Contacts of the helix formed by residues 84 - 99 (chain B) in PDB entry 3U9J
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 LYS 84 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A SER* 5.5 8.3 - - - -
82A ASP* 5.8 3.7 - - - +
83A ASN* 5.4 8.3 - - - +
84A LYS* 3.2 44.1 - - + +
122A ASP* 4.3 16.0 + - - +
82B ASP* 3.0 12.7 + - - +
83B ASN* 1.3 81.5 - - - +
85B LEU* 1.3 63.8 + - - +
87B GLU* 3.0 32.2 - - + +
88B MSE 3.2 23.0 + - + +
115B ARG* 4.6 25.9 - - - +
122B ASP* 5.3 4.8 + - - -
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Residues in contact with LEU 85 (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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51B PHE* 3.6 23.3 - - + +
54B PHE* 3.7 17.0 - - + +
55B LYS* 3.5 41.7 - - + +
58B GLU* 3.5 26.2 - - + +
82B ASP* 3.5 15.3 + - - +
83B ASN* 4.2 5.6 - - + -
84B LYS* 1.3 73.7 - - - +
86B SER* 1.3 65.9 + - - +
88B MSE 3.2 4.4 + - - +
89B LEU* 3.0 30.2 + - + +
119B PHE* 3.6 26.7 - - + -
123B PHE* 6.4 0.7 - - + -
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Residues in contact with SER 86 (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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55B LYS* 5.3 8.5 - - - +
84B LYS 3.3 0.4 - - - -
85B LEU* 1.3 79.2 - - - +
87B GLU* 1.3 70.9 + - - +
89B LEU* 3.5 10.2 + - - +
90B SER* 3.0 32.8 + - - -
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Residues in contact with GLU 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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82A ASP* 6.2 4.3 - - + -
82B ASP* 4.7 2.4 - - - +
84B LYS* 3.0 40.2 - - + +
85B LEU 3.2 0.2 - - - -
86B SER* 1.3 87.5 + - - +
88B MSE 1.3 65.3 + - - +
90B SER* 3.3 8.1 + - - -
91B LEU* 3.0 22.3 + - - +
115B ARG* 4.8 9.9 - - - +
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Residues in contact with MSE 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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51B PHE* 3.7 29.4 - - + -
83B ASN 4.7 0.2 - - - +
84B LYS 3.2 15.9 + - - +
85B LEU* 3.5 6.3 - - - +
87B GLU* 1.3 76.2 - - - +
89B LEU* 1.3 61.5 + - - +
91B LEU* 3.1 13.1 + - + +
92B PHE* 3.1 42.6 + - + -
115B ARG* 3.3 57.9 - - + +
116B LEU* 3.6 33.7 - - + -
119B PHE* 4.1 13.2 - - + -
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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
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48B TYR* 3.5 43.5 - - + +
51B PHE* 3.7 25.6 - - + +
52B LYS* 3.5 38.4 - - + +
55B LYS* 4.2 22.0 - - + +
85B LEU 3.0 21.9 + - - +
86B SER* 3.8 7.2 - - - +
88B MSE 1.3 75.7 - - - +
90B SER* 1.3 57.3 + - - +
92B PHE* 3.3 5.7 + - + +
93B GLU* 3.0 29.7 + - - +
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Residues in contact with SER 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 SER 3.0 19.3 + - - -
87B GLU* 3.6 8.6 - - - -
89B LEU* 1.3 76.0 - - - +
91B LEU* 1.3 62.8 + - - +
93B GLU* 3.4 13.4 + - - +
94B LYS* 3.0 24.6 + - - +
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Residues in contact with LEU 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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77A TYR* 3.6 33.0 - - + +
78A ASN* 4.1 12.6 - - + +
87B GLU 3.0 13.6 + - - +
88B MSE 3.1 13.4 + - + +
90B SER* 1.3 74.7 - - - +
92B PHE* 1.3 65.6 + - + +
94B LYS* 3.2 5.5 + - + +
95B GLY 3.1 12.1 + - - -
108B TYR* 2.7 39.6 + - + +
111B GLN* 5.3 1.6 - - + -
112B LEU* 4.1 24.5 - - + -
115B ARG* 4.0 32.8 - - + -
