Contacts of the helix formed by residues 63 - 74 (chain A) in PDB entry 3ZS4
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 63 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A VAL* 3.7 17.7 + - + -
14A GLU* 3.5 5.5 + - - -
15A GLY* 3.0 26.9 + - - -
53A ASP* 2.7 37.7 + - - +
55A ASP* 2.8 25.8 + - - +
62A SER* 1.3 74.7 - - - +
64A HIS* 1.3 64.3 - - - +
65A GLU 3.3 2.5 - - - -
66A LEU* 3.1 11.7 + - + +
67A LEU* 3.0 34.3 + - + +
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Residues in contact with HIS 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ASP* 3.6 4.8 + - - +
62A SER* 3.0 16.4 + - - +
63A ASN* 1.3 76.9 - - - +
65A GLU* 1.3 75.9 + - + +
67A LEU* 3.2 7.7 + - + +
68A ALA* 2.8 34.1 + - + +
80A LEU* 5.4 4.9 - - + -
92A ALA* 3.2 45.9 + - + +
93A ALA* 4.8 5.2 - - + -
96A THR* 3.8 15.9 - - + +
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Residues in contact with GLU 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ASN 3.3 0.6 - - - -
64A HIS* 1.3 95.2 + - + +
66A LEU* 1.3 61.5 + - - +
68A ALA* 3.4 9.4 + - - +
69A GLU* 3.2 21.1 + - - +
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Residues in contact with LEU 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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12A VAL* 4.4 6.5 - - + -
15A GLY* 3.3 39.7 - - - +
34A ALA* 4.2 13.2 - - + +
35A VAL* 5.2 7.9 - - + -
63A ASN* 3.1 13.0 + - + +
65A GLU* 1.3 78.6 - - - +
67A LEU* 1.3 60.0 + - + +
69A GLU* 3.1 28.8 + - - +
70A VAL* 3.0 36.9 + - + +
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Residues in contact with LEU 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A VAL* 3.7 28.5 - - + -
34A ALA* 5.3 1.6 - - + -
51A LEU* 3.9 19.4 - - + +
52A VAL 4.3 2.2 - - - -
53A ASP* 3.6 42.4 - - + +
63A ASN* 3.0 26.1 + - + +
64A HIS* 3.6 9.4 - - + +
66A LEU* 1.3 82.2 - - + +
68A ALA* 1.3 57.6 + - - +
70A VAL* 3.3 7.6 + - + +
71A VAL* 3.0 35.4 + - - +
80A LEU* 3.7 24.5 - - + -
96A THR* 5.0 0.9 - - - -
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Residues in contact with ALA 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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64A HIS* 2.8 24.3 + - + +
65A GLU* 3.5 13.7 - - - +
66A LEU 3.3 0.2 - - - -
67A LEU* 1.3 76.3 - - - +
69A GLU* 1.3 56.4 + - - +
71A VAL* 3.5 2.1 + - - +
72A GLY* 3.0 24.9 + - - -
96A THR* 3.8 32.3 - - + +
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Residues in contact with GLU 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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35A VAL* 4.1 15.2 - - - +
65A GLU 3.2 11.1 + - - +
66A LEU* 3.1 26.6 + - - +
68A ALA* 1.3 74.1 - - - +
70A VAL* 1.3 59.7 + - - +
72A GLY* 3.2 3.0 + - - -
73A LYS* 2.9 66.7 + - + +
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Residues in contact with VAL 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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34A ALA* 4.5 5.8 - - + +
35A VAL* 3.9 36.3 - - + +
38A ALA* 3.6 29.2 - - + -
39A LEU* 6.5 0.2 - - + -
51A LEU* 3.9 19.7 - - + -
66A LEU* 3.0 28.5 + - + +
67A LEU* 3.3 9.4 + - + +
69A GLU* 1.3 75.8 - - - +
71A VAL* 1.3 63.1 + - - +
73A LYS* 3.2 6.4 + - - +
74A LEU* 3.0 33.1 + - + +
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Residues in contact with VAL 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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51A LEU* 4.0 7.6 - - + -
67A LEU 3.0 22.5 + - - +
68A ALA 3.8 4.5 - - - +
70A VAL* 1.3 75.7 - - - +
72A GLY* 1.3 61.6 + - - +
73A LYS 3.4 0.2 + - - -
74A LEU* 3.4 17.2 + - - +
76A VAL 5.5 0.3 - - - +
78A VAL* 3.9 37.5 - - + +
80A LEU* 4.6 5.8 - - + -
96A THR* 3.4 35.0 - - - +
97A GLY 3.9 3.1 - - - +
98A CYS* 3.6 26.5 - - + +
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Residues in contact with GLY 72 (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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68A ALA 3.0 15.8 + - - -
69A GLU* 3.2 5.1 + - - -
71A VAL* 1.3 79.2 - - - +
73A LYS* 1.3 58.7 + - - +
74A LEU 3.7 4.0 + - - +
96A THR 4.6 4.9 + - - -
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Residues in contact with LYS 73 (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 VAL* 3.9 27.1 - - + +
39A LEU* 4.5 23.2 - - + +
42A GLN* 4.8 1.4 + - - -
69A GLU* 2.9 49.5 + - + +
70A VAL* 3.2 5.1 + - - +
72A GLY* 1.3 76.1 - - - +
74A LEU* 1.3 63.8 + - - +
75A ASP* 3.7 8.1 + - - +
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Residues in contact with LEU 74 (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 ALA* 3.7 28.7 - - + +
39A LEU* 4.1 7.4 - - + +
42A GLN* 3.5 30.3 - - + +
49A ILE* 4.0 20.2 - - + -
70A VAL* 3.0 37.3 + - + +
71A VAL 3.4 13.8 + - - +
72A GLY 4.0 4.0 - - - +
73A LYS* 1.3 79.9 - - - +
75A ASP* 1.3 62.2 + - - +
76A VAL* 4.2 14.5 - - + +
78A VAL* 3.5 26.7 - - + -
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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