Contacts of the helix formed by residues 83 - 102 (chain B) in PDB entry 3BUW
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 TYR 83 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B LEU* 4.1 18.8 + - + -
78B LYS 3.5 24.7 - - - -
79B ASN* 3.2 39.5 - - + +
80B SER 3.3 13.0 + - - +
81B PRO* 3.7 3.8 - - + +
82B PRO* 1.3 71.4 - - - +
84B ILE* 1.3 70.7 + - + +
85B LEU* 3.4 41.2 - - + +
86B ASP* 2.9 43.3 + - + +
87B LEU* 2.9 19.4 + - - +
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Residues in contact with ILE 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B VAL* 4.5 2.5 - - + -
67B VAL* 6.4 0.2 - - - -
70B CYS* 3.8 32.3 - - + -
77B LEU* 3.8 21.8 - - + -
82B PRO 3.9 3.8 + - - -
83B TYR* 1.3 72.4 - - + +
85B LEU* 1.3 65.1 + - + +
87B LEU* 4.0 7.3 - - + +
88B LEU* 3.1 48.7 + - + +
151B LEU* 5.7 5.6 - - + -
155B SER* 3.8 21.2 + - - +
158B PHE* 3.3 44.4 - - + -
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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
----------------------------------------------------------
67B VAL* 3.8 26.3 - - + +
70B CYS* 3.7 41.5 - - + +
71B GLN* 4.0 20.0 - - + +
77B LEU* 4.6 7.6 - - + +
83B TYR* 3.1 41.2 + - + +
84B ILE* 1.3 82.1 - - + +
86B ASP* 1.3 61.8 + - - +
89B PRO* 3.1 23.3 - - - +
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Residues in contact with ASP 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A SER 4.6 5.4 + - - -
79B ASN* 4.2 8.1 + - - +
83B TYR* 2.9 34.8 + - + +
85B LEU* 1.3 84.5 - - - +
87B LEU* 1.3 60.7 + - + +
88B LEU 3.4 0.9 - - - -
89B PRO* 3.4 3.0 - - - +
90B ASP* 2.9 46.3 + - - +
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Residues in contact with LEU 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B PRO* 3.9 3.6 - - + -
83B TYR 2.9 38.0 + - - +
84B ILE* 3.4 13.4 + - + +
86B ASP* 1.3 77.4 - - + +
88B LEU* 1.3 54.0 + - - +
90B ASP* 3.5 5.0 + - - +
91B THR* 2.7 37.6 + - - -
155B SER 3.5 25.1 - - - +
158B PHE* 4.5 10.5 - - + +
159B SER* 3.7 33.4 - - - +
162B LEU* 4.1 18.8 - - + +
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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
----------------------------------------------------------
63B MET* 3.6 43.1 - - + +
66B VAL* 3.3 42.4 - - + -
67B VAL* 3.8 14.4 - - + -
84B ILE* 3.1 23.8 + - + +
87B LEU* 1.3 74.3 - - - +
89B PRO* 1.3 76.0 - - + +
91B THR* 3.1 6.5 + - - +
92B TYR* 2.9 23.9 + - - +
122B LEU* 5.1 0.4 - - + -
158B PHE* 4.1 31.2 - - + -
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Residues in contact with PRO 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B VAL* 4.3 15.7 - - + -
85B LEU 3.1 28.9 - - - +
86B ASP* 3.4 7.4 - - - +
88B LEU* 1.3 94.5 - - + +
90B ASP* 1.3 59.4 + - - +
92B TYR* 3.2 12.7 + - + +
93B GLN* 2.9 29.3 + - - +
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Residues in contact with ASP 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ASP* 2.9 35.7 + - - +
87B LEU* 3.8 4.8 - - - +
89B PRO* 1.3 79.7 - - - +
91B THR* 1.3 57.9 + - - +
93B GLN* 3.4 7.5 + - - +
94B HIS* 3.0 27.5 + - - +
162B LEU* 3.8 19.8 - - + +
166B LYS* 4.9 9.5 + - - +
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Residues in contact with THR 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B MET* 4.1 13.7 - - - -
87B LEU* 2.7 22.8 + - - +
88B LEU* 3.5 8.0 - - - +
90B ASP* 1.3 73.5 - - - +
92B TYR* 1.3 68.0 + - - +
94B HIS* 3.3 2.1 + - - +
95B LEU* 2.9 41.8 + - + +
118B PHE* 4.6 13.2 - - + -
122B LEU* 4.3 13.2 - - + -
158B PHE* 4.8 5.9 + - + +
161B MET* 6.5 0.2 - - + -
162B LEU* 3.8 27.2 - - + +
165B LEU* 4.7 4.3 - - + -
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Residues in contact with TYR 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B TRP* 3.4 58.7 - + + +
63B MET* 4.4 9.3 - - + -
64B ASP* 6.1 0.4 - - - -
88B LEU 2.9 12.2 + - - +
89B PRO* 3.4 14.4 - - + +
91B THR* 1.3 78.4 - - - +
93B GLN* 1.3 67.8 + - + +
95B LEU* 3.2 2.9 + - - +
96B ARG* 2.9 77.6 + - + +
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Residues in contact with GLN 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B PRO 2.9 16.9 + - - +
