Contacts of the helix formed by residues 43 - 55 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41C PRO* 3.8 24.8 - - - +
42C ILE 3.2 16.4 - - - -
43C SER* 3.8 2.7 - - - +
44C VAL* 4.7 0.2 - - - -
41D PRO 4.1 0.8 + - - -
42D ILE* 1.3 76.4 - - - +
44D VAL* 1.3 64.9 + - - +
45D GLU* 3.4 8.5 - - - +
46D GLU* 2.8 44.1 + - - +
47D LEU* 3.0 21.9 + - - +
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Residues in contact with VAL 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C PHE* 6.4 0.4 - - + -
4C ILE* 3.5 26.2 - - + -
42C ILE* 3.0 16.6 + - + +
43C SER 4.7 0.2 - - - -
44C VAL* 4.3 19.7 - - + +
47C LEU* 4.2 16.8 - - + -
58C PHE* 6.2 0.4 - - + -
62C LEU* 4.0 7.4 - - + -
67C MSE 3.4 32.5 - - + -
42D ILE 4.0 0.2 + - - -
43D SER* 1.3 70.9 - - - +
45D GLU* 1.3 66.2 + - - +
47D LEU* 4.0 5.7 - - - +
48D SER* 3.0 24.6 + - - -
58D PHE* 4.2 12.2 - - + -
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Residues in contact with GLU 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C PHE* 3.7 52.1 - - + +
4C ILE* 5.0 1.3 - - - +
41C PRO* 4.0 20.4 - - + -
42C ILE* 3.4 26.9 + - - +
43D SER* 3.4 15.7 - - - +
44D VAL* 1.3 87.1 + - - +
46D GLU* 1.3 59.5 + - + +
48D SER* 3.6 4.1 - - - -
49D LYS* 3.2 32.3 + - - +
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Residues in contact with GLU 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D ILE* 4.9 8.9 - - + +
27D MSE 3.0 32.4 - - + +
40D ARG* 2.9 28.3 + - - -
42D ILE* 3.9 8.3 - - + +
43D SER* 2.8 41.1 + - - +
45D GLU* 1.3 75.6 - - + +
47D LEU* 1.3 68.6 + - - +
48D SER 3.0 1.1 - - - -
49D LYS* 2.7 23.3 + - + +
50D PHE* 2.9 16.9 + - + -
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Residues in contact with LEU 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C VAL* 4.1 14.4 - - + -
4D ILE* 3.8 26.0 - - + -
8D LEU* 4.2 13.0 - - + -
42D ILE* 3.7 20.7 - - + +
43D SER 3.0 12.7 + - - +
44D VAL* 4.0 4.0 - - - +
46D GLU* 1.3 75.0 - - - +
48D SER* 1.3 54.0 + - - +
50D PHE* 3.2 3.2 + - - -
51D SER* 2.8 36.0 + - - -
58D PHE* 3.8 20.6 - - + +
61D ILE* 4.1 21.5 - - + -
62D LEU* 3.7 32.1 - - + -
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Residues in contact with SER 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C PHE* 5.3 8.8 - - - -
67C MSE 5.3 9.0 - - - -
73C ASN* 5.9 3.3 - - - +
44D VAL* 3.0 21.2 + - - -
45D GLU* 3.6 9.2 - - - -
46D GLU 3.0 0.2 + - - -
47D LEU* 1.3 77.9 - - - +
49D LYS* 1.3 62.1 + - - +
51D SER* 3.2 15.4 + - - -
52D GLU* 3.2 9.2 + - - +
58D PHE* 3.8 20.8 - - - -
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Residues in contact with LYS 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C PHE* 4.9 16.6 - - + -
25D GLY 5.4 4.0 + - - -
26D ILE* 3.6 38.3 - - + +
45D GLU* 3.2 21.5 - - - +
46D GLU* 2.7 14.1 + - + +
48D SER* 1.3 71.1 - - - +
50D PHE* 1.3 64.9 + - - +
52D GLU* 3.1 19.6 + - - +
