Contacts of the helix formed by residues 96 - 110 (chain B) in PDB entry 4Y5O
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 96 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66B TYR* 3.5 18.7 - - - -
94B LEU 3.7 0.2 - - - -
95B LYS* 1.3 85.0 - - - +
97B GLN* 1.3 64.0 + - - +
98B ASP* 3.0 13.7 + - - +
99B ASP* 2.7 55.0 + - - +
100B LEU* 3.3 10.6 + - - +
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Residues in contact with GLN 97 (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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64B VAL 2.9 23.5 + - - -
65B LYS* 3.4 11.0 - - - +
66B TYR* 2.7 37.8 + - + +
67B GLU* 4.2 4.5 + - - +
96B ASN* 1.3 71.4 - - - +
98B ASP* 1.3 57.6 + - - +
100B LEU* 3.3 12.6 + - - +
101B ASP* 2.9 61.6 + - - +
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Residues in contact with ASP 98 (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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96B ASN* 2.9 13.9 + - - +
97B GLN* 1.3 75.7 - - - +
99B ASP* 1.3 69.1 + - - +
101B ASP* 3.2 10.3 + - - +
102B LYS* 3.0 23.1 + - - +
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Residues in contact with ASP 99 (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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92B ILE* 3.3 27.2 - - + +
93B LEU 3.5 6.8 - - - +
94B LEU* 3.6 25.4 - - + +
95B LYS* 3.0 28.1 + - - +
96B ASN* 2.7 30.7 + - - +
98B ASP* 1.3 75.7 - - - +
100B LEU* 1.3 62.8 + - - +
102B LYS* 3.2 10.0 + - - +
103B ALA* 3.0 20.6 + - - +
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Residues in contact with LEU 100 (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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47B ILE* 5.0 8.3 - - + -
64B VAL* 3.8 27.8 - - + +
66B TYR* 3.8 34.3 - - + -
69B VAL* 4.2 8.3 - - + -
83B LEU* 6.5 0.2 - - + -
94B LEU* 4.2 19.0 - - + +
96B ASN 3.3 6.7 + - - +
97B GLN* 3.3 21.0 + - - +
98B ASP 3.2 0.6 - - - -
99B ASP* 1.3 75.3 - - - +
101B ASP* 1.3 61.7 + - - +
103B ALA* 3.1 4.5 + - - +
104B ILE* 2.8 51.9 + - + +
116B LEU* 4.1 17.3 - - + -
118B ILE* 5.6 1.1 - - + -
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Residues in contact with ASP 101 (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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64B VAL 4.6 1.6 + - - +
97B GLN* 2.9 49.6 + - - +
98B ASP* 3.2 9.4 + - - +
100B LEU* 1.3 75.2 - - - +
102B LYS* 1.3 52.1 + - - +
104B ILE* 3.3 17.0 + - - +
105B ASP* 2.8 36.0 + - - +
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Residues in contact with LYS 102 (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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90B LEU* 4.7 14.0 - - - +
92B ILE* 5.8 11.2 - - + -
98B ASP 3.0 12.3 + - - +
99B ASP* 3.3 14.1 - - - +
101B ASP* 1.3 74.0 - - - +
103B ALA* 1.3 65.6 + - - +
105B ASP* 3.1 8.0 + - + +
106B ILE* 2.9 43.6 + - + +
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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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85B TYR* 3.8 42.3 + - + -
94B LEU* 4.8 4.3 - - + -
99B ASP 3.0 12.8 + - - +
100B LEU* 3.5 10.1 - - - +
102B LYS* 1.3 75.8 - - - +
104B ILE* 1.3 62.9 + - - +
106B ILE* 3.1 6.3 + - - +
107B LEU 3.0 18.7 + - - -
116B LEU* 3.5 25.5 - - + +
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Residues in contact with ILE 104 (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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45B VAL* 4.1 21.3 - - + -
62B ARG* 3.5 27.6 - - + +
64B VAL* 3.8 35.9 - - + +
100B LEU* 2.8 41.8 + - + +
101B ASP* 3.5 16.6 - - - +
103B ALA* 1.3 73.8 - - - +
105B ASP* 1.3 57.3 + - - +
107B LEU* 3.4 6.1 + - + +
108B ASP* 3.0 30.2 + - - +
116B LEU* 4.3 7.2 - - + -
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Residues in contact with ASP 105 (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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101B ASP 2.8 20.8 + - - +
102B LYS* 3.1 9.1 + - + +
104B ILE* 1.3 71.3 - - - +
106B ILE* 1.3 68.4 + - - +
108B ASP* 3.1 19.3 + - - +
109B ARG* 3.1 48.6 + - - +
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Residues in contact with ILE 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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85B TYR* 3.4 28.0 - - + +
87B ASN* 3.4 13.5 - - - +
90B LEU* 3.6 38.1 - - + +
102B LYS* 2.9 40.3 + - + +
103B ALA 3.4 7.0 - - - +
105B ASP* 1.3 77.3 - - + +
107B LEU* 1.3 62.5 + - - +
109B ARG* 3.3 9.0 + - - +
110B SER* 3.1 22.7 + - - -
113B MET* 4.3 7.0 - - - -
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Residues in contact with LEU 107 (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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45B VAL* 4.4 21.8 - - + -
46B ARG 4.7 3.6 - - - +
62B ARG* 6.0 2.2 - - - +
103B ALA 3.0 12.6 + - - +
104B ILE* 3.7 9.4 - - + +
106B ILE* 1.3 76.4 - - - +
108B ASP* 1.3 68.8 + - - +
109B ARG 3.4 0.3 + - - -
110B SER* 3.5 18.2 + - - +
113B MET* 3.5 36.1 - - + +
114B LYS* 3.9 3.8 - - - +
115B SER* 3.7 24.0 - - - +
116B LEU* 3.9 31.6 - - + +
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Residues in contact with ASP 108 (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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62B ARG* 2.9 43.3 + - - -
104B ILE* 3.0 20.9 + - - +
105B ASP* 3.1 16.0 + - - +
107B LEU* 1.3 80.5 - - - +
109B ARG* 1.3 64.5 + - + +
110B SER 3.8 3.3 + - - +
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Residues in contact with ARG 109 (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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105B ASP* 3.1 44.9 + - - +
106B ILE* 3.3 7.8 + - - +
107B LEU 3.2 0.2 - - - -
108B ASP* 1.3 80.3 - - + +
110B SER* 1.3 61.8 + - - +
111B SER* 3.8 1.4 + - - -
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Residues in contact with SER 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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106B ILE* 3.1 16.1 + - - -
107B LEU 3.9 13.1 - - - +
108B ASP 3.4 4.5 - - - +
109B ARG* 1.3 80.9 - - - +
111B SER* 1.3 62.0 + - - +
112B SER* 3.1 16.9 + - - -
113B MET* 3.2 35.3 + - - +
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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