Contacts of the helix formed by residues 81 - 98 (chain B) in PDB entry 1MBU
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 THR 81 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B PHE* 3.8 26.2 - - + -
25B MET 3.1 12.4 + - - +
26B THR* 4.0 6.7 - - + -
80B PRO* 1.3 77.9 - - - +
82B LEU* 1.3 65.5 + - - +
83B SER 3.5 1.3 + - - -
84B PHE* 3.1 19.1 + - - +
85B GLN* 3.0 20.7 + - - +
79D GLU* 2.8 42.8 + - + +
80D VAL* 4.8 3.4 - - + -
83D THR* 3.1 18.2 - - - +
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Residues in contact with LEU 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B PRO 3.9 0.2 + - - -
81B THR* 1.3 71.4 - - - +
83B SER* 1.3 64.9 + - - +
85B GLN* 3.0 25.8 + - + +
86B ARG* 2.8 44.0 + - + +
82D GLU* 3.7 33.9 - - + +
83D THR* 2.9 19.4 + - + +
86D ALA* 3.9 28.0 - - + -
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Residues in contact with SER 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B VAL* 3.4 13.9 - - - +
81B THR* 3.5 0.4 + - - -
82B LEU* 1.3 80.9 - - - +
84B PHE* 1.3 61.9 + - - +
86B ARG* 3.3 9.1 + - - +
87B VAL* 3.0 28.9 + - - +
115B GLU* 2.5 41.2 + - - +
118B SER* 4.5 4.0 - - - -
79D GLU* 3.7 26.5 - - - +
82D GLU* 4.4 3.5 + - - -
83D THR* 4.7 0.2 + - - -
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Residues in contact with PHE 84 (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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10B LEU* 4.2 15.0 - - + -
13B ALA* 5.4 0.7 - - + -
25B MET* 3.7 40.4 - - + +
26B THR 3.8 16.8 - - - -
27B VAL* 3.3 12.2 - - + +
30B LEU* 4.0 32.8 - - + -
80B PRO* 3.7 20.0 - - + -
81B THR* 3.1 22.8 + - - +
83B SER* 1.3 74.9 - - - +
85B GLN* 1.3 70.3 + - + +
87B VAL* 3.3 4.8 + - - +
88B LEU* 3.3 40.3 + - + +
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Residues in contact with GLN 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B GLN* 3.6 10.9 + - - -
80B PRO* 3.2 38.2 - - + +
81B THR 3.0 14.7 + - - +
82B LEU* 3.0 25.4 + - + +
84B PHE* 1.3 81.4 - - + +
86B ARG* 1.3 61.8 + - + +
88B LEU* 3.4 4.4 + - - +
89B GLN* 3.1 41.7 + - + +
83D THR* 5.6 0.5 - - - +
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Residues in contact with ARG 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B LEU* 2.8 28.5 + - + +
83B SER* 3.3 10.6 + - - +
85B GLN* 1.3 78.5 - - + +
87B VAL* 1.3 57.0 + - - +
89B GLN* 3.4 14.0 + - - +
90B ARG* 2.8 49.0 + - - +
115B GLU* 2.8 39.4 + - - +
82D GLU* 2.8 44.0 + - - -
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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
----------------------------------------------------------
27B VAL* 4.1 9.6 - - + -
30B LEU* 3.8 13.7 - - + -
83B SER 3.0 21.0 + - - +
84B PHE 3.7 5.2 - - - +
85B GLN 3.3 0.2 - - - -
86B ARG* 1.3 77.0 - - - +
88B LEU* 1.3 62.5 + - - +
90B ARG* 4.2 5.4 - - - +
91B ALA* 3.0 19.4 + - - +
108B VAL* 3.7 38.1 - - + +
111B ALA* 3.4 12.6 - - + +
112B ILE* 3.9 18.4 - - + -
115B GLU* 3.4 25.6 - - + -
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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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2B LEU* 4.6 17.0 - - + -
6B LEU* 5.0 0.4 - - + -
10B LEU* 4.1 31.6 - - + -
30B LEU* 4.3 14.4 - - + -
84B PHE* 3.3 40.1 + - + +
85B GLN* 3.9 7.6 - - - +
87B VAL* 1.3 79.3 - - - +
89B GLN* 1.3 58.0 + - + +
91B ALA* 3.1 6.2 + - + +
92B VAL* 2.8 38.8 + - + +
103B VAL* 5.5 0.4 - - + -
108B VAL* 4.5 20.0 - - + -
