Contacts of the helix formed by residues 27 - 42 (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 THR 27 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A LYS* 5.6 2.1 - - - -
83A ARG* 5.6 1.6 - - - -
90A ALA* 3.8 31.4 - - + -
23C LYS 5.2 0.4 - - - -
25C ARG 5.7 0.7 - - - +
26C ARG* 1.3 75.5 - - - +
28C PHE* 1.3 66.8 + - - +
29C GLU* 3.6 7.7 + - - +
30C GLN* 3.0 40.1 + - - +
31C ARG* 2.9 21.4 + - - +
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Residues in contact with PHE 28 (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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83A ARG* 3.8 6.7 - - - +
90A ALA 2.9 16.6 + - - +
91A ASN 3.6 15.5 - - - +
92A GLN 3.3 22.7 - - - +
93A ALA* 3.6 23.6 - - + -
94A PHE 3.3 29.2 - - - -
95A PHE* 3.8 20.0 - + - -
27C THR* 1.3 71.1 - - - +
29C GLU* 1.3 67.4 + - - +
31C ARG* 3.1 19.9 + - - +
32C VAL* 3.0 34.0 + - + +
119C ASP* 5.4 1.3 - - - -
120C GLU* 3.8 10.3 - - + -
121C ASP* 3.5 33.9 - - + -
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Residues in contact with GLU 29 (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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76A SER* 4.7 0.2 - - - -
79A ILE* 3.8 42.6 - - + +
80A LYS* 3.8 30.5 - - + +
83A ARG* 4.3 16.4 + - - +
94A PHE 4.2 11.8 - - - +
104A VAL* 4.1 9.5 - - - +
27C THR* 3.2 7.3 + - - +
28C PHE* 1.3 79.3 - - - +
30C GLN* 1.3 64.3 + - - +
32C VAL* 3.3 13.8 + - - +
33C GLU* 3.1 55.2 + - - +
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Residues in contact with GLN 30 (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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80A LYS* 5.5 11.2 - - - +
25C ARG 4.3 2.4 - - - +
26C ARG* 3.3 43.1 + - - +
27C THR* 3.0 45.4 + - - +
29C GLU* 1.3 77.5 - - - +
31C ARG* 1.3 61.7 + - - +
33C GLU* 3.7 11.1 - - - +
34C ASP* 3.1 24.8 + - - +
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Residues in contact with ARG 31 (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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91A ASN* 2.3 42.5 - - - +
22C PHE* 3.7 27.4 - - + -
23C LYS* 3.7 19.0 + - - +
26C ARG* 2.9 29.9 + - + +
27C THR* 2.9 9.9 + - - +
28C PHE* 3.2 37.9 - - - +
30C GLN* 1.3 76.2 - - - +
32C VAL* 1.3 58.5 + - - +
34C ASP* 3.1 6.2 + - - +
35C VAL* 2.9 26.2 + - - +
119C ASP* 5.2 0.8 + - - -
121C ASP* 2.6 51.0 + - - +
123C PHE* 3.4 16.4 - - + -
125C TYR* 3.5 10.8 - - - -
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Residues in contact with VAL 32 (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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95A PHE* 4.3 22.4 - - + -
104A VAL* 3.5 20.5 - - + +
132A GLU* 5.7 1.1 - - - +
28C PHE* 3.0 32.2 + - + +
29C GLU* 3.6 20.2 - - - +
31C ARG* 1.3 79.3 - - - +
33C GLU* 1.3 60.1 + - - +
35C VAL* 3.8 2.2 - - + +
36C ARG* 2.9 29.7 + - + +
120C GLU 4.8 0.2 - - - +
121C ASP* 3.4 31.9 - - + +
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Residues in contact with GLU 33 (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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76A SER* 3.2 28.2 + - - -
80A LYS* 4.1 8.3 + - - -
104A VAL* 3.5 23.4 - - + +
29C GLU* 3.1 44.1 + - - +
30C GLN* 3.7 12.2 - - - +
32C VAL* 1.3 75.0 - - - +
34C ASP* 1.3 66.6 + - - +
36C ARG* 3.3 2.4 + - - +
37C LEU* 3.0 28.8 + - + +
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Residues in contact with ASP 34 (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* 6.0 1.3 - - + -
