Contacts of the helix formed by residues 46 - 62 (chain A) in PDB entry 5A5J
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 GLY 46 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A ILE* 1.3 73.2 - - - +
47A ILE* 1.3 60.8 + - - -
48A LYS 3.3 2.7 - - - -
49A ASP* 3.1 16.5 + - - -
50A ILE* 2.8 33.8 + - - +
211A PRO* 4.9 0.2 - - - -
212A TRP* 5.4 0.4 - - - -
473A VAL* 3.9 16.2 - - - +
474A ASN 3.3 13.2 - - - -
475A GLY* 5.3 1.1 - - - -
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Residues in contact with ILE 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A GLY* 1.3 67.9 - - - -
48A LYS* 1.3 68.1 + - + +
50A ILE* 3.2 17.5 + - + +
51A SER* 2.9 32.1 + - - -
212A TRP* 5.2 1.6 - - - +
363A PRO* 3.4 32.0 - - + +
364A THR* 4.0 20.6 - - + +
474A ASN* 2.6 16.6 + - + +
475A GLY 3.4 18.3 + - - +
476A PHE* 3.6 22.4 - - + +
477A ALA 3.4 30.7 - - - +
478A SER 4.1 0.4 - - - +
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Residues in contact with LYS 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A GLY 3.3 0.8 - - - -
47A ILE* 1.3 87.2 - - + +
49A ASP* 1.3 59.0 + - - +
51A SER* 3.9 3.6 + - - -
52A LYS* 3.3 24.1 + - - +
358A TYR 5.8 0.9 - - - -
359A ILE 4.3 6.3 - - - -
360A ASP* 3.3 26.0 + - - -
363A PRO* 3.9 4.8 - - - +
392A THR* 4.4 7.3 + - - +
396A HIS* 6.4 1.6 - - - -
471A PRO* 3.8 29.2 - - + +
472A VAL 6.0 1.6 - - - +
473A VAL* 6.6 0.2 - - + -
474A ASN 5.9 0.2 - - - +
477A ALA 5.4 0.4 - - - +
478A SER* 3.1 31.2 + - - +
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Residues in contact with ASP 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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44A GLN 4.6 2.6 - - - +
45A ILE* 4.3 14.9 - - + -
46A GLY* 3.3 28.0 + - - +
47A ILE 3.1 0.2 - - - -
48A LYS* 1.3 79.7 + - - +
50A ILE* 1.3 64.0 + - - +
51A SER 3.3 0.2 - - - -
52A LYS* 3.2 8.8 + - - +
53A SER* 2.9 28.4 + - - +
473A VAL* 3.9 17.2 - - - +
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Residues in contact with ILE 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ILE* 4.1 19.5 - - + -
46A GLY 2.8 20.9 + - - +
47A ILE* 3.2 17.0 + - + +
49A ASP* 1.3 76.6 - - - +
51A SER* 1.3 56.9 + - - +
53A SER* 3.0 7.2 + - - -
54A LEU* 2.9 52.4 + - + +
212A TRP* 3.9 37.9 - - + +
364A THR* 5.0 9.2 - - + -
388A LEU* 5.3 5.6 - - + -
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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
----------------------------------------------------------
47A ILE 2.9 16.4 + - - -
48A LYS* 4.1 6.5 - - - -
50A ILE* 1.3 77.3 - - - +
52A LYS* 1.3 59.1 + - - +
54A LEU* 3.7 10.2 - - - +
55A THR* 3.3 23.9 + - - -
363A PRO* 3.7 14.3 + - - +
364A THR* 4.3 5.9 - - - +
390A SER* 3.3 10.7 + - - -
392A THR* 2.5 40.7 + - - +
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Residues in contact with LYS 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LYS 3.3 14.6 + - - +
49A ASP* 3.2 12.7 + - - +
50A ILE 3.1 0.6 - - - -
51A SER* 1.3 74.9 - - - +
53A SER* 1.3 64.3 + - - +
54A LEU 3.2 0.2 - - - -
55A THR* 3.0 27.5 + - + +
56A ASN* 3.0 23.7 + - - +
392A THR* 6.3 0.8 - - - +
405A GLU* 4.7 14.5 + - - -
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Residues in contact with SER 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ILE* 5.2 6.3 - - - +
49A ASP* 2.9 14.7 + - - +
50A ILE* 3.0 10.5 + - - -
52A LYS* 1.3 76.1 - - - +
54A LEU* 1.3 71.0 + - - +
55A THR 3.3 0.2 + - - -
56A ASN* 3.3 13.7 + - - +
57A LEU* 3.0 32.0 + - - +