90B ASP* 3.6 10.5 - - - +
92B TYR* 1.3 87.1 - - + +
94B HIS* 1.3 63.3 + - - +
96B ARG* 3.3 27.2 + - - +
97B THR* 3.0 26.5 + - - +
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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
----------------------------------------------------------
90B ASP 3.0 17.1 + - - +
91B THR 3.9 2.7 - - - +
93B GLN* 1.3 77.2 - - - +
95B LEU* 1.3 58.4 + - - +
97B THR* 3.2 13.3 + - + -
98B ILE* 2.9 39.6 + - + +
162B LEU* 4.5 2.0 - - + -
165B LEU* 3.7 22.5 - - + +
166B LYS* 3.8 45.4 - - + +
169B PHE* 3.0 41.8 + - + -
170B PRO* 4.9 0.2 - - - +
171B SER* 4.3 6.2 + - - -
172B GLY 4.2 7.0 + - - -
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Residues in contact with LEU 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B VAL* 5.6 2.7 - - + -
60B TRP* 3.8 25.8 - - + +
63B MET* 4.2 4.5 - - + -
91B THR* 2.9 25.2 + - + +
92B TYR 3.6 4.3 - - - +
94B HIS* 1.3 72.5 - - - +
96B ARG* 1.3 65.8 + - - +
98B ILE* 3.3 7.4 + - + +
99B LEU* 3.0 28.6 + - + +
115B PHE* 4.0 29.1 - - + -
118B PHE* 4.3 3.6 - - + -
119B MET* 4.0 17.0 - - + -
122B LEU* 3.6 30.1 - - + -
165B LEU* 3.9 22.0 - - + -
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Residues in contact with ARG 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B TRP* 3.9 17.1 - - + -
92B TYR* 2.9 66.0 + - + +
93B GLN* 3.4 26.0 + - - +
94B HIS 3.2 0.2 - - - -
95B LEU* 1.3 75.4 - - - +
97B THR* 1.3 59.9 + - - +
99B LEU* 3.4 5.5 + - - +
100B SER* 3.0 27.9 + - - -
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Residues in contact with THR 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 GLN* 3.0 22.7 + - - +
94B HIS* 3.2 17.3 + - + -
96B ARG* 1.3 76.2 - - - +
98B ILE* 1.3 65.3 + - - +
100B SER* 3.1 10.5 + - - -
101B ARG* 3.1 22.8 + - + +
171B SER* 4.0 23.3 - - - +
172B GLY* 4.1 5.4 - - - +
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Residues in contact with ILE 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B HIS* 2.9 30.4 + - - +
95B LEU* 3.3 13.9 + - + +
97B THR* 1.3 76.0 - - - +
99B LEU* 1.3 63.8 + - + +
101B ARG* 3.1 11.6 + - - +
102B TYR* 3.1 20.5 - - + -
109B LEU* 3.9 31.4 - - + -
115B PHE* 4.5 8.3 - - + -
165B LEU* 3.9 20.0 - - + -
169B PHE* 3.6 31.0 - - + -
172B GLY* 3.5 31.6 - - - +
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Residues in contact with LEU 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B LYS* 3.6 20.0 - - - +
56B VAL* 3.6 21.1 - - + -
60B TRP* 3.4 37.9 - - + -
95B LEU* 3.0 16.5 + - + +
96B ARG* 3.7 4.7 - - - +
98B ILE* 1.3 76.8 - - - +
100B SER* 1.3 60.9 - - - +
102B TYR* 3.2 12.5 + - - +
103B GLU* 3.5 12.3 + - - +
106B MET* 3.3 36.0 - - + +
109B LEU* 3.6 18.4 - - + -
115B PHE* 5.0 6.3 - - + -
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Residues in contact with SER 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B ARG 3.0 14.3 + - - -
97B THR* 3.2 15.0 - - - -
99B LEU* 1.3 77.4 - - - +
101B ARG* 1.3 61.3 + - - +
102B TYR 3.4 0.2 + - - -
103B GLU* 3.4 28.8 + - - +
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Residues in contact with ARG 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B THR* 3.1 13.2 + - + +
98B ILE 3.1 8.7 + - - +
100B SER* 1.3 77.2 - - - +
102B TYR* 1.3 62.9 + - + +
103B GLU* 3.3 3.0 + - - +
105B LYS* 3.2 18.4 + - - -
171B SER* 2.6 39.1 + - - +
172B GLY 3.1 5.8 - - - +
173B LEU* 3.1 46.6 - - + +
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Residues in contact with TYR 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ILE* 3.1 23.8 - - + +
99B LEU 3.2 8.5 + - - +
100B SER 3.2 0.8 - - - -
101B ARG* 1.3 78.3 - - + +
103B GLU* 1.3 64.3 + - - +
104B GLY 3.2 1.6 + - - -
105B LYS* 3.1 50.5 + - + +
106B MET* 3.4 8.8 + - - +
108B THR* 4.5 15.5 - - + -
109B LEU* 3.8 48.0 - - + -
169B PHE* 4.2 0.2 - + - -
172B GLY 3.5 19.5 - - - -
173B LEU* 3.1 20.4 - - + +
174B PHE* 2.9 38.3 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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