Contacts of the helix formed by residues 37 - 48 (chain A) in PDB entry 2VXO
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 TYR 37 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A ASP* 3.2 13.7 + - - +
34A GLY* 4.3 13.8 + - - -
38A GLY* 1.3 68.7 + - - +
39A LYS* 3.3 4.6 - - - +
40A VAL* 2.9 20.8 + - + +
41A ILE* 2.8 27.2 + - + +
75A SER* 3.9 10.5 - - - +
76A GLY* 4.4 14.8 - - - -
77A GLY* 4.2 20.2 - - - -
150A LEU* 5.5 4.0 - - + +
152A THR* 4.2 12.8 - - - +
190A HIS* 3.3 39.9 + + + -
192A GLU* 3.3 28.0 - - + +
193A VAL* 5.1 10.1 - - + -
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Residues in contact with GLY 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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30A ILE* 4.0 19.6 - - - +
32A ASP* 2.4 28.9 + - - -
37A TYR* 1.3 68.8 - - - +
39A LYS* 1.3 51.4 + - - +
41A ILE* 3.4 2.3 + - - +
42A ASP* 2.8 35.2 + - - +
54A ILE* 3.4 18.6 - - - +
75A SER* 4.4 0.2 + - - -
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Residues in contact with LYS 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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37A TYR 3.3 2.9 - - - +
38A GLY* 1.3 73.9 - - - +
40A VAL* 1.3 61.1 + - + +
42A ASP* 3.3 8.2 + - - +
43A ARG* 2.9 29.1 + - - +
46A ARG* 5.5 0.2 + - - -
54A ILE* 3.7 10.1 - - + +
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Residues in contact with VAL 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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37A TYR* 2.9 24.2 + - + +
39A LYS* 1.3 78.2 - - + +
41A ILE* 1.3 59.5 + - - +
43A ARG* 3.2 7.2 + - + +
44A ARG* 3.0 38.7 + - - +
192A GLU* 3.4 35.7 - - + +
193A VAL* 4.7 9.0 - - + +
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Residues in contact with ILE 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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30A ILE* 3.8 23.8 - - + -
37A TYR 2.8 22.4 + - - +
38A GLY 3.8 2.9 - - - +
40A VAL* 1.3 71.0 - - - +
42A ASP* 1.3 57.2 + - - +
44A ARG* 3.3 2.6 + - - +
45A VAL* 2.8 34.7 + - + +
73A ILE* 3.9 40.4 - - + -
75A SER* 3.4 35.0 - - - +
103A ILE* 4.2 8.1 - - + -
192A GLU* 3.8 28.7 - - + +
203A LEU* 5.2 5.8 - - + -
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Residues in contact with ASP 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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30A ILE* 3.6 11.0 - - + +
38A GLY 2.8 18.6 + - - +
39A LYS* 3.3 7.6 - - - +
40A VAL 3.2 0.2 - - - -
41A ILE* 1.3 76.4 - - - +
43A ARG* 1.3 56.7 + - - +
45A VAL* 4.0 1.0 - - - +
46A ARG* 3.0 44.0 + - - +
52A SER* 2.6 40.2 + - - +
54A ILE* 4.0 12.9 - - + +
415A HIS* 5.5 1.2 + - - -
493B GLU* 3.4 19.1 - - - +
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Residues in contact with ARG 43 (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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39A LYS 2.9 13.2 + - - +
40A VAL* 3.2 10.3 + - - +
42A ASP* 1.3 74.0 - - - +
44A ARG* 1.3 66.1 + - - +
46A ARG* 3.4 27.8 + - - +
47A GLU* 2.8 44.8 + - - +
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Residues in contact with ARG 44 (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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40A VAL* 3.0 30.7 + - - +
41A ILE* 3.8 3.8 - - - +
43A ARG* 1.3 81.0 - - - +
45A VAL* 1.3 63.3 + - - +
47A GLU* 2.9 45.2 + - - +
48A LEU* 3.0 29.7 + - + +
191A PRO 5.3 1.3 - - - -
192A GLU* 3.1 43.7 + - + +
193A VAL* 4.8 4.9 - - - +
194A GLY 4.9 4.6 - - - +
200A LYS* 5.8 12.3 - - + +
203A LEU* 3.5 22.4 - - + -
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Residues in contact with VAL 45 (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 VAL* 5.0 2.2 - - + -
41A ILE* 2.8 28.0 + - + +
44A ARG* 1.3 71.9 - - + +
46A ARG* 1.3 63.1 + - - +
48A LEU* 3.0 12.5 + - - +
49A PHE 3.2 0.2 + - - -
50A VAL* 3.2 50.4 + - + +
51A GLN 4.5 0.7 - - - +
52A SER* 3.4 27.6 - - - +
73A ILE* 4.0 23.3 - - + -
203A LEU* 5.3 5.4 - - + -
207A LEU* 4.0 26.0 - - + -
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Residues in contact with ARG 46 (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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42A ASP* 3.0 35.2 + - - +
43A ARG* 3.5 35.8 + - - +
45A VAL* 1.3 71.3 - - - +
47A GLU* 1.3 62.3 + - - +
48A LEU 3.0 5.2 - - - -
49A PHE* 2.9 25.3 + - - -
50A VAL 3.8 9.4 + - - -
52A SER* 5.0 1.3 - - - -
217A PHE* 4.3 22.9 - - + +
222A ARG* 4.2 11.0 - - - +
415A HIS* 3.4 41.9 + - - +
417A ASP* 5.3 4.4 + - - -
418A GLU* 3.1 26.0 + - - +
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Residues in contact with GLU 47 (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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43A ARG* 2.8 28.7 + - - +
44A ARG* 2.9 47.3 + - - +
46A ARG* 1.3 77.8 + - + +
48A LEU* 1.3 63.6 + - + +
49A PHE* 3.4 21.2 + - - -
200A LYS* 5.3 11.5 - - - +
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Residues in contact with LEU 48 (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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44A ARG* 3.0 16.7 + - + +
45A VAL 3.0 6.7 + - - +
46A ARG 3.0 0.6 - - - -
47A GLU* 1.3 80.1 - - + +
49A PHE* 1.3 67.8 + - + +
50A VAL* 3.3 4.1 + - - +
200A LYS* 4.0 36.8 - - + +
203A LEU* 3.8 31.2 - - + -
204A LYS* 3.8 39.3 - - + +
207A LEU* 4.3 14.4 - - + -
208A TYR* 2.4 36.4 + - + +
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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