Contacts of the helix formed by residues 102 - 113 (chain C) in PDB entry 1AYZ
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 VAL 102 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9C LEU* 4.7 0.2 - - + -
12C ASP* 3.2 16.5 + - + +
16C MET* 4.2 9.0 - - + -
26C ALA* 3.9 16.4 - - + -
36C TRP* 3.6 35.0 - - + -
57C LEU* 4.5 9.0 - - + -
59C PHE* 4.0 21.8 - - + -
63C TYR* 3.9 1.1 + - - +
101C ASP* 1.3 74.0 - - - +
103C ALA* 1.3 64.7 + - - +
105C ILE* 3.1 10.5 + - - +
106C LEU* 2.9 49.8 + - + +
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Residues in contact with ALA 103 (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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12C ASP 5.7 0.2 + - - -
15C ARG* 3.6 41.5 - - + +
16C MET* 3.9 19.1 - - - +
21C PRO* 3.9 10.7 - - + +
101C ASP* 3.6 8.0 - - - +
102C VAL* 1.3 80.6 - - - +
104C SER* 1.3 58.0 + - - +
106C LEU* 3.3 3.9 + - - +
107C THR* 3.0 34.4 + - - +
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Residues in contact with SER 104 (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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100C TYR* 3.2 25.9 - - - -
101C ASP* 2.7 40.8 + - - -
103C ALA* 1.3 75.5 - - - +
105C ILE* 1.3 56.9 + - - +
107C THR* 3.0 14.6 + - - -
108C SER* 2.5 32.0 + - - -
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Residues in contact with ILE 105 (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 LEU* 4.4 10.8 - - + -
59C PHE* 4.9 1.3 - - + -
63C TYR* 4.6 4.7 - - - +
68C PRO* 3.7 21.5 - - + -
70C VAL* 4.2 16.8 - - + -
91C ILE* 4.6 4.9 - - + +
92C LEU* 4.3 11.2 - - + -
96C TRP* 3.7 38.6 - - + -
100C TYR* 4.7 1.6 - - + -
101C ASP 3.0 27.5 + - - +
102C VAL* 3.3 11.9 - - - +
104C SER* 1.3 76.8 - - - +
106C LEU* 1.3 65.0 + - + +
108C SER* 3.5 4.9 - - - -
109C ILE* 3.0 44.1 + - + +
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Residues in contact with LEU 106 (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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16C MET* 4.0 13.7 - - + -
24C VAL* 3.9 20.2 - - + -
25C SER 4.0 7.9 - - - +
26C ALA* 3.6 30.5 - - + -
38C ALA* 4.1 16.2 - - + -
39C MET 5.6 0.7 - - - +
40C ILE* 3.5 23.1 - - + +
55C LEU* 4.6 6.1 - - + -
57C LEU* 4.7 14.6 - - + -
70C VAL* 5.8 0.2 - - + -
102C VAL* 2.9 27.2 + - + +
103C ALA 3.7 3.8 - - - +
105C ILE* 1.3 77.4 - - + +
107C THR* 1.3 60.0 + - - +
109C ILE* 3.3 6.4 + - + +
110C GLN* 2.8 29.4 + - - +
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Residues in contact with THR 107 (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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21C PRO* 3.8 28.3 - - + -
24C VAL* 4.6 2.2 - - + -
103C ALA 3.0 18.5 + - - +
104C SER* 3.0 16.3 + - - -
106C LEU* 1.3 74.2 - - - +
108C SER* 1.3 65.6 + - - +
110C GLN* 2.9 24.5 + - - +
111C SER* 2.8 35.6 + - - -
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Residues in contact with SER 108 (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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89C LEU* 4.4 8.6 - - - +
91C ILE* 3.4 34.1 - - - +
100C TYR* 4.1 8.1 - - - -
104C SER* 2.5 21.8 + - - -
105C ILE 3.5 2.2 - - - -
107C THR* 1.3 80.8 + - - +
109C ILE* 1.3 60.2 + - - +
111C SER* 3.6 17.1 + - - -
112C LEU* 3.8 10.4 + - - +
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Residues in contact with ILE 109 (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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40C ILE* 3.7 8.7 - - + -
55C LEU* 4.1 6.3 - - + -
70C VAL* 3.8 18.2 - - + -
72C PHE* 3.7 33.9 - - + -
87C ILE* 3.8 23.1 - - + -
89C LEU* 3.9 17.7 - - + -
92C LEU* 4.5 3.6 - - + -
105C ILE* 3.0 30.1 + - + +
106C LEU* 3.7 8.3 - - + +
108C SER* 1.3 74.1 - - - +
110C GLN* 1.3 67.8 + - - +
112C LEU* 3.0 32.1 + - + +
113C PHE* 4.0 4.6 + - + -
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Residues in contact with GLN 110 (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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22C PRO 3.2 23.4 + - - +
23C GLY* 3.9 8.5 - - - +
24C VAL* 3.4 16.0 - - + +
40C ILE* 3.8 16.8 - - + +
41C ILE 4.6 3.6 - - - +
43C PRO* 3.9 14.7 - - + +
106C LEU 2.8 13.1 + - - +
107C THR* 3.1 29.4 + - - +
109C ILE* 1.3 76.8 - - - +
111C SER* 1.3 58.6 + - - +
113C PHE* 2.9 40.1 + - - +
114C ASN* 3.9 2.4 - - - +
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Residues in contact with SER 111 (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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107C THR* 2.8 22.6 + - - -
108C SER* 3.7 12.4 - - - -
109C ILE 3.2 0.2 - - - -
110C GLN* 1.3 74.8 + - - +
112C LEU* 1.3 61.0 + - - +
114C ASN* 3.0 26.3 + - - +
115C ASP* 3.3 11.7 + - - +
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Residues in contact with LEU 112 (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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78C HIS* 2.6 34.4 - - + +
80C ASN* 4.3 26.0 - - + +
81C VAL* 5.5 3.4 - - + -
87C ILE* 4.2 24.7 - - + -
88C CYS 4.6 1.1 - - - +
89C LEU* 4.3 27.4 - - + -
108C SER 4.0 9.2 - - - +
109C ILE* 3.0 20.7 + - + +
110C GLN 2.9 0.4 + - - -
111C SER* 1.3 78.8 - - - +
113C PHE* 1.3 56.4 + - + +
114C ASN 3.1 0.2 - - - -
115C ASP* 3.1 30.8 + - + +
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Residues in contact with PHE 113 (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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40C ILE* 3.5 25.8 - - + -
43C PRO* 3.3 33.9 - - + -
46C THR* 3.6 13.2 - - - +
47C PRO* 5.6 0.3 - - - +
48C TYR* 3.4 49.3 - + + -
53C PHE* 3.6 20.2 - + - -
72C PHE* 4.0 15.7 - + - -
76C MET* 3.4 34.5 - - + -
78C HIS* 4.1 7.9 - + - -
109C ILE 4.2 3.4 - - - -
110C GLN* 2.9 24.1 + - - +
112C LEU* 1.3 78.4 - - + +
114C ASN* 1.3 60.6 - - - +
115C ASP 3.7 0.2 + - - -
116C PRO* 4.2 5.5 - - - +
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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