Contacts of the helix formed by residues 57 - 71 (chain A) in PDB entry 3NTY
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 ASN 57 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A THR* 2.8 42.6 + - - -
24A TYR* 4.4 0.2 - - - +
25A ALA 5.0 1.0 - - - +
31A LYS* 5.5 3.1 - - + +
34A ALA* 4.0 15.9 - - + +
51A SER* 2.8 23.4 + - - -
52A ALA 5.1 0.2 + - - -
55A TYR* 3.0 21.2 + - - +
56A ASN* 1.3 80.1 - - - +
58A GLU* 1.3 68.4 + - - +
59A GLU 2.9 5.4 + - - -
60A GLN* 3.0 19.2 + - - +
61A VAL* 3.0 19.3 + - - +
272A TYR* 3.9 4.4 + - - -
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Residues in contact with GLU 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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51A SER* 3.9 4.5 - - - +
52A ALA 3.7 23.5 - - - +
53A HIS* 4.0 11.8 + - - +
56A ASN* 3.7 1.3 - - - +
57A ASN* 1.3 81.8 + - - +
59A GLU* 1.3 56.3 + - - +
61A VAL* 4.7 1.3 - - - -
62A GLY* 3.0 22.2 + - - -
81A TYR* 3.2 19.3 + - - +
83A SER* 3.0 22.7 + - - -
102A SER* 2.5 44.9 + - - -
105A ASN* 4.2 19.4 + - + +
106A LEU* 3.2 24.1 - - + +
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Residues in contact with GLU 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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31A LYS* 4.6 9.5 + - - -
56A ASN 5.5 0.4 - - - -
57A ASN 2.9 0.8 + - - -
58A GLU* 1.3 75.8 - - - +
60A GLN* 1.3 82.2 + - - +
62A GLY* 3.4 1.0 + - - -
63A LEU* 2.9 40.7 + - + +
66A ARG* 5.2 0.5 + - - -
105A ASN* 3.4 29.4 - - + +
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Residues in contact with GLN 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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31A LYS* 3.2 53.3 - - - +
32A SER* 4.7 2.4 - - - +
34A ALA* 3.8 17.5 - - + -
35A LEU* 3.4 26.2 - - + +
56A ASN 3.8 6.8 - - - +
57A ASN* 3.0 22.9 + - - +
59A GLU* 1.3 97.0 + - - +
61A VAL* 1.3 59.5 + - - +
63A LEU* 3.1 13.9 + - + +
64A ALA* 2.9 26.7 + - - +
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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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23A THR* 4.0 12.8 - - + -
34A ALA* 4.7 4.7 - - + -
38A THR* 3.8 28.5 - - + +
49A ILE* 4.1 10.3 - - + -
51A SER* 4.2 4.0 - - - +
57A ASN* 3.0 39.2 + - + +
58A GLU* 4.1 3.6 - - - +
60A GLN* 1.3 75.4 - - - +
62A GLY* 1.3 57.6 + - - +
64A ALA* 3.3 7.2 + - - +
65A ILE* 2.9 34.5 + - + +
81A TYR* 3.9 26.2 - - + -
106A LEU* 4.8 0.7 - - + -
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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 GLU 3.0 18.8 + - - -
59A GLU 3.8 1.3 - - - -
61A VAL* 1.3 74.8 - - - +
63A LEU* 1.3 64.0 + - - +
65A ILE* 3.3 5.8 + - - +
66A ARG* 3.1 30.2 + - - +
106A LEU* 3.6 32.5 - - - -
108A LEU* 5.4 1.3 - - - -
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Residues in contact with LEU 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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35A LEU* 3.6 19.3 - - + -
39A LYS* 5.5 0.2 - - - -
59A GLU* 2.9 37.0 + - + +
60A GLN* 3.1 18.8 + - + +
62A GLY* 1.3 74.9 - - - +
64A ALA* 1.3 64.1 + - - +
66A ARG* 3.7 24.3 - - - +
67A SER* 2.9 25.3 + - - -
107A GLN* 4.7 4.7 - - - +
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Residues in contact with ALA 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 LEU* 3.5 19.9 - - + +
