Contacts of the helix formed by residues 71 - 84 (chain A) in PDB entry 1INZ
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 TRP 71 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A ASP* 4.9 0.4 - - - -
67A HIS 4.7 0.8 + - - -
69A LYS 4.0 5.3 - - - +
70A ASN* 1.3 75.0 - - - +
72A ARG* 1.3 81.1 + - + +
73A HIS 3.1 1.1 - - - -
74A VAL* 2.7 31.5 + - + +
75A TYR* 3.0 43.5 + + + -
109A PHE* 3.8 26.7 - - + -
111A TYR 5.8 4.0 - - - -
119A GLN* 3.5 52.5 + - + +
120A GLY* 4.1 10.2 - - - -
122A ASN* 4.1 18.8 - - + -
123A VAL* 3.6 25.8 - - + -
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Residues in contact with ARG 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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28A THR 5.2 0.2 - - - -
31A ASP* 5.3 10.1 + - - -
70A ASN* 2.9 25.0 - - - +
71A TRP* 1.3 101.5 - - + +
73A HIS* 1.3 73.7 + - + +
75A TYR* 3.4 2.4 + - - +
76A LYS* 3.2 26.2 + - + +
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Residues in contact with HIS 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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28A THR* 4.2 15.3 + - - +
29A SER* 4.8 12.5 + - - -
31A ASP* 5.3 5.4 - - - -
63A ARG* 3.5 34.8 + - + +
66A ASP* 3.3 38.8 - - - +
70A ASN* 4.2 16.4 + - + +
72A ARG* 1.3 87.8 - - + +
74A VAL* 1.3 62.9 + - - +
76A LYS* 3.5 2.3 + - - +
77A ALA* 2.9 22.9 + - - +
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Residues in contact with VAL 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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63A ARG 3.4 13.0 - - - +
64A LEU* 2.9 22.9 - - - +
66A ASP* 3.7 18.2 - - + +
71A TRP* 2.7 16.7 + - - +
73A HIS* 1.3 69.6 - - - +
75A TYR* 1.3 66.2 + - - +
77A ALA* 2.7 16.8 + - - +
78A MET* 2.9 17.9 + - + +
106A LEU* 3.1 23.6 - - + -
109A PHE* 4.0 14.4 - - + -
123A VAL* 2.8 29.8 - - + -
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Residues in contact with TYR 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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71A TRP* 3.0 32.2 + + + -
72A ARG 3.7 5.2 - - - +
74A VAL* 1.3 78.7 - - - +
76A LYS* 1.3 77.3 + - + +
78A MET* 3.0 19.5 + - - +
79A THR* 3.2 16.2 + - - -
122A ASN* 3.1 44.8 + - - -
123A VAL* 3.7 8.3 - - - -
126A LYS* 3.0 50.0 + - + +
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Residues in contact with LYS 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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27A ALA 3.7 8.6 - - - +
28A THR* 2.9 54.5 - - - +
29A SER* 3.7 6.3 - - - +
30A ASN* 5.4 5.6 - - - +
72A ARG* 3.2 16.1 + - + +
73A HIS 3.7 0.9 - - - +
74A VAL 3.2 0.4 - - - -
75A TYR* 1.3 92.9 - - + +
77A ALA* 1.3 62.6 + - - +
79A THR* 3.3 19.5 + - - +
80A LEU* 3.4 7.4 + - - +
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Residues in contact with ALA 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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28A THR* 3.4 16.6 - - + +
60A ILE* 3.8 13.2 - - - +
63A ARG* 4.1 4.0 - - + +
64A LEU* 3.2 33.2 - - + +
73A HIS 2.9 14.0 + - - +
74A VAL 2.7 18.2 + - - +
76A LYS* 1.3 73.2 - - - +
78A MET* 1.3 54.8 + - - -
80A LEU* 3.5 2.1 + - - +
81A MET* 3.1 28.2 + - - +
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Residues in contact with MET 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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64A LEU* 3.7 9.0 - - + -
