Contacts of the helix formed by residues 86 - 107 (chain B) in PDB entry 5XA0
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 ALA 86 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85B ASP* 1.3 79.1 - - + +
87B VAL* 1.3 70.3 + - + +
89B LEU* 3.5 8.7 + - - +
90B ASN* 3.3 16.7 + - - -
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Residues in contact with VAL 87 (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 ASP 4.3 1.9 - - - +
86B ALA* 1.3 78.2 - - + +
88B LEU* 1.3 66.7 + - - +
90B ASN* 2.9 21.3 + - + +
91B LYS* 3.1 21.5 + - + +
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Residues in contact with LEU 88 (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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75B ALA* 3.8 21.3 - - + -
85B ASP* 3.1 33.3 + - - +
86B ALA 3.2 0.6 - - - -
87B VAL* 1.3 78.9 - - - +
89B LEU* 1.3 57.4 + - - +
91B LYS* 3.6 7.9 + - + +
92B LEU* 2.9 47.4 + - + +
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Residues in contact with LEU 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B PHE* 2.7 60.5 - - + +
75B ALA* 2.5 40.6 - - + +
76B ALA* 3.1 24.7 - - + -
85B ASP 3.4 6.5 + - - +
86B ALA* 3.9 10.1 - - - +
87B VAL 3.1 0.8 - - - -
88B LEU* 1.3 77.8 - - - +
90B ASN* 1.3 62.7 + - - +
92B LEU* 4.3 0.4 - - - -
93B HIS* 3.0 6.6 + - - +
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Residues in contact with ASN 90 (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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86B ALA 3.3 23.6 + - - -
87B VAL* 2.9 13.9 + - + +
89B LEU* 1.3 82.3 - - - +
91B LYS* 1.3 65.9 + - - +
92B LEU 3.1 0.7 - - - -
93B HIS* 3.0 22.5 + - + +
94B HIS* 3.1 12.6 + - - +
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Residues in contact with LYS 91 (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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87B VAL* 3.1 20.5 + - + +
88B LEU* 4.1 9.6 - - + +
90B ASN* 1.3 74.9 - - - +
92B LEU* 1.3 61.9 + - - +
94B HIS* 3.0 18.6 + - + +
95B ALA* 3.1 12.1 + - - +
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Residues in contact with LEU 92 (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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68B ALA 4.1 2.0 - - - +
71B GLN* 3.0 56.5 - - + +
72B PHE* 3.0 29.3 - - + +
74B LYS* 4.9 0.9 - - + -
75B ALA* 3.3 26.7 - - + +
88B LEU* 2.9 32.6 + - + +
89B LEU 3.8 0.2 - - - +
91B LYS* 1.3 73.7 - - - +
93B HIS* 1.3 65.8 + - - +
95B ALA* 3.3 9.9 + - + +
96B ALA 3.0 19.4 + - - -
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Residues in contact with HIS 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B PHE* 3.1 35.7 - + + -
89B LEU 3.0 11.0 + - - +
90B ASN* 3.0 18.6 + - + +
92B LEU* 1.3 76.0 - - - +
94B HIS* 1.3 66.0 + - + +
97B ASP* 2.9 52.0 + - + +
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Residues in contact with HIS 94 (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 ASN 3.1 9.1 + - - +
91B LYS* 3.0 13.2 + - + +
93B HIS* 1.3 87.0 + + + +
95B ALA* 1.3 50.5 + - - +
97B ASP* 5.0 1.8 - - - +
98B LEU* 2.7 73.3 + - + +
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Residues in contact with ALA 95 (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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68B ALA* 3.0 23.1 - - + +
91B LYS 3.1 12.3 + - - +
92B LEU* 3.3 14.3 + - + +
94B HIS* 1.3 78.0 - - - +
96B ALA* 1.3 64.9 + - - +
98B LEU* 3.8 3.6 - - - +
99B GLU* 2.9 14.2 + - - +
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Residues in contact with ALA 96 (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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68B ALA* 3.0 34.7 - - - +
69B GLN* 3.6 9.4 - - + -
72B PHE* 3.4 26.7 - - + -
92B LEU 3.0 7.2 + - - +
95B ALA* 1.3 70.5 - - - +
97B ASP* 1.3 58.4 + - - +
99B GLU* 2.2 30.1 + - - +
100B LYS* 2.7 20.3 - - - +
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Residues in contact with ASP 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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93B HIS* 2.9 45.5 + - + +
