Contacts of the helix formed by residues 76 - 96 (chain C) in PDB entry 4ZIA
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 76 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C PHE* 3.0 19.2 + - + +
74C GLU* 3.2 12.9 + - + +
75C SER* 1.3 72.9 - - - +
77C VAL* 1.3 60.9 + - - +
78C LEU* 3.6 6.8 + - - +
79C TYR* 3.0 65.6 + - + +
80C GLN* 3.1 16.8 + - - +
8D GLN* 4.4 7.7 + - - +
32D GLN* 5.3 1.6 + - - +
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Residues in contact with VAL 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C SER 3.1 4.2 + - - +
76C ASN* 1.3 70.3 - - - +
78C LEU* 1.3 57.5 + - - +
80C GLN* 3.3 15.3 + - - +
81C HIS* 2.9 25.8 + - - +
4D TRP* 4.3 3.8 - - + -
7D LEU 4.3 1.6 - - - +
8D GLN* 3.7 43.3 - - + +
15D LEU* 3.7 23.6 - - + -
18D LEU* 3.7 16.6 - - + -
19D HIS* 3.6 9.4 - - + -
28D MET* 3.5 27.8 - - + -
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Residues in contact with LEU 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C ASN* 3.2 6.7 + - - +
77C VAL* 1.3 78.9 - - - +
79C TYR* 1.3 62.5 + - + +
81C HIS* 3.0 6.6 + - + +
82C ASN* 2.9 37.8 + - - +
4D TRP* 5.0 0.2 - - - -
8D GLN* 5.5 0.4 - - - +
28D MET* 3.8 22.2 - - + +
29D GLU* 3.7 43.5 - - - +
32D GLN* 3.6 40.5 + - - +
33D PHE* 4.0 17.5 - - + -
79D TYR* 3.5 21.1 - - + +
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Residues in contact with TYR 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C GLN* 5.8 2.2 + - - -
33C PHE* 3.7 18.8 - + + -
71C PHE* 3.5 46.7 - + + -
76C ASN* 3.0 43.1 + - - +
78C LEU* 1.3 77.5 - - + +
80C GLN* 1.3 67.3 + - - +
82C ASN* 3.2 5.8 + - - +
83C LEU* 3.0 28.4 + - - +
32D GLN* 6.2 0.7 - - - -
76D ASN* 5.8 0.7 + - - -
79D TYR* 3.3 33.5 + + - -
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Residues in contact with GLN 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C TYR* 3.3 28.5 + - + +
71C PHE* 3.1 34.1 + - + +
72C LEU* 2.9 37.1 + - + +
75C SER* 4.1 4.6 - - - +
76C ASN 3.1 19.4 + - - +
77C VAL* 3.4 18.3 - - - +
79C TYR* 1.3 76.0 - - - +
81C HIS* 1.3 58.4 + - - +
83C LEU* 3.3 3.1 + - - -
84C ARG* 2.9 31.0 + - - +
15D LEU* 3.5 15.0 - - - +
19D HIS* 4.1 14.1 + - + -
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Residues in contact with HIS 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C VAL 2.9 13.9 + - - +
78C LEU* 3.0 11.6 + - + +
80C GLN* 1.3 78.0 - - - +
82C ASN* 1.3 58.8 + - - +
84C ARG* 3.6 16.2 + - - +
85C ARG* 3.2 46.7 + - - +
19D HIS* 2.9 53.4 + - + +
22D TYR* 4.3 10.6 - - + +
27D PRO* 5.8 0.6 - - - +
28D MET* 3.7 40.2 + - + +
29D GLU* 4.9 2.2 - - - -
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Residues in contact with ASN 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C GLU* 3.5 22.8 - - + +
33C PHE* 3.7 29.7 - - + -
78C LEU* 2.9 41.6 + - - +
79C TYR* 3.2 5.0 + - - +
81C HIS* 1.3 75.0 - - - +
83C LEU* 1.3 66.8 + - - +
85C ARG* 2.7 35.9 + - - +
86C ILE* 3.0 25.5 + - - +
29D GLU* 2.9 8.0 + - - +
79D TYR* 3.8 11.2 + - - -
82D ASN* 5.1 0.2 + - - -
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Residues in contact with LEU 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C PHE* 4.0 22.9 - - + -
34C LEU* 4.5 7.4 - - + -
64C ILE* 4.0 15.9 - - + +
67C GLN* 3.9 6.3 - - + -
68C TYR* 3.6 44.0 - - + +
71C PHE* 3.6 31.9 - - + -
79C TYR 3.0 13.0 + - - +
82C ASN* 1.3 74.6 - - - +
84C ARG* 1.3 52.8 + - - +
86C ILE* 2.8 45.3 + - + +
87C LYS* 2.8 21.0 + - - +
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Residues in contact with ARG 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C TYR* 3.9 16.0 - - + +
80C GLN 2.9 18.6 + - - +
81C HIS* 3.6 16.0 + - - +
83C LEU* 1.3 76.9 - - - +
85C ARG* 1.3 60.1 + - - +
87C LYS* 3.5 6.9 + - - +
88C GLN* 2.9 60.0 + - + +
16D GLU* 2.7 37.6 + - - -
19D HIS* 3.5 46.1 + - - +
20D GLN* 4.0 15.4 - - - +
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Residues in contact with ARG 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C PRO* 5.6 6.1 - - + -
29C GLU* 3.3 26.6 + - - +
81C HIS* 3.2 28.4 + - + +
82C ASN* 2.7 29.5 + - - +
84C ARG* 1.3 78.6 - - - +
86C ILE* 1.3 67.5 + - - +
88C GLN* 3.5 10.4 + - - +
89C PHE* 3.1 25.0 + - + +
27D PRO* 5.3 5.1 - - - +
29D GLU* 2.6 40.9 + - - -
82D ASN* 5.6 0.7 - - - -
85D ARG* 6.1 1.1 - - - +