38A THR* 3.6 30.1 - - + -
39A LYS* 3.7 15.7 - - + +
42A ILE* 4.5 0.4 - - - -
60A GLN 2.9 12.4 + - - +
61A VAL 3.5 8.1 - - - +
63A LEU* 1.3 76.6 - - - +
65A ILE* 1.3 63.6 + - - +
67A SER* 3.3 4.5 - - - -
68A LYS* 3.1 27.9 + - - +
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Residues in contact with ILE 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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38A THR* 4.6 0.9 - - + -
42A ILE* 3.9 10.3 - - + -
49A ILE* 4.0 20.6 - - + -
61A VAL* 2.9 26.4 + - + +
62A GLY* 3.3 5.6 + - - +
64A ALA* 1.3 76.5 - - - +
66A ARG* 1.3 63.4 + - + +
68A LYS* 3.2 4.0 + - - +
69A ILE* 3.0 43.8 + - + +
74A VAL* 4.8 0.2 - - - +
76A ARG* 5.4 1.1 - - - -
79A ILE* 4.1 28.5 - - + -
81A TYR* 3.9 32.5 - - + -
106A LEU* 5.4 0.2 - - + -
108A LEU* 4.6 15.9 - - + -
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Residues in contact with ARG 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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59A GLU 5.2 0.8 + - - -
62A GLY 3.1 13.4 + - - +
63A LEU* 3.7 31.2 - - - +
65A ILE* 1.3 77.9 - - + +
67A SER* 1.3 60.2 + - - +
69A ILE* 3.2 11.0 + - + +
70A ALA* 2.8 32.0 + - - +
105A ASN 5.3 0.8 + - - -
106A LEU 2.8 19.0 + - - -
107A GLN* 2.8 71.1 + - - +
108A LEU* 3.9 18.2 - - + -
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Residues in contact with SER 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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39A LYS* 4.2 20.7 + - - +
63A LEU 2.9 13.2 + - - -
64A ALA* 3.3 13.2 - - - -
66A ARG* 1.3 76.7 - - - +
68A LYS* 1.3 59.2 + - - +
70A ALA* 3.3 5.2 + - - +
71A ASP* 2.9 35.9 + - - +
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Residues in contact with LYS 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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39A LYS* 4.2 20.4 - - + -
42A ILE* 3.3 29.6 - - + -
43A GLU* 2.7 43.8 + - - +
64A ALA 3.1 15.2 + - - +
65A ILE 3.2 6.7 + - - +
67A SER* 1.3 80.1 - - - +
69A ILE* 1.3 55.9 + - - +
71A ASP* 2.3 52.0 + - - +
73A SER* 3.1 26.9 + - - -
74A VAL* 3.2 22.8 + - + -
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Residues in contact with ILE 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 ILE* 3.0 30.7 + - + +
66A ARG* 3.2 14.8 + - + +
68A LYS* 1.3 75.1 - - - +
70A ALA* 1.3 63.5 + - - +
72A GLY* 3.3 10.2 + - - -
74A VAL* 3.1 28.8 - - + +
75A LYS* 4.1 2.2 - - - +
76A ARG* 3.6 52.7 - - + +
79A ILE* 4.9 1.3 - - + -
108A LEU* 5.2 1.6 - - + -
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Residues in contact with ALA 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 ARG 2.8 20.8 + - - +
67A SER* 3.9 5.2 - - - +
69A ILE* 1.3 71.2 - - - +
71A ASP* 1.3 61.9 + - - +
72A GLY* 3.0 6.9 + - - -
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Residues in contact with ASP 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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67A SER* 2.9 14.2 + - - +
68A LYS* 2.3 54.8 + - - +
70A ALA* 1.3 75.7 - - - +
72A GLY* 1.3 60.8 + - - +
73A SER* 2.5 37.5 + - - -
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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