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Residues in contact with PHE 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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44B LEU* 3.8 16.8 - - + +
47B LEU* 3.7 26.9 - - + -
48B TYR* 3.9 26.9 - - + -
51B PHE* 3.6 38.4 - + + -
88B MSE 3.1 42.1 + - + -
89B LEU* 3.3 11.2 + - + +
91B LEU* 1.3 78.1 - - + +
93B GLU* 1.3 63.0 + - - +
95B GLY* 3.1 3.8 + - - -
96B LEU* 3.0 28.1 + - + +
108B TYR* 3.4 5.8 - - - -
112B LEU* 3.6 31.9 - - + -
116B LEU* 4.2 2.2 - - + -
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Residues in contact with GLU 93 (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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48B TYR* 4.4 19.7 + - + -
89B LEU 3.0 15.3 + - - +
90B SER* 3.6 14.3 + - - +
92B PHE* 1.3 77.1 - - - +
94B LYS* 1.3 56.1 - - - +
96B LEU* 3.3 10.6 + - - +
97B LYS* 3.0 33.8 + - + +
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Residues in contact with LYS 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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74A GLN 6.1 0.4 - - - -
76A ILE 4.0 7.4 - - - -
77A TYR* 3.5 57.4 - - + +
90B SER 3.0 17.0 + - - +
91B LEU* 3.2 7.2 + - - +
93B GLU* 1.3 77.3 - - - +
95B GLY* 1.3 58.1 + - - +
97B LYS* 4.5 1.6 - - - -
98B ASN* 2.9 52.9 + - - +
99B VAL* 4.0 1.6 + - - +
108B TYR* 5.1 0.9 - - + -
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Residues in contact with GLY 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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40B PHE* 3.8 5.7 - - - -
41B ARG* 4.8 0.7 + - - -
44B LEU* 3.5 13.9 - - - -
91B LEU 3.1 6.7 + - - -
92B PHE 3.1 7.6 + - - -
94B LYS* 1.3 78.1 - - - +
96B LEU* 1.3 58.8 + - - +
99B VAL* 3.2 34.2 + - - +
108B TYR* 3.5 22.8 - - - -
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Residues in contact with LEU 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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40B PHE* 5.6 0.2 - - - -
41B ARG* 2.8 67.1 + - + +
44B LEU* 3.6 35.2 - - + +
45B GLN* 4.0 20.4 - - + +
48B TYR* 5.1 9.9 - - + -
92B PHE 3.0 21.6 + - - +
93B GLU* 3.3 8.3 + - - +
95B GLY* 1.3 77.2 - - - +
97B LYS* 1.3 60.7 + - - +
99B VAL 4.9 1.3 - - - +
100B LYS* 5.2 0.9 + - - -
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Residues in contact with LYS 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 GLU* 3.0 22.7 + - + +
94B LYS* 4.0 2.2 - - - +
96B LEU* 1.3 80.3 - - - +
98B ASN* 1.3 73.1 + - - +
99B VAL 5.4 0.2 - - - -
100B LYS* 2.7 25.7 + - - -
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Residues in contact with ASN 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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77A TYR* 5.2 6.3 - - + -
94B LYS* 2.9 46.3 + - + +
97B LYS* 1.3 103.3 + - - +
99B VAL* 1.3 66.5 + - + +
100B LYS* 3.4 17.4 + - - +
104B GLU* 4.0 9.5 - - - +
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Residues in contact with VAL 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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77A TYR* 3.9 29.8 - - + +
37B ASN* 4.4 8.3 + - - -
40B PHE* 3.7 13.0 - - + -
41B ARG* 4.9 8.3 + - - +
94B LYS 4.5 0.2 - - - +
95B GLY* 3.2 33.4 + - - +
96B LEU 5.1 1.0 - - - +
98B ASN* 1.3 74.7 - - - +
100B LYS* 1.3 65.0 + - - +
104B GLU* 3.8 5.6 - - + -
105B GLN* 3.4 46.2 - - + +
108B TYR* 4.0 11.9 - - + -
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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