26C ARG* 5.3 11.0 + - - -
30C GLN 3.1 14.8 + - - +
31C ARG* 3.1 10.4 + - - +
33C GLU* 1.3 76.3 - - - +
35C VAL* 1.3 63.7 + - - +
37C LEU* 3.9 6.7 - - - +
38C ILE* 3.0 29.3 + - + +
66C LYS* 2.6 38.2 + - - -
123C PHE* 4.0 12.6 - - + -
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Residues in contact with VAL 35 (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 ARG 2.9 8.4 + - - +
32C VAL* 3.8 3.4 - - + +
34C ASP* 1.3 75.4 - - - +
36C ARG* 1.3 67.5 + - - +
38C ILE* 3.5 6.2 - - - +
39C ARG* 2.9 44.1 + - + +
47C PRO* 4.6 4.7 - - + -
114C TYR* 4.1 2.7 - - - +
121C ASP 3.3 21.8 - - - +
122C GLY* 3.5 32.5 - - - +
123C PHE* 3.4 37.2 - - + -
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Residues in contact with ARG 36 (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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104A VAL* 3.8 20.6 - - + -
105A SER* 3.6 40.1 + - - -
132A GLU* 5.7 0.7 - - - -
32C VAL* 2.9 19.7 + - + +
33C GLU* 3.6 4.5 - - - +
35C VAL* 1.3 79.4 - - - +
37C LEU* 1.3 63.2 + - - +
39C ARG* 3.4 7.1 + - - +
40C GLU* 3.2 47.2 + - - +
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Residues in contact with LEU 37 (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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33C GLU* 3.0 18.4 + - + +
34C ASP* 3.9 6.7 - - - +
36C ARG* 1.3 78.2 - - - +
38C ILE* 1.4 58.8 + - + +
40C GLU* 3.3 16.0 + - - +
41C GLN* 2.9 70.2 + - - +
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Residues in contact with ILE 38 (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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34C ASP* 3.0 22.1 + - - +
35C VAL* 3.5 10.1 - - - +
37C LEU* 1.4 74.6 - - + +
39C ARG* 1.3 62.9 + - - +
41C GLN* 3.5 18.7 - - - +
42C HIS* 2.9 37.8 + - + +
47C PRO* 4.3 24.7 - - + -
68C LEU* 3.8 39.3 - - + +
123C PHE* 6.0 1.3 - - + -
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Residues in contact with ARG 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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35C VAL* 2.9 35.4 + - + +
36C ARG* 3.6 10.8 - - - +
38C ILE* 1.3 74.4 - - - +
40C GLU* 1.3 66.3 + - - +
42C HIS 3.0 2.1 + - - -
43C PRO* 3.0 56.5 + - + +
45C LYS 2.9 25.3 + - - -
46C ILE* 4.2 12.1 - - - +
47C PRO* 4.2 19.0 - - + +
114C TYR* 4.2 26.4 + - - +
115C GLU* 5.3 3.0 + - - -
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Residues in contact with GLU 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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36C ARG* 3.2 33.9 + - - +
37C LEU* 3.6 16.1 - - - +
39C ARG* 1.3 79.6 - - - +
41C GLN* 1.3 63.8 + - - +
42C HIS 3.3 0.9 + - - -
43C PRO* 3.7 10.5 - - - +
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Residues in contact with GLN 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 LEU* 2.9 43.9 + - - +
38C ILE* 3.5 19.2 - - - +
39C ARG 3.1 0.2 - - - -
40C GLU* 1.3 79.4 + - - +
42C HIS* 1.3 87.0 + - + +
43C PRO* 3.9 2.4 - - - +
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Residues in contact with HIS 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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38C ILE* 2.9 27.1 + - + +
39C ARG* 3.0 6.9 + - - +
41C GLN* 1.3 115.4 - - + +
43C PRO* 1.3 68.8 - - - +
44C THR* 3.0 4.6 + - - +
45C LYS* 3.1 56.6 + - + +
68C LEU* 4.3 13.4 - - + +
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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