Contacts of the helix formed by residues 56 - 71 (chain A) in PDB entry 1A76
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 56 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A PHE* 3.8 3.2 + - - +
36A LEU* 3.9 21.9 + - - -
39A ILE* 2.5 42.1 + - - +
46A PRO* 4.1 4.0 - - - +
47A LEU* 3.2 25.5 + - - +
54A ILE* 3.6 15.7 - - - -
55A THR* 1.3 76.6 + - - +
57A ALA* 1.3 61.9 + - - +
59A ASN* 3.4 4.4 + - - +
60A GLY 3.3 16.6 + - - -
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Residues in contact with ALA 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 4.3 21.1 - - + +
35A PHE* 3.7 12.8 - - - +
36A LEU* 4.8 4.3 - - + +
54A ILE* 5.0 0.6 - - - +
55A THR 3.2 0.6 - - - -
56A SER* 1.3 75.9 - - - +
58A TYR* 1.3 68.7 + - + +
60A GLY 3.3 1.2 + - - -
61A VAL* 3.0 30.1 + - - +
131A MET* 4.0 23.1 - - - -
135A CYS* 3.8 20.0 - - - -
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Residues in contact with TYR 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A GLU* 6.3 1.3 - - + -
54A ILE 3.8 14.7 + - - -
55A THR* 3.1 18.8 + - - +
57A ALA* 1.3 76.9 - - + +
59A ASN* 1.3 62.0 + - - +
61A VAL* 4.4 1.1 - - - -
62A PHE* 3.0 27.7 + - - +
130A LYS* 5.7 0.2 - - - +
131A MET* 3.6 38.5 - - + +
134A ASN* 3.1 41.5 + - + +
135A CYS* 3.7 14.4 - - - -
138A LEU* 3.5 18.6 - - + +
289A PHE* 4.2 15.0 - + - -
290A LEU* 4.3 5.4 - - + -
294A ASN* 3.8 28.9 - - + -
296A PHE* 4.0 11.2 - - + -
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Residues in contact with ASN 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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39A ILE* 3.8 17.3 - - + +
47A LEU* 3.6 26.8 - - + +
55A THR 3.1 11.5 + - - +
56A SER 3.5 10.1 - - - +
58A TYR* 1.3 77.6 - - - +
60A GLY* 1.3 63.4 + - - +
63A TYR* 3.1 50.6 + - - +
296A PHE* 3.5 20.5 - - + -
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Residues in contact with GLY 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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35A PHE* 3.3 20.9 - - - -
39A ILE* 3.5 20.6 - - - +
56A SER 3.3 8.5 + - - -
57A ALA 3.3 0.6 + - - -
59A ASN* 1.3 77.0 + - - +
61A VAL* 1.3 60.5 + - - +
63A TYR* 5.3 0.4 - - - -
64A LYS* 2.6 40.6 + - - +
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Residues in contact with VAL 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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32A LEU* 3.8 25.4 - - + -
35A PHE* 3.4 5.8 - - + -
57A ALA 3.0 21.7 + - - +
58A TYR 3.7 4.0 - - - +
59A ASN 3.4 0.2 - - - -
60A GLY* 1.3 77.2 - - - +
62A PHE* 1.3 58.8 + - - +
65A THR* 2.5 34.9 + - - +
77A TRP* 4.1 10.3 - - + -
135A CYS* 3.9 18.4 - - + +
138A LEU* 3.8 20.2 - - + -
139A LEU* 3.6 34.3 - - + -
142A MET* 4.0 1.2 - - - +
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Residues in contact with PHE 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 TYR 3.0 17.8 + - - +
59A ASN* 4.0 2.0 - - - +
61A VAL* 1.3 79.2 - - - +
63A TYR* 1.3 93.4 + + + +
66A ILE* 3.2 45.4 + - + +
138A LEU* 4.3 5.2 - - + -
142A MET* 3.7 31.3 - - + +
286A ILE* 3.8 19.3 - - + -
290A LEU* 3.6 24.7 - - + -
296A PHE* 5.0 0.2 - - + -
301A VAL* 4.1 9.4 - - + -
304A HIS* 3.6 21.3 - - + -
305A VAL* 3.6 24.7 - - + -
308A LEU* 4.9 2.5 - - + -
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Residues in contact with TYR 63 (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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59A ASN* 3.1 41.7 + - - +
60A GLY* 5.3 0.2 - - - -
62A PHE* 1.3 95.1 - + - +
64A LYS* 1.3 62.0 + - + +
66A ILE* 3.4 4.2 + - - +
67A HIS* 2.9 29.9 + - - +
296A PHE* 3.8 19.9 - + - +
297A ASN 5.5 0.5 + - - -
300A ARG* 3.2 34.2 - - + +
301A VAL* 3.7 19.1 + - - +
304A HIS* 3.5 45.2 - + - -