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Residues in contact with GLN 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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85B GLN* 3.1 38.3 + - + +
86B ARG* 3.8 12.4 - - - +
88B LEU* 1.3 77.0 - - + +
90B ARG* 1.3 54.6 + - - +
92B VAL* 3.2 7.3 + - - +
93B PHE* 2.7 39.0 + - - +
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Residues in contact with ARG 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 ARG* 2.8 44.5 + - - +
87B VAL* 3.6 7.8 - - - +
89B GLN* 1.3 74.8 - - - +
91B ALA* 1.3 57.4 + - - +
93B PHE* 3.7 8.9 - - + +
94B HIS* 2.8 31.4 + - + +
111B ALA* 3.3 25.1 + - + +
114B SER* 3.2 39.9 + - - -
115B GLU* 3.1 29.9 + - - -
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Residues in contact with ALA 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 3.0 15.0 + - - +
88B LEU* 3.1 6.5 + - + +
90B ARG* 1.3 75.9 - - - +
92B VAL* 1.3 64.1 + - - +
94B HIS* 3.3 6.9 + - - +
95B VAL* 3.1 28.2 + - - +
103B VAL* 3.9 20.4 - - + -
107B ASN* 3.9 23.6 - - + +
108B VAL* 3.9 15.5 - - + -
111B ALA* 4.1 4.4 - - + +
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Residues in contact with VAL 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B LEU* 4.5 15.3 - - + -
88B LEU* 2.8 25.7 + - + +
89B GLN* 3.6 7.2 - - - +
91B ALA* 1.3 75.4 - - - +
93B PHE* 1.3 64.8 + - - +
95B VAL* 3.1 3.5 + - - +
96B GLN* 3.0 33.0 + - + +
103B VAL* 4.0 21.8 - - + -
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Residues in contact with PHE 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B GLN 2.7 21.2 + - - +
90B ARG* 3.7 8.7 - - + +
92B VAL* 1.3 74.8 - - - +
94B HIS* 1.3 66.6 + - + +
96B GLN* 3.8 30.2 - - - +
97B SER* 2.9 45.0 + - - -
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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 ARG* 2.8 18.6 + - + +
91B ALA* 3.7 5.2 - - - +
93B PHE* 1.3 81.7 - - + +
95B VAL* 1.3 71.1 + - + +
97B SER* 3.5 7.3 + - - -
98B SER* 3.1 37.7 + - - -
107B ASN* 3.8 29.9 + - + -
110B VAL* 6.5 1.1 - - + -
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Residues in contact with VAL 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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91B ALA 3.1 15.2 + - - +
92B VAL 3.1 1.8 + - - +
94B HIS* 1.3 83.8 - - + +
96B GLN* 1.3 58.9 + - - +
98B SER* 3.5 6.6 + - - -
100B ARG* 3.0 56.4 + - + +
101B ASN 3.8 10.1 - - - +
102B GLU 3.8 16.2 - - - +
103B VAL* 3.6 22.4 - - + -
107B ASN* 3.5 30.7 - - - +
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Residues in contact with GLN 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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92B VAL* 3.0 23.1 + - + +
93B PHE* 3.8 36.7 - - - -
95B VAL* 1.3 78.2 - - - +
97B SER* 1.3 68.2 + - - +
99B GLY* 3.1 14.7 + - - -
100B ARG 4.3 6.2 - - - +
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Residues in contact with SER 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 PHE* 2.9 41.4 + - - -
94B HIS* 3.5 9.0 + - - -
96B GLN* 1.3 82.8 - - - +
98B SER* 1.3 60.2 + - - +
99B GLY 3.1 1.9 + - - -
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Residues in contact with SER 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* 3.1 33.1 + - - -
95B VAL* 3.5 7.3 + - - -
96B GLN 3.2 0.6 - - - -
97B SER* 1.3 77.4 - - - +
99B GLY* 1.3 59.3 + - - +
100B ARG* 3.1 30.7 + - - +
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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