Contacts of the helix formed by residues 43 - 55 (chain B) in PDB entry 2AXZ
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A PRO* 4.0 15.9 - - - +
42A ILE 3.2 17.0 - - - -
43A SER* 3.6 2.9 - - - +
44A VAL* 4.6 1.3 - - - -
41B PRO 4.1 0.8 + - - -
42B ILE* 1.3 76.9 - - - +
44B VAL* 1.3 65.2 + - - +
45B GLU* 3.4 14.9 - - - +
46B GLU* 2.9 44.4 + - - +
47B LEU* 3.0 20.3 + - - +
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Residues in contact with VAL 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A PHE* 5.5 0.4 - - + -
4A ILE* 3.5 26.0 - - + -
42A ILE* 3.0 15.8 + - + +
44A VAL* 4.2 23.3 - - + +
47A LEU* 4.1 16.8 - - + -
58A PHE* 6.1 0.4 - - + -
62A LEU* 4.0 7.9 - - + -
67A MSE 3.5 31.9 - - + -
42B ILE 4.0 0.4 + - - -
43B SER* 1.3 71.3 - - - +
45B GLU* 1.3 66.6 + - - +
47B LEU* 4.0 3.0 - - - +
48B SER* 3.0 24.4 + - - -
58B PHE* 4.2 12.9 - - + -
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Residues in contact with GLU 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MSE 3.6 31.1 + - + +
2A PHE* 4.3 18.8 + - - +
4A ILE* 5.0 3.1 - - - +
41A PRO* 3.9 17.9 - - + -
42A ILE* 3.3 39.3 + - - +
43B SER* 3.4 15.7 - - - +
44B VAL* 1.3 79.5 + - - +
46B GLU* 1.3 61.6 + - + +
48B SER* 3.6 4.9 - - - -
49B LYS* 3.2 30.2 + - - +
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Residues in contact with GLU 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ILE* 4.8 8.7 - - + +
27B MSE 3.0 31.5 - - + +
40B ARG* 2.9 27.8 + - - -
42B ILE* 3.9 9.0 - - + +
43B SER* 2.9 40.6 + - - +
45B GLU* 1.3 75.0 - - + +
47B LEU* 1.3 67.0 + - - +
48B SER 3.0 1.3 - - - -
49B LYS* 2.7 22.5 + - + +
50B PHE* 2.9 17.7 + - + -
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Residues in contact with LEU 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A VAL* 4.2 13.5 - - + -
4B ILE* 3.8 25.8 - - + -
8B LEU* 4.2 13.0 - - + -
42B ILE* 3.7 19.3 - - + +
43B SER 3.0 13.4 + - - +
44B VAL* 4.0 4.3 - - - +
46B GLU* 1.3 74.6 - - - +
48B SER* 1.3 51.8 + - - +
50B PHE* 3.2 4.0 + - - +
51B SER* 2.8 36.3 + - - -
58B PHE* 3.8 22.4 - - + -
61B ILE* 4.1 22.7 - - + -
62B LEU* 3.7 31.6 - - + -
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Residues in contact with SER 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MSE 5.0 4.1 - - - -
2A PHE* 3.9 24.7 - - - -
67A MSE 5.4 2.6 - - - -
44B VAL* 3.0 20.6 + - - -
45B GLU* 3.6 9.0 - - - -
47B LEU* 1.3 76.7 - - - +
49B LYS* 1.3 62.2 + - - +
51B SER* 3.2 15.8 - - - -
52B GLU* 3.2 8.8 + - - +
58B PHE* 3.8 20.3 - - - +
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Residues in contact with LYS 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MSE 4.6 20.2 - - + -
25B GLY 5.4 3.8 + - - -
26B ILE* 3.6 38.0 - - + +
45B GLU* 3.2 19.3 - - - +
46B GLU* 2.7 14.7 + - - +
48B SER* 1.3 70.7 - - - +
50B PHE* 1.3 65.4 + - - +
52B GLU* 3.1 19.5 + - - +
53B ARG* 3.1 23.2 + - - +
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Residues in contact with PHE 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B LEU* 4.0 28.5 - - + -
22B LEU* 3.7 37.2 - - + -
23B TYR* 4.2 2.5 - - - -
26B ILE* 3.9 11.7 - - + -
27B MSE 3.4 35.0 - - + -
32B TYR* 3.4 33.7 - + - -
35B VAL* 4.8 3.4 - - + -
42B ILE* 3.9 27.4 - - + -
46B GLU* 2.9 20.6 + - + -
47B LEU* 3.6 4.7 - - - +
49B LYS* 1.3 76.4 - - - +
51B SER* 1.3 58.2 + - - +
53B ARG* 2.9 6.6 + - - +
54B LEU* 2.9 36.1 + - + +
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Residues in contact with SER 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B LEU 2.8 13.4 + - - -
48B SER* 3.2 15.0 - - - -
50B PHE* 1.3 78.2 - - - +
52B GLU* 1.3 53.3 + - - +
54B LEU* 3.8 0.6 + - - -
55B GLY* 3.1 21.5 + - - -
56B VAL 2.9 28.2 + - - +
57B ASN 3.6 0.2 - - - -
58B PHE* 3.1 32.6 + - - +
61B ILE* 3.7 19.6 - - - +
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Residues in contact with GLU 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A ASN* 4.1 26.2 - - - +
74A GLU* 3.9 22.3 - - - +
75A THR* 5.7 7.0 - - + +
106A SER* 4.8 6.6 + - - -
108A GLN* 6.0 0.2 - - - +
109A TYR* 6.1 0.5 - - - -
48B SER 3.2 7.4 + - - +
49B LYS* 3.1 13.6 + - - +
51B SER* 1.3 76.3 - - - +
53B ARG* 1.3 72.6 + - + +
55B GLY* 3.6 9.4 + - - -
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Residues in contact with ARG 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A THR 5.3 0.7 - - - +
106A SER* 4.9 4.5 - - - -
17B TYR* 3.9 17.2 + - - -
21B ASP 3.3 26.2 + - - +
22B LEU* 3.5 24.7 + - + +
24B SER* 2.8 29.9 + - - -
25B GLY* 4.5 2.4 - - - -
26B ILE* 3.4 31.4 - - - +
49B LYS* 3.1 20.6 + - - +
50B PHE* 2.9 12.3 + - - +
52B GLU* 1.3 86.0 + - - +
54B LEU* 1.3 61.5 + - - +
55B GLY* 4.5 0.2 - - - -
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Residues in contact with LEU 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A SER* 5.0 1.6 - - - -
107A LEU* 5.0 4.0 + - - +
8B LEU* 3.6 32.3 - - + +
11B ILE* 3.7 36.1 - - + -
12B ARG* 3.8 24.2 - - + +
15B LEU* 3.3 20.6 - - - +
17B TYR* 3.6 18.9 + - + -
22B LEU* 3.8 22.2 - - + -
50B PHE 2.9 18.0 + - - +
51B SER 4.2 1.3 - - - +
53B ARG* 1.3 79.0 - - - +
55B GLY* 1.3 57.6 + - - +
56B VAL* 3.3 8.7 - - + +
61B ILE* 4.1 15.3 - - + -
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Residues in contact with GLY 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A SER* 4.4 11.2 - - - -
107A LEU* 4.5 3.1 - - - +
108A GLN* 3.0 42.4 + - - +
151A ILE* 4.0 12.2 - - - +
51B SER 3.1 10.7 + - - -
52B GLU* 3.6 8.5 + - - -
53B ARG 3.4 2.4 - - - -
54B LEU* 1.3 78.1 - - - +
56B VAL* 1.3 60.0 + - - +
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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