Contacts of the helix formed by residues 102 - 114 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B LEU* 4.6 0.4 - - + -
12B ASP* 3.2 23.0 + - + +
16B MET* 4.2 7.6 - - + -
26B ALA* 3.8 28.9 - - + -
36B TRP* 3.8 27.4 - - + -
57B LEU* 4.5 8.5 - - + -
59B PHE* 3.7 28.0 - - + -
63B TYR* 3.6 1.2 + - - +
101B ASP* 1.3 73.8 - - - +
103B ALA* 1.3 63.6 + - - +
105B ILE* 3.1 9.9 + - - +
106B LEU* 2.9 34.9 + - + +
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Residues in contact with ALA 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ARG* 3.8 35.9 - - + +
16B MET* 3.9 19.4 - - - +
21B PRO* 3.9 14.6 - - + -
101B ASP* 3.2 8.5 + - - +
102B VAL* 1.3 78.1 - - - +
104B SER* 1.3 59.3 + - - +
106B LEU* 3.1 7.7 + - - +
107B THR* 2.9 33.6 + - - +
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Residues in contact with SER 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B THR 5.7 0.2 - - - -
100B TYR* 3.3 25.8 - - - -
101B ASP* 2.7 41.4 + - - -
103B ALA* 1.3 74.6 - - - +
105B ILE* 1.3 58.3 + - - +
107B THR* 2.9 16.9 + - - -
108B SER* 2.4 30.7 + - - -
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Residues in contact with ILE 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B LEU* 4.5 11.4 - - + -
59B PHE* 4.8 2.9 - - + -
63B TYR* 4.7 3.4 - - - +
68B PRO* 3.8 24.9 - - + -
70B VAL* 4.4 12.1 - - + -
91B ILE* 5.6 0.4 - - + -
92B LEU* 4.3 15.7 - - + +
96B TRP* 3.7 37.9 - - + -
100B TYR* 4.8 2.2 - - + -
101B ASP 2.8 23.9 + - - +
102B VAL* 3.3 12.8 - - - +
104B SER* 1.3 79.9 + - - +
106B LEU* 1.3 64.3 - - + +
108B SER* 3.2 12.0 + - - -
109B ILE* 3.2 33.3 + - + +
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Residues in contact with LEU 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B MET* 3.9 17.7 - - + -
24B VAL* 3.9 21.5 - - + -
25B SER 3.9 7.4 - - - +
26B ALA* 3.7 28.3 - - + -
38B ALA* 3.7 19.7 - - + -
40B ILE* 3.3 26.7 - - + +
55B LEU* 4.6 8.7 - - + -
57B LEU* 4.8 11.4 - - + -
102B VAL* 2.9 21.4 + - + +
103B ALA 3.1 6.5 + - - +
105B ILE* 1.3 80.7 - - + +
107B THR* 1.3 56.6 + - - +
109B ILE* 3.4 2.8 + - + -
110B GLN* 3.0 27.7 + - - +
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Residues in contact with THR 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B PRO* 3.8 30.1 - - + -
24B VAL* 4.7 2.9 - - + -
103B ALA 2.9 16.3 + - - +
104B SER* 2.9 23.6 + - - -
106B LEU* 1.3 71.4 - - - +
108B SER* 1.3 59.0 + - - +
110B GLN* 3.1 24.4 + - - +
111B SER* 2.9 34.8 + - - -
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Residues in contact with SER 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B LEU* 4.0 15.4 - - - +
91B ILE* 3.6 36.2 - - - +
92B LEU* 5.3 0.2 - - - -
100B TYR* 4.3 3.8 - - - -
104B SER* 2.4 25.7 + - - -
105B ILE* 3.3 6.3 - - - -
107B THR* 1.3 79.1 + - - +
109B ILE* 1.3 59.7 + - - +
111B SER* 3.5 16.6 + - - -
112B LEU* 3.7 10.2 + - - +
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Residues in contact with ILE 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B ILE* 3.8 6.7 - - + -
55B LEU* 3.9 8.1 - - + -
70B VAL* 3.9 16.6 - - + -
72B PHE* 3.6 34.8 - - + -
87B ILE* 3.6 24.7 - - + -
89B LEU* 4.1 18.4 - - + -
92B LEU* 4.3 5.8 - - + -
105B ILE* 3.2 27.1 + - + +
106B LEU* 3.7 9.4 - - + +
108B SER* 1.3 73.3 - - - +
110B GLN* 1.3 66.1 + - - +
112B LEU* 3.0 28.3 + - + +
113B PHE* 3.9 6.5 - - + -
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Residues in contact with GLN 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B PRO 3.1 23.8 + - - +
23B GLY* 4.1 6.6 - - - -
24B VAL* 3.7 9.6 - - + +
40B ILE* 3.8 19.1 - - + +
41B ILE 5.0 2.4 - - - +
43B PRO* 4.1 13.8 - - + +
106B LEU 3.0 15.3 + - - +
107B THR* 3.2 32.1 + - - +
109B ILE* 1.3 77.1 - - - +
111B SER* 1.3 63.2 + - - +
113B PHE* 3.1 30.3 + - - +
114B ASN* 4.0 6.2 - - - +
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Residues in contact with SER 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B THR* 2.9 14.0 + - - -
108B SER* 3.6 11.9 - - - -
109B ILE 3.2 0.2 - - - -
110B GLN* 1.3 80.1 + - - +
112B LEU* 1.3 58.3 + - - +
114B ASN* 2.9 33.9 + - - +
115B ASP* 3.5 7.5 + - - +
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Residues in contact with LEU 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B HIS* 2.8 27.5 - - + +
80B ASN* 4.1 30.3 - - + +
81B VAL* 5.6 2.2 - - + -
87B ILE* 3.9 28.3 - - + -
88B CYS 4.4 4.7 - - - +
89B LEU* 4.3 24.0 - - + -
108B SER 3.7 8.9 + - - +
109B ILE* 3.0 20.8 + - + +
111B SER* 1.3 78.7 - - - +
113B PHE* 1.3 57.4 + - + +
115B ASP* 3.0 29.3 + - + +
117B ASN* 6.3 0.7 - - + -
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Residues in contact with PHE 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B ILE* 3.7 24.9 - - + -
43B PRO* 3.3 32.1 - - + -
46B THR* 3.7 13.0 - - - +
47B PRO* 5.8 0.2 - - - +
48B TYR* 3.5 48.6 - + + -
53B PHE* 3.8 16.6 - + - -
72B PHE* 3.9 15.5 - + - -
76B MET* 3.3 34.8 - - + -
78B HIS* 3.9 9.4 - + - -
109B ILE 3.9 9.4 - - - -
110B GLN* 3.1 20.2 + - - +
111B SER 3.1 0.8 - - - -
112B LEU* 1.3 77.6 - - - +
114B ASN* 1.3 60.3 + - - +
115B ASP 3.2 1.4 + - - -
116B PRO* 4.1 5.9 - - - +
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Residues in contact with ASN 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B PRO* 3.6 22.3 - - - +
44B ALA* 5.2 1.2 - - - +
45B ASP 5.7 1.0 - - - +
46B THR* 3.3 26.4 - - - +
110B GLN* 4.0 8.1 - - - +
111B SER* 2.9 18.3 + - - +
113B PHE* 1.3 77.5 - - - +
115B ASP* 1.3 61.1 + - + +
116B PRO* 3.8 4.3 - - - +
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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