Contacts of the helix formed by residues 68 - 84 (chain A) in PDB entry 1Z83
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 PRO 68 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A LEU* 4.9 2.7 - - + -
60A ILE* 4.2 17.3 - - + -
66A LEU 4.5 0.9 - - - +
67A VAL* 1.4 95.8 - - + +
69A LEU* 1.3 66.3 + - - +
70A GLU* 4.6 4.7 - - + +
71A THR* 3.2 26.9 + - - +
72A VAL* 3.3 11.8 + - - +
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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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67A VAL 3.4 3.5 + - - -
68A PRO* 1.3 70.9 - - - +
70A GLU* 1.3 70.3 + - + +
71A THR 3.3 0.2 + - - -
72A VAL* 3.3 9.7 - - - +
73A LEU* 2.9 32.0 + - + +
95A TYR* 4.5 2.2 - - - +
98A GLU* 3.9 13.9 - - - +
100A GLN* 3.5 50.7 - - + +
101A GLN* 3.9 19.3 - - + +
104A GLU* 4.0 26.9 - - + +
108A ARG* 5.7 1.6 - - - +
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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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68A PRO* 3.3 4.3 - - + +
69A LEU* 1.3 86.3 - - + +
71A THR* 1.3 61.5 + - - +
73A LEU* 4.9 1.6 - - - -
74A ASP* 2.8 40.6 + - - +
108A ARG* 5.3 3.6 - - - +
70B GLU* 3.4 7.5 - - - +
104B GLU* 3.4 9.5 - - - +
107B ARG* 4.1 6.0 + - - -
642B ZN 2.1 38.4 - - - -
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Residues in contact with THR 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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43A LEU* 4.6 1.1 - - + -
46A GLU* 5.3 1.1 - - - +
53A ARG* 5.3 12.0 + - + +
57A LEU* 4.0 23.1 - - + +
67A VAL* 3.9 17.7 - - + -
68A PRO* 3.2 24.3 + - - +
70A GLU* 1.3 83.3 + - - +
72A VAL* 1.3 64.6 + - - +
74A ASP* 3.9 4.3 - - - +
75A MET* 3.3 32.9 + - + +
107B ARG* 6.4 0.4 - - - +
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Residues in contact with VAL 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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39A THR* 3.4 35.6 - - + +
43A LEU* 4.8 8.3 - - + -
67A VAL* 4.8 6.1 - - + -
68A PRO 3.3 11.2 + - - +
69A LEU* 3.3 15.7 - - - +
71A THR* 1.3 79.6 - - - +
73A LEU* 1.3 61.0 + - - +
75A MET* 3.4 9.1 + - + +
76A LEU* 3.0 27.9 + - - +
95A TYR* 3.9 12.8 - - + -
101A GLN* 4.2 1.8 - - - +
631A AP5 3.8 33.2 - - + +
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Residues in contact with LEU 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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69A LEU* 2.9 25.9 + - + +
70A GLU 4.3 0.4 - - - +
72A VAL* 1.3 70.5 - - - +
74A ASP* 1.3 61.2 + - - +
76A LEU* 4.3 7.4 - - + -
77A ARG* 2.8 32.1 + - + +
95A TYR* 3.7 29.2 - - + +
104A GLU* 3.7 37.0 - - + +
105A PHE* 4.2 11.0 - - + -
108A ARG* 3.8 29.4 - - + +
109A ILE* 4.0 26.7 - - + -
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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 GLU* 2.8 29.9 + - - +
71A THR* 3.9 5.4 - - - +
73A LEU* 1.3 74.4 - - - +
75A MET* 1.3 57.7 + - + +
77A ARG* 4.0 0.9 - - - +
78A ASP* 3.1 36.4 + - - +
108A ARG* 2.9 35.8 + - - +
70B GLU* 3.2 5.5 - - - +
104B GLU* 3.0 3.5 - - - +
107B ARG* 4.2 5.4 + - - +
108B ARG* 3.4 22.1 + - - +
642B ZN 2.1 32.4 - - - -
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Residues in contact with MET 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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39A THR* 6.3 0.2 - - + -
42A LEU* 4.2 30.3 - - + +
43A LEU* 3.7 34.3 - - + -
46A GLU* 2.7 46.0 - - + +
57A LEU* 4.4 4.0 - - + -
71A THR* 3.3 20.9 + - + +
72A VAL* 3.6 6.7 - - + +
74A ASP* 1.3 80.2 - - + +
76A LEU* 1.3 62.9 + - - +
78A ASP* 3.9 6.4 - - - +
79A ALA* 3.2 24.6 + - - +
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Residues in contact with LEU 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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37A LEU* 4.2 31.4 - - + +
39A THR* 4.1 14.4 - - + -
42A LEU* 4.3 9.8 - - + +
72A VAL 3.0 17.8 + - - +
73A LEU* 3.7 6.7 - - + +
75A MET* 1.3 75.1 - - - +
77A ARG* 1.3 59.7 + - - +