74A VAL* 3.1 11.7 - - + +
75A TYR* 3.0 9.4 + - - +
77A ALA* 1.3 76.7 - - - +
79A THR* 1.3 59.8 + - - +
81A MET* 4.2 3.1 - - - -
82A GLU* 2.9 25.8 + - - +
106A LEU* 3.4 18.4 - - + -
123A VAL* 2.8 56.1 - - + +
126A LYS* 3.5 20.6 - - + -
127A ALA* 2.8 37.9 - - + +
130A LEU* 3.0 23.2 - - + +
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Residues in contact with THR 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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27A ALA 6.0 0.7 - - - -
40A MET* 3.4 32.5 - - + -
75A TYR* 3.2 17.8 + - - -
76A LYS* 3.6 16.7 + - - +
77A ALA 3.3 0.2 - - - -
78A MET* 1.3 78.8 - - - +
80A LEU* 1.3 57.6 + - - +
82A GLU* 4.0 7.6 - - - +
83A TYR* 3.0 31.4 + - - +
126A LYS* 5.4 8.5 - - - +
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Residues in contact with LEU 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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24A VAL* 3.1 42.4 - - + +
27A ALA* 4.1 4.5 - - + -
28A THR* 4.0 12.6 - - + -
40A MET* 4.0 16.8 - - + +
43A ILE* 3.1 28.7 - - + -
60A ILE* 3.0 26.5 - - + -
76A LYS 3.4 2.5 + - - +
77A ALA 3.9 6.3 - - - +
78A MET 3.3 0.4 - - - -
79A THR* 1.3 79.5 - - - +
81A MET* 1.3 62.5 + - - +
83A TYR* 4.4 1.6 - - - -
84A LEU* 2.7 56.1 + - + +
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Residues in contact with MET 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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57A MET* 4.1 17.9 - - + -
60A ILE* 3.7 9.6 - - + +
61A TRP* 3.0 35.0 - - - -
64A LEU* 3.4 25.4 - - + -
77A ALA 3.1 18.3 + - - +
78A MET* 3.9 4.9 - - + +
80A LEU* 1.3 78.4 - - - +
82A GLU* 1.3 53.8 + - - +
84A LEU* 4.7 0.2 - - - -
85A ILE* 2.6 47.5 + - + +
96A CYS* 5.6 0.2 - - - -
103A VAL* 3.3 42.0 - - + -
106A LEU* 5.6 0.7 - - + -
130A LEU* 3.7 16.6 - - + -
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Residues in contact with GLU 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 MET 2.9 19.6 + - - +
79A THR* 4.0 7.3 - - - +
81A MET* 1.3 78.0 - - - +
83A TYR* 1.3 65.8 + - - +
85A ILE* 3.6 5.2 + - + +
86A LYS* 3.5 26.8 + - + +
126A LYS* 4.1 24.1 + - - -
129A GLN* 4.5 14.2 - - - +
130A LEU* 3.4 27.4 + - + +
133A LEU* 5.2 11.6 - - + +
134A LEU* 6.4 0.2 - - + -
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Residues in contact with TYR 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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40A MET* 3.1 57.0 - - + -
41A SER* 2.9 29.9 + - - -
44A ALA* 3.4 9.2 - - + -
79A THR 3.0 20.1 + - - +
80A LEU 4.1 1.6 - - - +
82A GLU* 1.3 81.2 + - - +
84A LEU* 1.3 67.2 + - + +
86A LYS* 3.2 13.2 + - - +
87A THR* 3.1 41.7 + - + +
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Residues in contact with LEU 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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40A MET 4.0 0.2 - - - +
43A ILE* 3.1 31.4 - - + +
44A ALA* 2.8 47.8 - - + +
47A THR* 3.9 5.2 - - + -
56A ILE* 3.3 16.2 - - + -
57A MET* 5.1 2.2 - - - -
60A ILE* 3.8 3.8 - - + -
80A LEU* 2.7 39.2 + - + +
81A MET* 4.7 0.9 - - - -
83A TYR* 1.3 77.4 - - + +
85A ILE* 1.3 61.9 + - - +
86A LYS 2.9 5.4 - - - -
88A GLY* 2.7 27.7 + - - -
89A SER 3.1 5.9 + - - -
92A VAL* 3.4 17.6 - - + +
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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