Contacts of the helix formed by residues 33 - 51 (chain A) in PDB entry 2A6O
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 VAL 33 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A LYS* 4.2 14.1 - - + +
31A VAL* 2.7 16.5 + - - +
32A LEU* 1.3 80.4 - - - +
34A GLY* 1.3 72.9 + - - +
35A ALA 3.4 0.3 + - - -
36A VAL* 3.2 6.9 + - - +
37A GLU* 3.2 19.6 + - - +
62A LYS* 3.8 28.5 - - + +
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Residues in contact with GLY 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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33A VAL* 1.3 76.3 - - - +
35A ALA* 1.3 64.8 + - - -
37A GLU* 3.0 18.7 + - - +
38A MET* 3.0 27.6 + - - +
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Residues in contact with ALA 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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33A VAL 3.4 0.6 + - - -
34A GLY* 1.3 69.5 - - - +
36A VAL* 1.3 62.4 + - + +
38A MET* 3.4 14.1 + - - +
39A ARG* 3.1 28.9 + - + +
96A PHE* 3.3 27.4 - - + -
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Residues in contact with VAL 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A VAL* 3.4 26.2 - - + +
32A LEU* 4.1 18.4 - - + -
33A VAL 3.2 3.6 + - - +
35A ALA* 1.3 77.0 - - + +
37A GLU* 1.3 58.9 + - - +
39A ARG* 3.4 1.0 + - - +
40A LEU* 2.9 28.6 + - - +
92A LEU* 4.0 11.1 - - + +
96A PHE* 3.8 36.1 - - + -
98A HIS* 4.5 10.5 - - + +
99A LEU* 3.8 25.6 - - + -
106A LEU* 6.2 0.4 - - + -
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Residues in contact with GLU 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 3.7 12.1 - - + +
33A VAL* 3.2 21.5 + - - +
34A GLY* 3.0 21.1 + - - +
36A VAL* 1.3 78.6 - - - +
38A MET* 1.3 66.9 + - + +
40A LEU* 3.4 7.4 + - - +
41A LYS* 3.1 48.9 + - - +
60A THR* 2.6 35.8 + - - +
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Residues in contact with MET 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 GLY* 3.0 27.8 + - - +
35A ALA* 3.6 14.4 - - - +
37A GLU* 1.3 79.5 - - + +
39A ARG* 1.3 63.1 + - + +
41A LYS* 3.3 9.8 + - - +
42A GLU* 3.1 33.1 + - - +
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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 ALA* 3.1 15.6 + - + +
38A MET* 1.3 77.5 - - + +
40A LEU* 1.3 61.0 + - - +
42A GLU* 2.6 51.4 + - - +
43A ILE* 2.8 58.0 + - - +
46A GLU* 5.0 8.5 + - - -
91A ILE* 3.9 7.1 - - - +
92A LEU* 3.6 19.1 - - + -
95A GLU* 2.8 40.7 + - - +
96A PHE* 3.9 9.6 - - + -
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Residues in contact with LEU 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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23A TRP* 5.3 0.7 - - + -
32A LEU* 4.0 34.5 - - + -
36A VAL* 2.9 19.6 + - + +
37A GLU* 3.5 4.7 - - - +
38A MET 3.3 0.2 - - - -
39A ARG* 1.3 78.8 - - - +
41A LYS* 1.3 58.3 + - - +
43A ILE* 3.3 2.8 + - - +
44A ILE* 2.9 43.5 + - + +
60A THR* 4.1 9.0 - - + -
65A ILE* 3.6 27.6 - - + -
88A SER* 3.8 26.2 - - - -
92A LEU* 3.9 14.9 - - + +
107A TRP* 3.8 20.0 - - + -
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Residues in contact with LYS 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 GLU* 3.1 32.9 + - + +
38A MET* 3.7 8.5 - - - +
40A LEU* 1.3 76.5 - - + +
42A GLU* 1.3 62.0 + - + +
44A ILE* 3.4 0.6 + - - -
45A GLN* 2.9 32.6 + - + +
58A MET* 3.3 34.4 + - + +
59A GLN* 4.3 10.6 - - - +
60A THR* 3.3 44.4 + - + +
65A ILE* 5.4 0.2 - - + -
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Residues in contact with GLU 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 MET* 3.1 22.7 + - + +
39A ARG* 2.6 45.0 + - - +
41A LYS* 1.3 78.8 - - + +
43A ILE* 1.3 62.5 + - - +
45A GLN* 3.0 18.4 + - - +
46A GLU* 3.1 21.6 + - + +