79A ALA* 3.3 2.1 + - - +
80A MET* 2.9 42.4 + - + +
92A ILE* 3.9 12.1 - - + -
95A TYR* 3.6 44.9 - - + -
105A PHE* 3.9 20.0 - - + -
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Residues in contact with ARG 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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2A GLU* 3.0 26.5 + - - +
5A LEU* 4.0 7.2 - - + +
73A LEU* 2.8 23.3 + - + +
74A ASP 4.1 2.0 - - - +
76A LEU* 1.3 73.2 - - - +
78A ASP* 1.3 63.5 + - - +
80A MET* 3.2 4.3 + - + +
81A VAL* 2.9 44.3 + - + +
108A ARG* 2.9 34.2 + - - +
109A ILE* 3.6 28.3 - - + +
74B ASP* 3.7 42.9 + - - +
77B ARG* 6.3 0.2 - - - +
78B ASP* 2.9 42.4 + - - -
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Residues in contact with ASP 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 23.2 + - - +
75A MET* 3.9 6.8 + - - +
77A ARG* 1.3 80.2 + - - +
79A ALA* 1.3 61.1 + - - +
81A VAL* 3.5 1.5 + - - -
82A ALA* 3.2 22.9 + - - +
74B ASP* 5.3 0.9 - - - +
77B ARG* 3.6 50.1 + - - +
108B ARG* 2.9 46.4 + - - +
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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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37A LEU* 4.2 21.5 - - + +
42A LEU* 4.3 18.4 - - + -
75A MET 3.2 18.9 + - - +
76A LEU 3.6 4.0 - - - +
77A ARG 3.2 0.2 - - - -
78A ASP* 1.3 74.4 - - - +
80A MET* 1.3 66.5 + - - +
82A ALA* 3.6 11.0 + - - +
83A LYS* 3.6 25.2 - - - +
703B SO4 5.4 4.0 - - - +
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Residues in contact with MET 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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5A LEU* 4.2 11.7 - - + -
10A ILE* 4.2 14.8 - - + -
37A LEU* 3.6 17.7 - - + -
76A LEU* 2.9 23.4 + - + +
77A ARG* 3.6 4.9 - - - +
79A ALA* 1.3 76.2 - - - +
81A VAL* 1.3 62.8 + - + +
83A LYS 3.1 2.1 + - - -
84A VAL* 3.0 22.9 + - - +
90A PHE* 3.5 47.6 - - + -
92A ILE* 4.1 11.7 - - + -
105A PHE* 4.0 24.7 - - + -
109A ILE* 4.0 31.0 - - + -
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Residues in contact with VAL 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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1A MET* 3.3 34.7 - - + +
5A LEU* 3.9 21.1 - - + -
77A ARG* 2.9 33.7 + - - +
78A ASP* 3.9 4.5 - - - +
79A ALA 3.4 0.2 - - - -
80A MET* 1.3 77.2 - - - +
82A ALA* 1.3 60.4 + - - +
83A LYS 3.4 0.7 + - - -
84A VAL* 3.7 8.4 + - - +
77B ARG* 4.5 5.2 - - - +
78B ASP* 3.3 29.8 - - - +
81B VAL* 3.9 31.3 - - + +
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Residues in contact with ALA 82 (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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78A ASP 3.2 17.0 + - - +
79A ALA* 3.6 9.0 - - - +
80A MET 3.3 0.2 - - - -
81A VAL* 1.3 77.4 - - - +
83A LYS* 1.3 59.0 + - - +
85A ASN* 5.3 2.0 + - - +
1B MET* 3.8 36.9 - - + +
77B ARG* 5.4 1.1 - - - +
81B VAL* 4.6 4.4 - - - +
703B SO4 3.5 26.0 + - - +
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Residues in contact with LYS 83 (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 THR* 3.9 31.1 - - + +
36A HIS 5.2 1.2 + - - -
37A LEU* 3.6 24.9 - - + +
42A LEU* 6.0 1.4 - - - +
79A ALA* 3.6 19.4 + - - +
80A MET 3.1 4.6 + - - +
82A ALA* 1.3 76.0 - - - +
84A VAL* 1.3 65.0 + - - +
85A ASN* 3.2 3.2 + - - -
86A THR* 3.2 10.5 + - - +
87A SER* 3.1 21.4 + - - -
90A PHE* 4.5 2.9 - - + -
703B SO4 3.3 37.2 + - - +
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Residues in contact with VAL 84 (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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1A MET* 3.3 34.8 - - + +
4A LYS* 3.9 25.7 - - + +
5A LEU* 3.8 25.4 - - + -
8A THR* 3.6 24.0 + - - +
80A MET 3.0 13.2 + - - +
81A VAL* 3.7 9.2 - - - +
82A ALA 3.7 0.2 - - - -
83A LYS* 1.3 76.7 - - - +
85A ASN* 1.3 62.1 + - - +
86A THR 3.1 1.2 + - - -
87A SER* 3.2 15.3 + - - +
90A PHE* 4.0 12.6 - - + -
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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