Contacts of the helix formed by residues 40 - 52 (chain A) in PDB entry 2O2V
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 LEU 40 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A GLN* 4.1 17.7 - - + +
39A LEU* 1.3 78.2 - - - +
41A PHE* 1.3 65.5 + - - +
42A ARG* 4.0 13.0 - - + +
43A ASP* 3.0 39.5 + - - +
44A VAL* 3.2 14.6 + - - +
75A ASP* 3.5 18.8 - - - +
78A MET* 3.7 4.5 - - - -
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Residues in contact with PHE 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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40A LEU* 1.3 69.9 - - - +
42A ARG* 1.3 64.6 + - + +
44A VAL* 3.2 5.8 + - - +
45A LEU* 3.1 50.5 + - + +
58A THR 3.6 13.0 - - - -
60A PHE* 3.6 27.4 - + - -
72A VAL* 3.3 34.5 - - + -
73A ARG* 3.5 31.9 - - - -
74A SER* 3.9 9.2 - - - +
75A ASP* 2.8 34.3 + - - +
78A MET* 3.6 13.0 - - + +
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Residues in contact with ARG 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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40A LEU* 3.2 11.5 - - + +
41A PHE* 1.3 84.6 - - + +
43A ASP* 1.3 57.6 + - - +
45A LEU* 3.4 20.7 + - - +
46A ASP* 2.9 57.2 + - - +
75A ASP* 5.1 1.2 + - - -
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Residues in contact with ASP 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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31A TRP* 4.5 5.2 - - + -
38A GLN 3.7 9.4 - - - +
39A LEU* 4.0 14.1 - - + +
40A LEU* 3.0 42.6 + - - +
42A ARG* 1.3 76.0 - - - +
44A VAL* 1.3 65.5 + - - +
46A ASP* 3.3 12.3 + - - +
47A VAL* 3.0 28.8 + - + +
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Residues in contact with VAL 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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19A ILE* 4.5 8.1 - - + -
21A ILE* 5.5 1.1 - - + +
31A TRP* 4.1 24.9 - - + -
39A LEU* 4.2 13.0 - - + -
40A LEU 3.7 11.7 - - - +
41A PHE 3.2 7.0 + - - +
43A ASP* 1.3 74.7 - - - +
45A LEU* 1.3 59.0 + - - +
47A VAL* 3.2 4.0 + - - +
48A ILE* 3.0 36.5 + - + +
60A PHE* 3.5 27.1 - - + -
78A MET* 3.8 20.2 - - - -
81A MET* 6.2 0.4 - - + -
104A ILE* 3.8 22.7 - - + -
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Residues in contact with LEU 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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41A PHE* 3.1 47.6 + - + +
42A ARG* 3.7 22.9 - - - +
43A ASP 3.3 0.2 - - - -
44A VAL* 1.3 76.6 - - - +
46A ASP* 1.3 57.1 + - - +
48A ILE* 3.4 5.4 + - + +
49A GLY* 2.9 26.2 + - - -
57A THR* 4.1 21.6 - - + +
58A THR* 3.8 15.9 - - + +
59A ALA 3.9 20.9 - - - +
60A PHE* 4.1 21.5 - - + -
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Residues in contact with ASP 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 ARG* 2.9 46.0 + - - +
43A ASP* 3.5 13.1 - - - +
44A VAL 3.2 0.2 - - - -
45A LEU* 1.3 77.7 - - - +
47A VAL* 1.3 61.1 + - + +
49A GLY* 3.2 4.0 + - - -
50A GLN* 3.1 33.1 + - - +
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Residues in contact with VAL 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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21A ILE* 4.0 15.0 - - + -
31A TRP* 3.6 54.3 - - + +
43A ASP 3.0 15.4 + - - +
44A VAL 3.8 6.3 - - - +
46A ASP* 1.3 73.0 - - + +
48A ILE* 1.3 66.3 + - - +
50A GLN* 3.1 24.7 + - + +
51A VAL* 3.0 27.6 + - + +
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Residues in contact with ILE 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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21A ILE* 4.2 23.1 - - + -
44A VAL* 3.0 28.5 + - + +
45A LEU* 3.7 7.0 - - + +
47A VAL* 1.3 75.8 - - - +
49A GLY* 1.3 51.6 + - - +
51A VAL* 3.1 4.9 + - - -
52A LEU* 2.7 43.1 + - + +
57A THR* 3.6 37.7 - - + +
60A PHE* 3.9 31.9 - - + -
104A ILE* 4.0 8.5 - - + -
106A PRO* 3.7 22.9 - - + -
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Residues in contact with GLY 49 (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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45A LEU 2.9 15.4 + - - -
46A ASP* 3.2 5.8 + - - -
48A ILE* 1.3 76.0 - - - +
50A GLN* 1.3 60.2 + - - +
52A LEU 4.3 6.1 - - - -
53A PRO* 3.3 26.4 - - - +
55A ALA 5.7 2.5 - - - -
57A THR* 5.5 4.2 - - - -
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Residues in contact with GLN 50 (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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46A ASP* 3.1 21.9 + - - +
47A VAL* 3.1 27.7 + - + +
49A GLY* 1.3 77.7 - - - +
51A VAL* 1.3 65.7 + - + +
52A LEU 3.6 0.2 + - - -
53A PRO* 3.7 11.9 - - - +
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Residues in contact with VAL 51 (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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21A ILE* 4.6 10.3 - - + -
23A ILE* 3.6 30.2 - - + +
29A VAL* 3.8 35.4 - - + -
47A VAL* 3.0 31.9 + - + +
48A ILE* 3.8 6.1 - - - +
50A GLN* 1.3 78.7 - - + +
52A LEU* 1.3 64.4 + - + +
53A PRO* 3.4 7.8 - - - +
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Residues in contact with LEU 52 (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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21A ILE* 5.0 1.1 - - + -
22A LYS 4.1 9.0 - - - +
23A ILE* 3.9 10.1 - - + -
24A PRO* 3.7 30.5 - - + -
48A ILE* 2.7 21.4 + - + +
49A GLY* 3.5 8.2 - - - +
51A VAL* 1.3 85.2 - - + +
53A PRO* 1.3 64.7 - - - +
54A GLU 3.3 2.9 - - - -
55A ALA* 3.1 33.9 + - + +
57A THR* 4.8 3.4 + - - +
106A PRO* 3.7 34.3 - - + -
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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