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Residues in contact with ILE 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 ARG* 2.8 39.9 + - - +
40A LEU* 3.7 4.0 - - - +
42A GLU* 1.3 72.0 - - - +
44A ILE* 1.3 62.7 + - - +
46A GLU* 3.3 12.4 + - + +
47A VAL* 3.0 28.9 + - + +
87A ARG* 3.8 27.1 - - + -
88A SER* 3.8 23.3 - - - +
91A ILE* 3.3 41.5 - - + -
92A LEU* 4.0 21.8 - - + -
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Residues in contact with ILE 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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23A TRP* 4.4 8.7 - - + -
40A LEU* 2.9 47.0 + - + +
41A LYS 3.8 4.7 - - - +
42A GLU 3.3 0.2 - - - -
43A ILE* 1.3 77.8 - - + +
45A GLN* 1.3 57.1 + - - +
47A VAL* 3.3 5.3 + - - +
48A ALA* 3.0 27.2 + - - +
55A ILE* 4.0 8.3 - - + -
58A MET* 3.8 21.1 - - - -
65A ILE* 4.1 12.1 - - + -
67A ILE* 3.8 15.3 - - + -
80A PHE* 4.2 12.1 - - + -
84A ALA* 3.8 35.0 - - + +
88A SER* 4.3 3.8 - - - -
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Residues in contact with GLN 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 LYS* 2.9 27.5 + - + +
42A GLU* 3.2 11.2 - - - +
44A ILE* 1.3 77.2 - - - +
46A GLU* 1.3 63.6 + - + +
48A ALA* 3.3 4.0 + - - +
49A LYS* 3.2 23.2 + - - +
55A ILE* 3.2 30.4 - - - +
58A MET* 4.1 12.6 - - + +
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Residues in contact with GLU 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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39A ARG* 5.0 10.6 + - - -
42A GLU* 3.1 18.2 + - - +
43A ILE* 3.7 11.4 - - - +
45A GLN* 1.3 76.2 - - + +
47A VAL* 1.3 64.3 + - - +
49A LYS* 3.5 5.3 + - - +
50A GLU* 3.1 25.9 + - - +
87A ARG* 4.5 11.9 - - - +
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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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43A ILE* 3.0 19.7 + - + +
44A ILE* 3.6 7.6 - - - +
45A GLN 3.2 0.2 - - - -
46A GLU* 1.3 77.2 - - - +
48A ALA* 1.3 52.7 + - - +
50A GLU* 3.2 2.9 + - - -
51A LEU* 2.7 52.5 + - + +
80A PHE* 4.4 7.0 - - + +
83A THR* 3.5 33.7 - - + -
84A ALA* 3.9 22.4 - - + +
87A ARG* 3.6 33.9 - - - +
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Residues in contact with ALA 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 ILE 3.0 16.3 + - - +
45A GLN* 3.3 5.6 + - - +
47A VAL* 1.3 74.2 - - - +
49A LYS* 1.3 55.7 + - - +
52A ARG 2.7 14.2 + - - -
53A VAL* 2.5 58.1 + - + +
55A ILE* 3.6 24.0 - - + -
80A PHE* 4.2 8.0 - - + -
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Residues in contact with LYS 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 GLN 3.2 12.6 + - - +
46A GLU* 4.0 6.3 - - - +
48A ALA* 1.3 77.9 - - - +
50A GLU* 1.3 64.4 + - - +
52A ARG* 3.3 11.6 + - - +
53A VAL 4.9 1.6 - - - -
155A LEU* 4.0 41.1 - - + +
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Residues in contact with GLU 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 GLU 3.1 16.5 + - - +
47A VAL 3.5 3.1 - - - +
49A LYS* 1.3 80.8 - - - +
51A LEU* 1.3 69.1 + - + +
52A ARG* 3.2 8.2 + - - +
83A THR* 5.6 0.5 - - - +
87A ARG* 3.3 36.8 + - - -
155A LEU* 4.7 5.8 - - - +
10C T 5.0 1.9 + - - -
17D T 3.8 4.7 - - - +
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Residues in contact with LEU 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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47A VAL* 2.7 38.4 + - + +
48A ALA* 4.8 0.2 - - - -
50A GLU* 1.3 94.2 - - + +
52A ARG* 1.3 64.8 + - - +
53A VAL* 3.3 14.2 + - + +
75A PHE* 3.6 30.1 - - + -
80A PHE* 3.6 21.8 - - + -
83A THR* 3.5 31.4 - - + +
17D T 2.8 33.4 + - - +
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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