues in contact with VAL 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ARG 2.9 14.4 + - - +
32A VAL 3.3 6.5 - - - +
34A ASP* 1.3 69.7 - - - +
36A ARG* 1.3 68.7 + - - +
37A LEU 3.2 0.2 + - - -
38A ILE* 3.4 7.3 + - - +
39A ARG* 3.0 35.5 + - + +
47A PRO* 4.5 5.2 - - + -
114A TYR* 3.8 10.3 - - - +
121A ASP 3.4 21.5 - - - +
122A GLY* 3.5 32.3 - - - +
123A PHE* 3.5 21.1 - - + -
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Residues in contact with ARG 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A VAL* 2.9 22.4 + - + +
33A GLU* 2.9 35.5 + - - +
35A VAL* 1.3 75.2 - - - +
37A LEU* 1.3 89.1 + - - +
39A ARG* 3.5 4.4 + - - +
40A GLU* 3.0 47.9 + - - +
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Residues in contact with LEU 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A GLU* 3.1 26.8 + - + +
34A ASP* 3.8 4.5 - - - +
36A ARG* 1.3 105.6 - - - +
38A ILE* 1.3 67.4 + - - +
39A ARG 3.2 0.2 + - - -
40A GLU* 3.4 16.1 + - - +
41A GLN* 3.1 51.0 + - - +
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Residues in contact with ILE 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ASP* 3.1 25.6 + - + +
35A VAL* 3.5 9.2 - - - +
37A LEU* 1.3 78.4 - - - +
39A ARG* 1.3 65.7 - - + +
41A GLN* 3.5 6.5 + - - -
42A HIS* 2.7 41.0 + - + +
45A LYS 4.7 3.4 - - - +
47A PRO* 3.8 31.0 - - + -
66A LYS* 5.8 4.3 - - - -
68A LEU* 3.9 31.6 - - + -
123A PHE* 4.5 11.9 - - + -
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Residues in contact with ARG 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A VAL* 3.0 32.2 + - + +
36A ARG* 3.9 5.4 - - - +
38A ILE* 1.3 86.4 - - + +
40A GLU* 1.3 62.3 + - - +
42A HIS 4.1 3.4 - - - +
43A PRO* 3.2 50.5 + - - +
45A LYS 3.7 13.8 + - - -
46A ILE* 4.4 11.8 - - - +
47A PRO* 4.3 10.5 - - - -
114A TYR* 3.7 33.0 + - - -
115A GLU* 4.2 8.9 + - - -
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Residues in contact with GLU 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A ARG* 3.0 37.3 + - - +
37A LEU* 3.5 24.8 - - + +
39A ARG* 1.3 77.2 - - - +
41A GLN* 1.3 71.5 + - + +
42A HIS 3.4 0.6 + - - -
43A PRO* 3.9 11.5 - - - +
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Residues in contact with GLN 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A LEU* 3.1 52.0 + - - +
38A ILE* 3.7 4.4 + - - +
40A GLU* 1.3 84.5 + - + +
42A HIS* 1.3 86.5 + - + +
43A PRO* 3.8 3.6 - - - +
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Residues in contact with HIS 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ILE* 2.7 23.4 + - + +
39A ARG* 4.6 1.6 - - - -
40A GLU 3.4 0.2 - - - -
41A GLN* 1.3 103.8 + - + +
43A PRO* 1.3 59.7 - - - +
44A THR* 3.1 4.9 - - - -
45A LYS* 2.8 59.4 + - + +
68A LEU* 4.1 25.1 - - + +
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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