Contacts of the helix formed by residues 44 - 57 (chain A) in PDB entry 1X58
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 ARG 44 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A LEU* 3.6 10.6 - - - +
42A GLY 4.5 7.3 + - - +
43A ARG* 1.3 81.5 - - - +
45A ALA* 1.3 65.3 + - - +
46A VAL* 3.8 25.4 - - + +
47A ASP* 3.1 29.2 + - - +
48A LEU* 4.1 1.9 + - - +
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Residues in contact with ALA 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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30A TRP* 3.7 11.9 - - + +
31A ASN* 3.2 54.2 + - - +
34A LEU* 3.4 16.4 - - + +
44A ARG* 1.3 72.1 - - - +
46A VAL* 1.3 64.1 + - + +
48A LEU* 3.2 21.7 + - - +
49A ALA 3.5 3.3 + - - -
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Residues in contact with VAL 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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44A ARG* 3.1 21.2 - - + -
45A ALA* 1.3 79.6 - - + +
47A ASP* 1.3 65.9 + - - +
49A ALA* 3.0 11.2 + - + +
50A HIS* 2.7 40.3 + - + +
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Residues in contact with ASP 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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11A PHE* 3.4 8.9 - - + -
43A ARG* 3.5 34.8 + - - +
44A ARG* 3.1 26.5 + - - +
46A VAL* 1.3 88.0 - - - +
48A LEU* 1.3 56.3 + - - +
50A HIS* 3.8 6.2 - - - +
51A LYS* 2.9 33.1 + - - +
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Residues in contact with LEU 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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11A PHE* 4.0 11.9 - - + -
19A LEU* 3.4 25.6 - - + +
30A TRP* 3.2 44.0 - - + +
33A ILE* 3.8 10.8 - - + -
34A LEU* 3.6 27.4 - - + +
39A PHE* 3.8 24.2 - - + -
43A ARG* 4.2 9.4 - - - +
44A ARG 4.4 4.3 - - - +
45A ALA 3.4 10.8 - - - +
46A VAL 3.1 0.2 - - - -
47A ASP* 1.3 75.1 - - - +
49A ALA* 1.3 59.4 + - - +
51A LYS* 3.8 1.2 - - - +
52A TYR* 2.8 31.4 + - - +
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Residues in contact with ALA 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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30A TRP* 3.5 42.4 - - + +
45A ALA 3.5 2.3 + - - +
46A VAL* 3.0 14.9 + - + +
48A LEU* 1.3 77.4 - - - +
50A HIS* 1.3 56.8 + - - +
52A TYR* 3.6 2.1 - - - +
53A HIS* 2.8 29.6 + - - +
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Residues in contact with HIS 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 VAL* 2.7 25.1 + - + +
47A ASP* 3.8 7.2 - - - +
49A ALA* 1.3 71.8 - - - +
51A LYS* 1.3 64.9 + - - +
53A HIS* 3.5 17.7 + - + +
54A ARG* 3.3 43.6 + - - +
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Residues in contact with LYS 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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10A ASP* 2.8 35.3 + - - +
11A PHE* 3.6 38.8 + - + -
16A VAL* 4.4 12.6 - - + -
19A LEU* 5.4 0.4 - - + -
47A ASP 2.9 19.1 + - - +
48A LEU 3.9 1.1 - - - +
50A HIS* 1.3 73.6 - - - +
52A TYR* 1.3 52.7 + - - +
54A ARG* 3.0 17.1 + - + +
55A LEU* 2.8 67.6 + - + +
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Residues in contact with TYR 52 (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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19A LEU* 3.5 20.6 - - + +
20A PHE* 3.5 33.7 - + - -
23A VAL* 3.9 25.9 - - + +
28A ASN* 5.2 8.8 + - - -
30A TRP* 3.4 26.2 - + + -
48A LEU 2.8 18.3 + - - +
49A ALA 3.6 3.8 - - - +
51A LYS* 1.3 72.4 - - - +
53A HIS* 1.3 56.3 + - - +
55A LEU* 2.9 10.8 + - - +
56A ILE* 2.8 64.4 + - + +
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Residues in contact with HIS 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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49A ALA 2.8 19.6 + - - +
50A HIS* 3.5 21.8 + + + +
52A TYR* 1.3 75.6 - - - +
54A ARG* 1.3 83.7 + - - +
56A ILE* 3.1 16.3 + - + +
57A SER* 2.8 44.1 + - - -
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Residues in contact with ARG 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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50A HIS* 3.3 32.0 + - + +
51A LYS* 3.0 19.9 + - + +
53A HIS* 1.3 93.4 + - - +
55A LEU* 1.3 62.0 + - - +
57A SER* 3.3 12.9 + - - -
58A GLY 3.3 20.3 + - - +
62A GLY 5.4 10.8 + - - -
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Residues in contact with LEU 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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16A VAL* 3.9 21.8 - - + -
19A LEU* 4.8 7.9 - - + -
20A PHE* 3.7 38.1 - - + -
51A LYS* 2.8 54.6 + - + +
52A TYR* 2.9 13.9 + - - +
54A ARG* 1.3 73.1 - - - +
56A ILE* 1.3 58.0 + - - +
58A GLY* 3.1 19.1 + - - -
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Residues in contact with ILE 56 (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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20A PHE* 5.2 4.3 - - + -
52A TYR* 2.8 60.9 + - + +
53A HIS* 3.3 19.7 - - + +
55A LEU* 1.3 71.9 - - + +
57A SER* 1.3 57.9 + - - +
58A GLY* 3.3 3.4 + - - -
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Residues in contact with SER 57 (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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53A HIS* 2.8 35.1 + - - -
54A ARG* 3.5 19.3 - - - -
55A LEU 3.3 0.4 - - - -
56A ILE* 1.3 76.4 - - - +
58A GLY* 1.3 63.6 + - - +
59A PRO 4.4 1.2 - - - +
60A SER 3.9 10.7 - - - +
61A SER 4.6 8.4 - - - +
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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