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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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50A ILE* 2.9 37.7 + - + +
51A SER* 3.7 11.4 - - - +
52A LYS 3.2 0.2 - - - -
53A SER* 1.3 85.2 - - - +
55A THR* 1.3 60.2 + - - +
57A LEU* 3.7 9.1 + - + -
58A SER* 3.2 15.9 + - - -
65A PHE* 3.5 17.2 - - + -
67A LEU* 4.3 20.0 - - + -
76A VAL* 3.8 36.6 - - + -
78A HIS* 4.8 4.8 - - + -
364A THR* 5.2 5.8 - - + -
388A LEU* 4.0 17.7 - - + -
389A ILE 6.5 0.2 - - - -
390A SER* 5.1 11.7 - - - +
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Residues in contact with THR 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 3.3 11.7 + - - -
52A LYS* 3.0 25.0 + - + +
54A LEU* 1.3 74.8 - - - +
56A ASN* 1.4 59.3 - - - +
58A SER* 2.7 39.9 + - - +
59A LYS* 3.2 24.7 + - - +
78A HIS* 3.0 24.4 + - + +
390A SER* 5.0 1.7 + - - -
392A THR* 5.5 4.3 - - - +
393A SER* 5.1 3.3 + - - -
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Residues in contact with ASN 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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52A LYS* 3.0 23.1 + - - +
53A SER* 3.3 16.0 - - - +
55A THR* 1.4 75.9 - - - +
57A LEU* 1.3 58.5 + - + +
59A LYS* 3.0 44.3 + - - +
60A VAL* 3.4 11.3 + - - +
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Residues in contact with LEU 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A PRO* 3.8 26.5 - - + -
53A SER* 3.0 27.4 + - - +
54A LEU* 4.2 8.5 - - + -
56A ASN* 1.3 76.3 - - + +
58A SER* 1.3 64.5 + - - +
60A VAL* 3.9 10.1 - - + -
61A TYR* 3.0 42.1 + - + +
65A PHE* 3.8 21.6 - - + -
67A LEU* 3.9 24.2 - - + -
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Residues in contact with SER 58 (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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54A LEU 3.2 10.4 + - - -
55A THR* 2.7 22.5 + - - +
57A LEU* 1.3 73.5 - - - +
59A LYS* 1.3 68.6 + - - +
62A GLY* 3.0 39.9 + - - +
65A PHE* 4.1 2.9 - - - -
78A HIS* 3.3 42.1 + - - -
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Residues in contact with LYS 59 (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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55A THR* 3.4 31.6 - - + +
56A ASN* 3.0 27.7 + - - +
58A SER* 1.3 84.2 - - - +
60A VAL* 1.3 60.6 + - + +
62A GLY 4.6 0.9 + - - -
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Residues in contact with VAL 60 (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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56A ASN 3.7 13.5 - - - +
57A LEU* 3.9 11.9 - - + +
58A SER 3.3 0.2 - - - -
59A LYS* 1.3 79.3 - - + +
61A TYR* 1.3 88.5 + - + +
62A GLY 3.5 0.9 + - - -
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Residues in contact with TYR 61 (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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31A PRO* 4.2 21.1 - - + +
32A GLY* 3.1 27.0 + - - -
33A PRO* 2.9 46.9 - - + +
57A LEU* 3.0 34.7 + - + +
60A VAL* 1.3 95.0 - - + +
62A GLY* 1.3 59.1 + - - +
63A PRO* 4.8 0.5 - - - +
64A VAL 4.3 8.8 - - - +
65A PHE* 3.9 17.9 - - + -
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Residues in contact with GLY 62 (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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58A SER* 3.0 32.0 + - - +
59A LYS 4.6 1.0 + - - -
60A VAL 3.5 2.6 + - - -
61A TYR* 1.3 80.0 - - - +
63A PRO* 1.3 72.4 - - - +
64A VAL 3.6 1.8 - - - -
65A PHE* 4.0 4.3 - - - -
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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