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Residues in contact with ILE 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C PRO* 4.9 9.4 - - + -
29C GLU* 4.1 17.9 - - + +
30C LEU* 3.4 55.9 - - + +
33C PHE* 4.8 1.6 - - + -
34C LEU* 4.8 1.1 - - + -
64C ILE* 3.9 7.9 - - + -
82C ASN 3.0 15.1 + - - +
83C LEU* 2.8 38.7 + - + +
85C ARG* 1.3 78.3 - - + +
87C LYS* 1.3 62.2 + - - +
89C PHE* 3.4 6.2 + - + +
90C LEU* 3.1 34.7 + - + +
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Residues in contact with LYS 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C LEU* 4.2 32.0 + - - +
64C ILE* 3.8 23.1 - - + -
65C ASP* 3.0 33.7 + - - +
68C TYR* 5.4 7.2 - - + -
83C LEU* 2.8 18.1 + - + +
84C ARG* 3.9 8.3 - - - +
85C ARG 3.3 0.2 - - - -
86C ILE* 1.3 77.2 - - - +
88C GLN* 1.3 63.9 + - + +
90C LEU* 3.2 8.7 + - - +
91C GLN* 2.9 35.6 + - + +
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Residues in contact with GLN 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C ARG* 2.9 52.4 + - + +
85C ARG* 3.9 8.7 - - - +
87C LYS* 1.3 77.2 - - + +
89C PHE* 1.3 61.0 + - - +
91C GLN* 3.7 11.7 - - - +
92C SER* 3.5 19.1 + - - -
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Residues in contact with PHE 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C SER 3.8 15.7 - - - -
26C PHE* 3.9 6.3 - - + -
27C PRO* 3.4 42.0 - - + -
30C LEU* 5.9 0.9 - - + -
85C ARG* 3.1 19.8 + - + +
86C ILE* 3.6 4.7 - - + +
88C GLN* 1.3 79.1 - - - +
90C LEU* 1.3 74.2 + - + +
92C SER* 3.9 2.0 + - - -
93C ARG* 3.4 56.5 + - - +
94C TYR* 3.5 24.5 - + - -
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Residues in contact with LEU 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C LEU* 4.7 6.3 - - + -
57C PHE* 3.5 23.9 - - + -
60C LEU* 4.1 18.2 - - + -
61C LEU* 4.0 22.9 - - + -
64C ILE* 4.0 9.2 - - + -
86C ILE* 3.1 38.7 + - + +
87C LYS 3.8 2.7 - - - +
89C PHE* 1.3 82.0 - - + +
91C GLN* 1.3 67.0 + - - +
94C TYR* 2.9 49.5 + - + +
101C ILE* 4.2 16.6 - - + -
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Residues in contact with GLN 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C PHE* 4.6 0.9 - - - -
61C LEU* 4.5 20.0 - - + +
87C LYS* 2.9 27.6 + - + +
88C GLN* 3.7 9.4 - - - +
90C LEU* 1.3 75.0 - - - +
92C SER* 1.3 66.8 + - - +
95C LEU* 3.0 58.7 - - - +
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Residues in contact with SER 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C GLN 3.5 14.1 + - - -
89C PHE 4.5 2.0 - - - -
90C LEU 3.5 0.4 - - - -
91C GLN* 1.3 83.4 - - - +
93C ARG* 1.3 63.5 + - - +
94C TYR 3.5 0.2 + - - -
95C LEU* 4.2 2.8 + - - +
96C GLU* 4.7 7.6 + - - +
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Residues in contact with ARG 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C ASP* 4.7 11.5 + - - -
25C SER 4.4 5.9 + - - -
89C PHE* 3.4 49.7 + - - +
91C GLN 3.7 0.2 - - - -
92C SER* 1.3 79.7 - - - +
94C TYR* 1.3 103.7 + - + +
95C LEU 3.7 0.4 - - - -
96C GLU* 4.9 1.7 - - - +
97C LYS* 4.2 14.7 + - - +
100C GLU* 5.1 2.9 + - - +
104C ILE* 4.2 9.5 - - - +
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Residues in contact with TYR 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C SER 4.2 4.9 + - - -
57C PHE* 3.2 28.9 - - + -
89C PHE* 3.5 21.8 - + - -
90C LEU* 2.9 28.7 + - + +
93C ARG* 1.3 121.0 + - + +
95C LEU* 1.3 63.3 + - - +
96C GLU 3.4 0.9 - - - -
97C LYS 3.7 11.4 - - - +
98C PRO* 3.6 14.6 - - - +
100C GLU* 3.5 11.0 - - + -
101C ILE* 3.1 59.5 - - + +
104C ILE* 2.8 27.8 - - + +
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Residues in contact with LEU 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C THR* 6.1 4.4 - - + +
57C PHE* 3.8 22.2 - - + -
91C GLN* 3.0 51.9 + - - +
92C SER 4.8 0.4 - - - +
93C ARG 3.7 0.2 - - - -
94C TYR* 1.3 79.1 - - - +
96C GLU* 1.3 65.8 + - + +
97C LYS 3.4 0.2 - - - -
98C PRO* 3.8 8.5 - - - +
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Residues in contact with GLU 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C GLU* 4.8 7.3 - - - +
92C SER 4.7 8.2 + - - +
93C ARG 5.7 0.9 - - - +
94C TYR* 4.3 0.6 - - - +
95C LEU* 1.3 84.6 - - + +
97C LYS* 1.3 69.7 + - + +
98C PRO* 3.6 5.2 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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