Contacts of the helix formed by residues 65 - 81 (chain A) in PDB entry 1ZJY
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 ASP 65 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A HIS* 3.0 25.2 + - + +
62A ASP* 2.9 25.6 + - + +
63A SER 3.2 0.4 - - - -
64A SER* 1.3 74.2 + - - +
66A GLU* 1.3 65.5 + - - +
67A ASP* 3.3 8.5 + - - +
68A GLY* 3.1 25.5 + - - -
69A TRP* 3.3 5.3 + - - -
71A LYS* 5.9 0.5 - - - -
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Residues in contact with GLU 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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64A SER 3.4 4.9 + - - -
65A ASP* 1.3 72.7 + - - +
67A ASP* 1.3 64.6 + - - +
69A TRP* 3.2 20.2 + - - +
70A THR* 3.9 4.5 + - - -
119A PHE* 3.7 43.2 - - + -
122A ARG* 3.0 28.7 + - - +
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Residues in contact with ASP 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ASP* 3.3 7.2 + - - +
66A GLU* 1.3 80.6 - - - +
68A GLY* 1.3 64.2 + - - +
70A THR* 3.1 23.4 + - - +
71A LYS* 3.5 32.5 + - - +
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Residues in contact with GLY 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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59A PHE* 4.3 1.9 - - - -
61A HIS* 3.4 19.9 + - - -
65A ASP* 3.1 20.1 + - - -
66A GLU 3.2 0.4 - - - -
67A ASP* 1.3 77.5 - - - +
69A TRP* 1.3 66.5 + - - +
71A LYS* 2.9 19.0 + - - +
72A LEU* 2.9 23.7 + - - +
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Residues in contact with TRP 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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12A THR* 3.5 24.5 - - + -
61A HIS* 3.1 25.3 + - - -
63A SER* 2.7 32.3 + - - -
65A ASP 3.4 15.0 - - - -
66A GLU 3.2 9.5 + - - +
67A ASP 3.2 0.6 - - - -
68A GLY* 1.3 75.2 - - - +
70A THR* 1.3 61.9 + - - +
72A LEU* 3.2 23.9 + - + +
73A PHE* 3.1 38.0 + + - -
86A LEU* 3.9 16.6 - - + -
88A ASN* 3.2 22.9 - - - -
116A GLY 3.4 22.4 + - - -
119A PHE* 3.6 20.0 - - + +
120A GLY* 3.5 19.5 - - - -
123A LEU* 3.5 18.9 - - + +
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Residues in contact with THR 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 GLU 4.5 4.2 + - - -
67A ASP* 3.1 17.6 + - - +
68A GLY 3.0 0.8 - - - -
69A TRP* 1.3 75.7 - - - +
71A LYS* 1.3 67.0 + - + +
73A PHE* 3.4 3.2 + - - +
74A ASP* 3.1 30.6 + - - +
123A LEU* 4.0 17.6 - - - +
127A ARG* 3.7 20.9 - - - +
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Residues in contact with LYS 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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59A PHE* 3.6 19.2 - - + -
65A ASP* 5.9 0.7 - - - -
67A ASP* 3.5 34.7 + - - +
68A GLY* 2.9 15.2 + - - +
70A THR* 1.3 78.3 - - - +
72A LEU* 1.3 58.7 + - - +
74A ASP* 3.3 7.1 + - - +
75A ALA* 2.9 30.3 + - - +
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Residues in contact with LEU 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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10A ILE* 3.8 27.8 - - + -
12A THR* 4.7 0.9 - - + -
34A MET* 4.0 5.2 - - + -
36A THR* 3.7 23.6 - - + -
59A PHE* 3.7 33.6 - - + -
61A HIS* 3.7 24.7 - - + -
68A GLY 2.9 10.6 + - - +
69A TRP* 3.4 28.0 - - + +
70A THR 3.1 0.2 - - - -
71A LYS* 1.3 74.4 - - - +
73A PHE* 1.3 64.7 + - - +
75A ALA* 3.3 1.6 + - - +
76A THR* 2.8 38.5 + - - +
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Residues in contact with PHE 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE* 3.8 21.3 - - + -
69A TRP* 3.1 31.7 + + - +