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Residues in contact with LYS 64 (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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35A PHE* 3.9 20.9 - - + -
39A ILE* 6.1 1.6 - - + -
60A GLY* 2.6 29.7 + - - +
63A TYR* 1.3 75.1 - - + +
65A THR* 1.3 62.3 + - - +
67A HIS* 3.3 30.0 + - - +
68A LEU* 3.1 32.2 + - + +
77A TRP* 5.6 1.6 - - + -
188A LEU 3.0 28.7 + - - +
189A THR* 4.2 18.6 + - + +
190A THR* 4.5 0.8 - - - +
191A THR* 3.3 25.5 + - - +
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Residues in contact with THR 65 (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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61A VAL 2.5 25.5 + - - -
62A PHE 3.8 1.6 - - - -
64A LYS* 1.3 78.9 - - - +
66A ILE* 1.3 60.8 + - - +
68A LEU* 3.3 11.7 + - - +
69A LEU* 3.1 24.3 + - + +
75A PRO* 4.1 16.8 - - + -
77A TRP* 3.3 25.8 + - - +
139A LEU* 4.3 2.1 - - + +
142A MET* 3.9 7.6 - - + -
144A ILE* 3.8 37.0 - - + -
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Residues in contact with ILE 66 (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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62A PHE* 3.2 39.8 + - + +
63A TYR* 3.9 4.3 - - - +
65A THR* 1.3 73.5 - - - +
67A HIS* 1.3 67.3 + - - +
69A LEU* 3.1 8.3 + - - +
70A GLU* 2.9 40.3 + - + +
142A MET* 4.3 5.2 - - + -
304A HIS* 3.6 53.6 - - + +
307A LYS* 5.1 3.4 - - + -
308A LEU* 4.0 22.2 - - + +
311A LEU* 4.3 10.8 - - + -
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Residues in contact with HIS 67 (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 PHE* 3.5 43.1 - + - -
63A TYR 2.9 18.5 + - - +
64A LYS* 3.4 33.5 + - - +
66A ILE* 1.3 78.3 - - - +
68A LEU* 1.3 67.7 + - + +
70A GLU* 3.5 25.7 + - - +
71A ASN 3.6 3.8 + - - -
188A LEU* 5.1 1.3 - - + -
191A THR* 5.0 8.3 - - - +
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Residues in contact with LEU 68 (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 PHE* 3.9 26.9 - - + -
24A VAL* 5.0 2.2 - - + -
26A ILE* 4.1 27.4 - - + -
64A LYS* 3.1 21.8 + - + +
65A THR* 3.5 10.8 - - - +
67A HIS* 1.3 84.6 - - + +
69A LEU* 1.3 56.2 + - - +
71A ASN* 3.0 12.6 + - - +
73A ILE* 3.0 50.7 + - + +
75A PRO* 4.3 11.7 - - + -
170A VAL* 5.8 2.2 - - + -
188A LEU* 4.5 26.2 - - + +
189A THR* 6.6 0.4 - - + -
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Residues in contact with LEU 69 (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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65A THR* 3.1 19.9 + - + +
66A ILE* 3.1 6.7 + - - +
68A LEU* 1.3 71.6 - - - +
70A GLU* 1.3 60.8 + - - +
71A ASN 3.0 5.2 - - - -
72A ASP 3.1 6.2 + - - -
73A ILE 3.5 16.8 - - - +
74A THR* 4.1 3.4 - - - -
75A PRO* 3.8 15.0 - - + -
144A ILE* 3.8 20.4 - - + -
278A LEU* 4.3 8.1 - - + -
308A LEU* 3.7 29.8 - - + -
311A LEU* 3.6 14.4 - - + +
312A ILE* 4.6 7.2 - - + -
315A LYS* 2.8 54.3 + - + +
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Residues in contact with GLU 70 (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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66A ILE* 2.9 22.8 + - + +
67A HIS* 3.6 25.7 + - - +
68A LEU 3.2 0.2 - - - -
69A LEU* 1.3 76.0 - - - +
71A ASN* 1.3 57.3 + - - +
72A ASP 3.3 2.3 + - - -
304A HIS* 5.5 4.3 - - - -
307A LYS* 4.0 24.4 + - + +
311A LEU* 3.8 27.1 - - + +
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Residues in contact with ASN 71 (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 PHE* 2.7 67.0 + - + +
17A GLU* 4.4 3.4 - - - +
20A LYS* 3.1 33.8 - - - +
67A HIS 3.6 0.6 + - - +
68A LEU 3.0 7.2 + - - +
69A LEU 3.0 0.6 - - - -
70A GLU* 1.3 79.6 - - - +
72A ASP* 1.3 65.4 + - - +
73A ILE* 3.1 6.5 + - + +
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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