94B HIS* 4.8 2.9 - - - +
96B ALA* 1.3 71.8 - - - +
98B LEU* 1.4 63.9 + - + +
100B LYS* 3.0 26.4 + - + +
101B LYS* 3.0 12.0 + - - +
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Residues in contact with LEU 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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94B HIS* 2.7 67.7 + - + +
95B ALA* 3.8 4.9 - - - +
97B ASP* 1.4 76.8 - - + +
99B GLU* 1.3 61.5 + - - +
101B LYS* 3.1 11.7 + - + +
102B GLN* 2.9 21.7 + - - +
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Residues in contact with GLU 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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65B ARG* 2.1 65.7 + - - +
66B TYR* 2.8 32.2 - - + -
67B SER* 4.8 1.1 - - - +
68B ALA* 3.9 14.1 - - + +
95B ALA 2.9 12.2 + - - +
96B ALA 2.2 29.0 + - - +
98B LEU* 1.3 64.3 - - - +
100B LYS* 1.3 57.2 - - - +
102B GLN* 2.9 19.0 + - - +
103B ASN* 2.2 26.3 + - - +
106B GLU* 3.3 1.6 - - - +
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Residues in contact with LYS 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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66B TYR* 2.9 51.8 - - + +
69B GLN* 2.8 47.9 + - - +
96B ALA* 2.7 29.5 + - - +
97B ASP* 3.1 20.4 - - - +
99B GLU* 1.3 70.5 - - - +
101B LYS* 1.3 60.3 + - - +
103B ASN* 2.1 37.5 + - - +
104B GLU* 2.9 6.1 + - - +
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Residues in contact with LYS 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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97B ASP 3.0 12.3 + - - +
98B LEU* 3.3 15.7 - - + +
99B GLU 3.1 0.2 - - - -
100B LYS* 1.3 73.3 - - - +
102B GLN* 1.4 71.7 + - - +
104B GLU* 2.7 17.8 + - - +
105B THR* 2.8 15.6 + - - +
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Residues in contact with GLN 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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98B LEU 2.9 11.2 + - - +
99B GLU* 2.9 17.8 + - - +
101B LYS* 1.4 77.3 - - - +
103B ASN* 1.3 66.7 + - - +
105B THR* 2.5 15.5 + - - +
106B GLU* 2.2 73.9 + - - +
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Residues in contact with ASN 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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64B ASN* 3.1 21.7 - - - +
65B ARG* 3.2 1.6 + - - -
66B TYR* 2.5 32.5 + - - -
99B GLU 2.2 27.0 - - - +
100B LYS* 2.1 29.8 + - - +
102B GLN* 1.3 70.3 - - - +
104B GLU* 1.3 65.9 + - - +
106B GLU* 2.2 12.4 + - - +
107B ASN* 2.7 53.2 + - - +
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Residues in contact with GLU 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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100B LYS 2.9 12.6 + - - +
101B LYS* 2.7 15.3 + - - +
102B GLN 2.7 3.2 + - - -
103B ASN* 1.3 73.5 - - - +
105B THR* 1.3 51.6 - - - +
108B ARG* 2.0 47.9 + - + +
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Residues in contact with THR 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 LYS* 2.8 10.9 + - - +
102B GLN* 2.5 19.0 + - - -
104B GLU* 1.3 78.4 - - - +
106B GLU* 1.4 57.8 + - - -
107B ASN 3.6 0.2 - - - -
108B ARG* 3.6 3.4 - - + -
109B LYS* 2.7 53.1 + - - +
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Residues in contact with GLU 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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65B ARG* 2.0 56.5 + - - -
102B GLN* 2.2 68.1 + - - +
103B ASN 2.2 14.8 + - - -
105B THR* 1.4 70.8 - - - +
107B ASN* 1.3 81.2 + - - +
109B LYS* 4.2 10.5 + - - +
110B LEU* 4.3 8.5 - - - +
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Residues in contact with ASN 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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62B PRO* 4.0 26.0 - - + +
63B MET 2.5 34.4 + - - +
64B ASN* 3.9 3.6 - - - +
65B ARG* 3.5 3.3 + - - +
103B ASN* 2.7 32.5 + - - +
106B GLU* 1.3 96.2 - - - +
108B ARG* 1.3 59.9 + - - +
109B LYS 3.1 7.2 + - - -
110B LEU* 3.6 24.4 + - - +
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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