Contacts of the helix formed by residues 43 - 55 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41C PRO 4.1 0.8 + - - -
42C ILE* 1.3 75.7 - - - +
44C VAL* 1.3 64.6 + - - +
45C GLU* 3.4 8.5 - - - +
46C GLU* 2.8 43.9 + - - +
47C LEU* 3.0 22.5 + - - +
41D PRO* 3.8 25.0 - - - +
42D ILE 3.2 15.9 - - - -
43D SER* 3.8 2.5 - - - +
44D VAL* 4.7 0.4 - - - -
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Residues in contact with VAL 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C ILE 4.0 0.4 + - - -
43C SER* 1.3 72.1 - - - +
45C GLU* 1.3 67.2 - - - +
47C LEU* 4.0 6.5 - - - +
48C SER* 3.0 24.6 + - - -
58C PHE* 4.2 12.6 - - + -
4D ILE* 3.5 26.2 - - + -
42D ILE* 3.0 15.8 + - + +
44D VAL* 4.3 19.7 - - + +
47D LEU* 4.1 16.4 - - + -
58D PHE* 6.2 0.7 - - + -
62D LEU* 4.0 7.9 - - + -
67D MSE 3.4 32.5 - - + -
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Residues in contact with GLU 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C SER* 3.4 16.4 - - - +
44C VAL* 1.3 87.5 + - - +
46C GLU* 1.3 60.0 + - + +
48C SER* 3.6 3.7 - - - -
49C LYS* 3.2 27.9 + - - +
1D MSE 3.4 48.9 - - + +
2D PHE 4.2 10.2 - - - +
4D ILE* 5.0 2.5 - - - +
41D PRO* 4.0 20.0 - - + -
42D ILE* 3.4 26.1 + - - +
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Residues in contact with GLU 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C ILE* 4.9 8.7 - - + +
27C MSE 3.0 31.9 - - + +
40C ARG* 2.9 27.6 + - - -
41C PRO 4.5 0.2 - - - +
42C ILE* 3.9 9.1 - - + +
43C SER* 2.8 40.6 + - - +
45C GLU* 1.3 75.7 - - + +
47C LEU* 1.3 69.2 + - - +
48C SER 3.0 1.1 - - - -
49C LYS* 2.7 22.1 + - + +
50C PHE* 2.9 17.8 + - + -
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Residues in contact with LEU 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C ILE* 3.8 25.8 - - + -
8C LEU* 4.2 13.7 - - + -
42C ILE* 3.7 18.9 - - + +
43C SER 3.0 12.9 + - - +
44C VAL* 4.0 5.2 - - - +
46C GLU* 1.3 75.5 - - - +
48C SER* 1.3 53.5 + - - +
50C PHE* 3.2 3.5 + - - +
51C SER* 2.8 36.0 + - - -
58C PHE* 3.8 20.6 - - + -
61C ILE* 4.1 23.3 - - + -
62C LEU* 3.7 31.6 - - + -
44D VAL* 4.2 13.9 - - + -
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Residues in contact with SER 48 (chain C).
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* 3.0 21.9 + - - -
45C GLU* 3.6 8.1 - - - -
47C LEU* 1.3 77.5 - - - +
49C LYS* 1.3 62.9 + - - +
51C SER* 3.2 15.8 + - - -
52C GLU* 3.2 8.8 + - - +
58C PHE* 3.8 20.8 - - - +
1D MSE 5.1 8.0 - - - -
2D PHE* 4.9 12.1 - - - -
67D MSE 5.3 6.3 - - - -
73D ASN* 5.7 0.7 + - - -
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Residues in contact with LYS 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C GLY 5.4 4.0 + - - -
26C ILE* 3.6 38.0 - - + +
45C GLU* 3.2 14.1 - - - +
46C GLU* 2.7 13.5 + - + +
48C SER* 1.3 71.5 - - - +
50C PHE* 1.3 64.7 + - - +
52C GLU* 3.1 19.8 + - - +
53C ARG* 3.1 24.0 + - - +
1D MSE 3.3 28.7 - - + +
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Residues in contact with PHE 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C LEU* 4.0 27.1 - - + -
22C LEU* 3.7 37.5 - - + -
23C TYR* 4.2 2.2 - - - -
26C ILE* 3.9 12.1 - - + -
27C MSE 3.4 34.8 - - + -
32C TYR* 3.5 33.2 - + - -
35C VAL* 4.8 3.8 - - + -
42C ILE* 3.9 28.3 - - + -
46C GLU* 2.9 21.0 + - + -
47C LEU* 3.6 4.7 - - - +
49C LYS* 1.3 75.6 - - - +
51C SER* 1.3 57.6 + - - +
53C ARG* 3.0 6.6 + - - +
54C LEU* 2.9 35.7 + - + +
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Residues in contact with SER 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C LEU 2.8 12.8 + - - -
48C SER* 3.2 15.3 - - - -
49C LYS 3.1 0.2 - - - -
50C PHE* 1.3 78.6 - - - +
52C GLU* 1.3 54.0 + - - +
54C LEU* 4.1 0.8 - - - -
55C GLY* 3.1 21.1 + - - -
56C VAL 2.9 28.6 + - - +
58C PHE* 3.1 31.5 + - - +
61C ILE* 3.7 19.6 - - - +
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Residues in contact with GLU 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C SER 3.2 7.4 + - - +
49C LYS* 3.1 14.2 + - - +
51C SER* 1.3 76.8 - - - +
53C ARG* 1.3 72.9 + - + +
55C GLY* 3.6 10.5 + - - +
73D ASN* 4.5 19.4 - - - +
74D GLU* 3.4 35.6 - - - +
75D THR* 5.1 11.3 - - + +
106D SER* 4.8 6.8 + - - -
108D GLN* 6.0 0.2 - - - +
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Residues in contact with ARG 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C TYR* 3.9 16.7 + - - -
21C ASP 3.3 25.7 + - - +
22C LEU* 3.5 25.1 + - + +
24C SER* 2.8 29.9 + - - -
25C GLY* 4.5 2.6 - - - -
26C ILE* 3.4 31.0 - - - +
49C LYS* 3.1 21.5 + - - +
50C PHE* 3.0 12.3 + - - +
52C GLU* 1.3 85.5 + - - +
54C LEU* 1.3 63.2 + - - +
55C GLY* 4.5 0.2 - - - -
105D THR 5.2 0.7 - - - +
106D SER* 4.8 4.5 - - - -
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Residues in contact with LEU 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C LEU* 3.6 31.2 - - + +
11C ILE* 3.6 38.1 - - + -
12C ARG* 3.7 22.7 - - + +
15C LEU* 3.3 20.7 - - - +
17C TYR* 3.6 21.1 + - + -
22C LEU* 3.8 21.5 - - + -
50C PHE 2.9 18.0 + - - +
51C SER 4.2 1.1 - - - +
53C ARG* 1.3 80.3 - - - +
55C GLY* 1.3 58.3 + - - +
56C VAL* 3.3 8.3 - - + +
61C ILE* 4.1 14.6 - - + -
106D SER* 4.8 1.6 - - - -
107D LEU* 4.9 4.0 + - - +
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Residues in contact with GLY 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C SER 3.1 10.7 + - - -
52C GLU* 3.6 8.0 + - - -
53C ARG 3.4 2.4 - - - -
54C LEU* 1.3 77.3 - - - +
56C VAL* 1.3 61.7 + - - +
106D SER* 4.4 10.8 - - - -
107D LEU* 4.5 3.3 - - - +
108D GLN* 2.9 43.0 + - - +
151D ILE* 3.9 11.2 - - - +
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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