53D ARG* 3.1 23.7 + - - +
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Residues in contact with PHE 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D LEU* 4.0 27.6 - - + -
22D LEU* 3.7 36.8 - - + -
23D TYR* 4.2 0.9 - - - -
26D ILE* 3.9 13.5 - - + -
27D MSE 3.4 34.5 - - + -
32D TYR* 3.5 33.2 - + - -
35D VAL* 4.8 3.6 - - + -
42D ILE* 3.9 28.3 - - + -
46D GLU* 2.9 19.9 + - + -
47D LEU* 3.6 5.2 - - - +
49D LYS* 1.3 76.7 - - - +
51D SER* 1.3 58.5 + - - +
53D ARG* 3.0 6.6 + - - +
54D LEU* 2.9 36.0 + - + +
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Residues in contact with SER 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C GLN* 3.7 4.0 + - - +
47D LEU 2.8 13.9 + - - -
48D SER 3.2 14.6 - - - -
49D LYS 3.1 0.2 - - - -
50D PHE* 1.3 77.7 - - - +
52D GLU* 1.3 54.3 + - - +
54D LEU* 4.8 0.7 - - - -
55D GLY 3.1 19.4 + - - -
56D VAL 2.9 29.3 + - - +
57D ASN 3.6 0.2 - - - -
58D PHE* 3.1 31.6 + - - +
61D ILE* 3.7 19.9 - - - +
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Residues in contact with GLU 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C ASN* 3.3 39.8 + - - +
74C GLU* 2.8 31.9 - - - +
75C THR* 5.2 1.1 - - + +
106C SER* 4.8 5.2 - - - -
108C GLN* 4.2 16.8 + - - +
109C TYR* 6.6 0.2 - - + -
48D SER 3.2 7.8 + - - +
49D LYS* 3.1 13.8 + - - +
51D SER* 1.3 76.9 - - - +
53D ARG* 1.3 72.2 + - + +
55D GLY* 3.6 8.8 + - - -
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Residues in contact with ARG 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C THR 5.2 1.0 - - - +
106C SER* 4.8 4.5 - - - -
17D TYR* 3.9 16.8 + - - -
21D ASP 3.3 25.8 + - - +
22D LEU* 3.5 24.4 + - + +
24D SER* 2.8 29.5 + - - -
25D GLY* 4.5 2.2 - - - -
26D ILE* 3.4 31.4 - - - +
49D LYS* 3.1 21.2 + - - +
50D PHE* 3.0 12.3 + - - +
52D GLU* 1.3 84.5 + - - +
54D LEU* 1.3 62.4 + - - +
55D GLY* 4.5 0.2 - - - -
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Residues in contact with LEU 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C SER* 4.9 1.3 - - - -
107C LEU* 4.9 3.6 + - - +
8D LEU* 3.6 31.0 - - + +
11D ILE* 3.6 39.3 - - + -
12D ARG* 3.7 22.2 - - + +
15D LEU* 3.3 20.5 - - - +
17D TYR* 3.6 21.0 + - + -
22D LEU* 3.8 21.8 - - + -
50D PHE 2.9 17.4 + - - +
51D SER* 4.2 1.6 - - - +
53D ARG* 1.3 78.4 - - - +
55D GLY* 1.3 57.2 + - - +
56D VAL* 3.3 7.6 - - + +
61D ILE* 4.1 14.8 - - + -
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Residues in contact with GLY 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C SER* 4.4 9.6 - - - -
107C LEU* 4.8 2.5 - - - -
108C GLN* 3.0 49.1 + - - +
151C ILE* 3.9 17.2 - - - +
51D SER 3.1 6.7 + - - -
52D GLU 3.6 4.0 + - - -
53D ARG 3.4 2.2 - - - -
54D LEU* 1.3 77.3 - - - +
56D VAL* 1.3 59.2 + - - +
57D ASN 4.0 0.3 + - - -
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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