Contacts of the helix formed by residues 101 - 114 (chain B) in PDB entry 4U2M
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 MET 101 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45B CYS* 3.9 22.9 - - + +
46B SER* 4.3 3.4 - - - -
73B VAL* 3.8 13.7 - - + -
76B PHE* 3.7 21.1 - - + -
77B MET* 3.6 34.8 - - + -
96B ALA* 2.8 15.9 + - + +
99B LEU* 3.8 25.4 - - + +
100B GLN* 1.3 69.6 - - - +
102B GLN* 1.3 58.7 - - - +
103B ASP* 3.4 3.8 - - + -
104B ILE* 3.1 33.3 + - + +
105B ILE* 3.0 29.3 + - - +
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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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100B GLN 3.4 8.3 + - - +
101B MET* 1.3 69.0 - - - +
103B ASP* 1.3 66.9 + - - +
105B ILE* 3.2 28.7 + - + +
106B THR* 2.9 42.1 + - - -
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Residues in contact with ASP 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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76B PHE* 4.9 9.2 - - + -
101B MET* 5.1 1.1 - - + -
102B GLN* 1.3 79.4 - - - +
104B ILE* 1.3 64.1 + - + +
106B THR* 3.6 5.3 + - - -
107B ALA* 3.1 23.0 + - - +
134B PHE* 3.9 30.9 - - + -
114C LEU* 4.0 2.9 - - - +
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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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73B VAL* 4.0 17.9 - - + -
76B PHE* 3.5 44.0 - - + -
82B LEU* 4.1 17.5 - - + -
92B VAL* 3.5 26.2 - - + -
96B ALA* 3.4 19.1 - - + -
101B MET* 3.1 31.6 + - + +
103B ASP* 1.3 74.4 - - + +
105B ILE* 1.3 66.3 + - - +
107B ALA* 3.2 6.2 + - - +
108B CYS* 3.0 23.0 + - - -
134B PHE* 5.7 0.2 - - + -
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Residues in contact with ILE 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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93B LEU* 4.0 12.9 - - + +
96B ALA* 3.8 29.4 - - + +
97B THR* 3.9 19.5 - - + +
100B GLN* 4.7 4.3 - - - -
101B MET 3.0 23.7 + - - +
102B GLN* 3.2 35.0 + - - +
104B ILE* 1.3 76.7 - - - +
106B THR* 1.3 62.7 + - - +
108B CYS* 3.3 4.7 + - - +
109B HIS* 3.1 46.9 + - + +
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Residues in contact with THR 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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102B GLN* 2.9 29.0 + - - -
103B ASP* 4.0 2.2 - - - -
105B ILE* 1.3 75.9 - - - +
107B ALA* 1.3 59.0 + - - +
109B HIS* 3.2 8.3 + - + +
110B ALA* 2.8 28.6 + - - +
113C SER* 3.6 28.9 - - - +
114C LEU* 3.6 20.9 - - + +
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Residues in contact with ALA 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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82B LEU* 3.8 17.5 - - + -
84B LEU* 3.8 3.9 - - + +
103B ASP 3.1 18.4 + - - +
104B ILE 3.2 5.3 + - - +
106B THR* 1.3 75.6 - - - +
108B CYS* 1.3 56.9 - - - +
110B ALA* 3.3 5.7 + - - +
111B LEU* 2.9 28.2 + - - +
132B ILE* 3.6 28.4 - - + +
134B PHE* 4.5 3.8 - - + -
114C LEU* 3.5 14.0 - - + +
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Residues in contact with CYS 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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84B LEU* 4.1 11.0 - - - -
89B VAL* 3.8 23.2 - - + +
92B VAL* 3.7 29.8 - - - -
93B LEU* 3.7 33.0 - - + -
104B ILE* 3.0 19.7 + - - -
105B ILE 3.6 7.2 - - - +
106B THR 3.2 0.2 - - - -
107B ALA* 1.3 77.2 - - - +
109B HIS* 1.3 62.4 + - - +
111B LEU* 3.2 3.3 + - - +
112B LYS* 3.0 29.2 + - - +
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Residues in contact with HIS 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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93B LEU* 3.8 27.3 - - + +
105B ILE* 3.1 40.4 + - + +
106B THR* 3.7 9.7 - - + +
108B CYS* 1.3 76.5 - - - +
110B ALA* 1.3 58.8 + - - +
112B LYS* 3.2 11.9 + - + +
113B SER* 2.8 30.6 + - - -
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Residues in contact with ALA 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 THR 2.8 21.6 + - - +
107B ALA* 3.4 8.7 - - - +
109B HIS* 1.3 72.7 - - - +
111B LEU* 1.3 62.2 + - - +
113B SER* 2.7 27.2 + - - -
114B LEU* 3.6 4.0 + - - +
110C ALA* 3.8 35.2 - - + +
113C SER* 3.9 9.2 - - - +
114C LEU* 4.7 7.2 - - + -
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Residues in contact with LEU 111 (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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84B LEU* 3.8 30.5 - - + -
85B SER 4.3 8.7 - - - +
86B PRO* 4.7 1.8 - - + -
89B VAL* 4.2 20.2 - - + -
107B ALA 2.9 13.5 + - - +
108B CYS* 3.6 7.4 - - - +
110B ALA* 1.3 77.8 - - - +
112B LYS* 1.3 63.0 + - - +
114B LEU* 3.0 39.4 + - + +
115B ALA* 4.2 1.0 + - - +
128B ALA* 3.7 29.8 - - + +
130B SER* 3.9 24.5 - - - -
132C ILE* 5.5 0.2 - - + -
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Residues in contact with LYS 112 (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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89B VAL* 4.2 23.3 - - + -
90B ASP* 2.8 32.0 + - - -
93B LEU* 4.5 13.0 - - + +
108B CYS 3.0 24.6 + - - +
109B HIS* 3.7 16.6 - - + +
111B LEU* 1.3 77.5 - - + +
113B SER* 1.3 62.4 + - - +
114B LEU 3.0 1.6 + - - -
115B ALA* 3.0 22.2 + - - +
126B GLY 6.3 0.9 - - - +
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Residues in contact with SER 113 (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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109B HIS 2.8 14.4 + - - -
110B ALA* 2.7 20.7 + - - -
112B LYS* 1.3 75.3 - - - +
114B LEU* 1.3 61.1 + - - +
115B ALA 3.2 6.5 + - - +
106C THR* 3.7 15.2 - - - +
110C ALA* 3.8 15.2 - - - +
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Residues in contact with LEU 114 (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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110B ALA 4.1 8.1 - - - +
111B LEU* 3.0 34.2 + - + +
112B LYS 3.0 1.6 - - - -
113B SER* 1.3 81.0 + - - +
115B ALA* 1.3 59.1 + - - +
128B ALA* 4.2 18.2 - - + -
103C ASP* 4.1 8.1 - - - +
106C THR* 3.9 14.6 - - + +
107C ALA* 3.6 35.4 - - + +
110C ALA* 4.8 4.3 - - + -
132C ILE* 4.3 22.7 - - + -
134C PHE* 4.4 11.6 - - + -
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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