Contacts of the helix formed by residues 43 - 55 (chain A) in PDB entry 2AXV
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 SER 43 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A PRO 4.4 0.2 + - - -
42A ILE* 1.3 75.6 - - - +
44A VAL* 1.3 65.4 + - - +
45A GLU* 3.5 10.4 - - - +
46A GLU* 2.8 39.2 + - - +
47A LEU* 3.0 20.5 + - - +
41B PRO* 3.8 26.3 - - - +
42B ILE 3.3 15.3 - - - -
43B SER* 4.0 2.2 - - - +
44B VAL* 4.7 0.2 - - - -
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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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42A ILE 3.7 1.4 + - - -
43A SER* 1.3 71.3 - - - +
45A GLU* 1.3 58.9 + - - +
47A LEU* 3.4 3.5 + - - +
48A SER* 2.9 34.6 + - - -
58A PHE* 3.9 11.4 - - + -
2B PHE 5.6 5.2 - - - +
4B ILE* 3.6 34.3 - - + -
42B ILE* 3.0 19.7 + - + +
44B VAL* 4.3 23.6 - - + +
47B LEU* 4.2 17.3 - - + -
58B PHE* 5.7 0.7 - - + -
62B LEU* 4.1 15.5 - - + -
67B MET* 5.4 4.9 - - + -
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Residues in contact with GLU 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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43A SER* 3.5 11.2 + - - +
44A VAL* 1.3 81.8 - - - +
46A GLU* 1.3 65.0 + - + +
48A SER* 3.3 7.7 + - - -
49A LYS* 3.0 51.1 + - + +
2B PHE* 3.5 34.8 - - + -
41B PRO* 5.4 7.7 - - + +
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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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26A ILE* 4.6 12.1 - - + +
27A MET* 3.2 21.1 - - + +
40A ARG* 2.9 36.3 + - - -
42A ILE* 3.6 4.3 - - + +
43A SER* 2.8 41.4 + - - +
45A GLU* 1.3 81.4 - - + +
47A LEU* 1.3 58.6 + - - +
49A LYS* 3.1 11.4 + - - +
50A PHE* 2.9 48.8 + - + -
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Residues in contact with LEU 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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4A ILE* 3.6 27.4 - - + -
8A LEU* 4.4 9.4 - - + -
42A ILE* 3.9 11.6 - - + +
43A SER 3.0 14.2 + - - +
44A VAL 3.6 2.7 - - - +
46A GLU* 1.3 77.7 - - - +
48A SER* 1.3 57.8 + - - +
50A PHE* 3.4 7.9 + - - +
51A SER* 2.9 29.8 + - - -
58A PHE* 3.4 25.6 - - + +
61A ILE* 4.2 20.4 - - + -
62A LEU* 3.7 19.3 - - + -
44B VAL* 3.7 26.0 - - + -
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Residues in contact with SER 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 VAL* 2.9 22.0 + - - -
45A GLU* 3.4 7.6 - - - -
47A LEU* 1.3 75.6 - - - +
49A LYS* 1.3 64.7 + - - +
51A SER* 3.3 4.5 + - - -
52A GLU* 3.1 20.7 + - - +
58A PHE* 3.6 21.5 - - - -
67B MET* 4.9 10.9 - - - +
72B VAL* 5.8 3.3 - - - +
73B ASN* 5.0 12.5 + - - +
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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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25A GLY 5.4 3.8 - - - -
26A ILE* 3.6 40.8 - - + +
45A GLU* 3.0 50.0 + - + +
46A GLU* 3.1 9.4 + - - +
48A SER* 1.3 76.9 + - - +
50A PHE* 1.3 62.6 + - - +
52A GLU* 3.0 20.8 + - - +
53A ARG* 2.9 23.6 - - + +
2B PHE* 5.9 0.8 - - - -
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Residues in contact with PHE 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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8A LEU* 3.7 22.0 - - + -
22A LEU* 3.6 46.8 - - + +
23A TYR* 4.4 0.2 - - - -
26A ILE* 3.8 22.2 - - + -
27A MET* 3.8 25.8 - - + -
32A TYR* 3.7 24.5 - + - -
35A VAL* 4.5 3.6 - - + -
42A ILE* 3.6 29.2 - - + -
46A GLU* 2.9 33.1 + - + +
47A LEU* 3.8 4.0 - - - +
49A LYS* 1.3 72.9 - - - +
51A SER* 1.3 61.9 + - - +
53A ARG* 3.1 5.0 + - - +
54A LEU* 3.0 30.3 + - - +
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Residues in contact with SER 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 LEU 2.9 18.2 + - - -
48A SER* 3.3 9.5 + - - -
50A PHE* 1.3 76.8 - - - +
52A GLU* 1.3 56.8 + - - +
54A LEU* 3.4 1.6 + - - +
55A GLY* 2.9 26.0 + - - -
56A VAL 2.9 22.9 + - - +
57A ASN* 4.2 0.3 - - - -
58A PHE* 3.2 22.9 + - - +
61A ILE* 3.5 26.2 - - - +
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Residues in contact with GLU 52 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A SER 3.1 7.2 + - - +
49A LYS* 3.0 18.7 + - - +
51A SER* 1.3 78.3 + - - +
53A ARG* 1.3 66.3 + - + +
55A GLY* 3.4 12.1 + - - -
73B ASN* 3.0 40.9 + - - +
74B GLU* 3.2 12.6 + - - +
75B THR* 3.1 38.8 + - + +
106B SER* 4.2 9.9 + - - -
108B GLN* 5.3 3.3 - - - +
109B TYR* 5.9 0.7 - - - -
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Residues in contact with ARG 53 (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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17A TYR* 3.0 26.9 + - - -
21A ASP 3.4 20.0 + - - +
22A LEU* 2.9 36.9 + - + +
24A SER* 2.8 32.1 + - - +
25A GLY 5.4 0.6 + - - -
26A ILE* 3.4 25.1 - - + +
49A LYS* 2.9 25.0 - - - +
50A PHE* 3.1 8.9 + - - +
52A GLU* 1.3 78.8 - - + +
54A LEU* 1.3 61.8 + - - +
55A GLY 3.6 0.2 + - - -
105B THR 4.8 0.5 - - - +
106B SER* 4.2 5.2 - - - -
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Residues in contact with LEU 54 (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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8A LEU* 3.7 29.8 - - + +
11A ILE* 4.0 25.4 - - + -
12A ARG* 3.8 32.8 - - + +
15A LEU* 3.4 18.4 - - + +
17A TYR* 3.7 23.9 + - + -
22A LEU* 4.0 18.4 - - + -
50A PHE 3.0 18.5 + - - +
51A SER* 3.9 7.0 - - - +
53A ARG* 1.3 77.2 - - - +
55A GLY* 1.3 59.9 + - - +
56A VAL* 3.4 6.7 + - + +
61A ILE* 4.7 6.1 - - + -
106B SER* 4.6 1.8 - - - -
107B LEU* 4.2 8.7 + - - +
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Residues in contact with GLY 55 (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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51A SER 2.9 8.9 + - - -
52A GLU* 3.4 9.4 + - - -
53A ARG 3.3 2.4 - - - -
54A LEU* 1.3 78.0 - - - +
56A VAL* 1.3 61.0 + - - +
106B SER* 4.1 9.4 - - - -
107B LEU* 4.6 1.8 - - - -
108B GLN* 3.0 41.9 - - - +
151B ILE* 3.6 13.2 - - - +
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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