70A THR 3.4 2.4 + - - +
72A LEU* 1.3 78.6 - - - +
74A ASP* 1.3 62.9 + - - +
76A THR* 3.3 2.6 + - - -
77A GLU* 3.0 24.9 + - - +
83A VAL* 3.8 37.5 - - + +
86A LEU* 4.4 11.0 - - + -
123A LEU* 3.4 28.3 - - + -
124A GLY* 3.8 23.3 - - - -
127A ARG* 3.7 47.5 + - + +
128A MET* 4.4 6.7 - - + -
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Residues in contact with ASP 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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70A THR* 3.1 25.8 + - - +
71A LYS* 3.7 9.8 - - - +
73A PHE* 1.3 75.4 - - - +
75A ALA* 1.3 63.1 + - - +
77A GLU* 3.5 7.9 + - - +
78A LYS* 3.1 24.6 + - - +
127A ARG* 2.8 28.4 + - - +
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Residues in contact with ALA 75 (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 MET* 3.9 9.2 - - + +
59A PHE* 3.4 40.4 - - + -
71A LYS 2.9 8.2 + - - +
72A LEU 3.8 2.0 - - - +
73A PHE 3.3 0.2 - - - -
74A ASP* 1.3 76.5 - - - +
76A THR* 1.3 58.6 + - - +
78A LYS* 3.6 9.7 + - - +
79A ALA* 3.0 28.8 + - - +
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Residues in contact with THR 76 (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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8A VAL* 3.9 16.6 - - + -
9A ALA 4.5 2.0 - - - +
10A ILE* 3.6 19.5 - - + +
34A MET* 3.5 37.3 - - + +
72A LEU* 2.8 18.3 + - - +
73A PHE 3.7 3.4 - - - -
74A ASP 3.3 0.2 - - - -
75A ALA* 1.3 76.8 - - - +
77A GLU* 1.3 57.8 + - - +
79A ALA* 3.2 1.6 + - - +
80A PHE* 2.9 35.1 + - + +
81A GLY 3.7 0.6 - - - +
83A VAL* 3.7 20.6 - - + -
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Residues in contact with GLU 77 (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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73A PHE 3.0 15.8 + - - +
74A ASP* 4.1 7.3 - - - +
76A THR* 1.3 77.1 - - - +
78A LYS* 1.3 57.8 + - - +
81A GLY* 2.8 46.3 + - - +
82A PRO* 3.7 24.0 - - + +
83A VAL* 4.4 4.4 - - + +
127A ARG* 4.7 12.6 + - - -
131A LYS* 5.6 2.9 + - - -
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Residues in contact with LYS 78 (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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74A ASP 3.1 18.1 + - - +
75A ALA* 3.9 8.1 - - - +
77A GLU* 1.3 74.1 - - - +
79A ALA* 1.3 65.6 + - - +
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Residues in contact with ALA 79 (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 MET* 4.4 3.8 - - + -
57A GLN* 3.8 28.7 + - - +
75A ALA 3.0 18.3 + - - +
76A THR 3.2 2.9 + - - +
78A LYS* 1.3 79.9 - - - +
80A PHE* 1.3 80.9 + - + +
81A GLY 3.9 0.2 - - - -
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Residues in contact with PHE 80 (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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8A VAL* 3.6 26.0 - - + +
32A LYS* 3.6 30.2 - - + +
33A VAL 3.4 32.8 - - - -
34A MET* 4.2 9.2 - - + -
53A PRO 3.5 25.1 - - - -
54A ASP* 3.7 17.0 - - - -
55A GLN 4.1 1.8 - - - -
56A ILE 4.1 4.3 - - - -
57A GLN* 3.9 22.0 - - - -
76A THR* 2.9 23.8 + - + +
79A ALA* 1.3 94.4 - - + +
81A GLY* 1.3 62.1 + - - +
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Residues in contact with GLY 81 (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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8A VAL* 3.7 8.4 - - - +
77A GLU* 2.8 38.0 + - - -
79A ALA 3.9 0.2 - - - -
80A PHE* 1.3 77.2 - - - +
82A PRO* 1.3 79.5 - - - +
83A VAL 3.4 0.9 + - - -
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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