Contacts of the helix formed by residues 80 - 93 (chain B) in PDB entry 4U0L
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 SER 80 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79B LEU* 1.3 75.5 - - - +
81B ASP* 1.3 59.1 + - - +
82B SER* 3.3 9.6 + - - -
83B GLU* 2.8 41.5 + - - +
84B GLN* 2.9 27.1 + - - +
163B LYS* 4.9 2.1 - - - +
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Residues in contact with ASP 81 (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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79B LEU 3.9 0.2 + - - -
80B SER* 1.3 72.6 - - - +
82B SER* 1.3 57.7 + - - +
84B GLN* 3.5 19.8 + - - +
85B ARG* 3.0 46.0 + - - +
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Residues in contact with SER 82 (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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80B SER* 3.3 11.0 + - - -
81B ASP* 1.3 74.1 - - - +
83B GLU* 1.3 59.5 + - - +
85B ARG* 3.2 24.4 + - - +
86B GLU* 2.7 37.3 + - - +
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Residues in contact with GLU 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B LEU* 3.5 23.1 - - + +
80B SER* 2.8 44.8 + - - +
82B SER* 1.3 84.6 + - - +
84B GLN* 1.3 55.9 + - - +
86B GLU* 3.3 13.7 + - - +
87B VAL* 2.9 32.1 + - - +
156B LEU* 4.0 19.3 - - + +
159B ASP* 4.6 6.1 - - - +
163B LYS* 3.2 27.6 + - - -
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Residues in contact with GLN 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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68B GLN* 6.0 1.6 - - + -
71B VAL* 4.0 13.8 - - + +
72B SER* 4.2 19.9 - - - -
76B ILE* 3.4 20.4 - - + +
77B LYS* 2.8 29.0 + - - +
79B LEU* 2.7 24.8 + - + +
80B SER 2.9 16.7 + - - +
81B ASP* 3.7 21.8 + - - +
82B SER 3.3 0.2 - - - -
83B GLU* 1.3 72.5 - - - +
85B ARG* 1.3 65.9 + - - +
87B VAL* 3.2 7.4 + - - +
88B ALA* 3.0 24.7 + - - +
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Residues in contact with ARG 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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64B PHE* 3.9 20.7 - - + -
68B GLN* 4.0 22.4 - - - +
81B ASP* 3.0 29.2 + - - +
82B SER* 3.3 34.0 - - - +
84B GLN* 1.3 74.7 - - - +
86B GLU* 1.3 57.6 + - - +
88B ALA* 3.3 7.3 + - - +
89B LYS* 2.9 31.8 + - + +
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Residues in contact with GLU 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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82B SER 2.7 15.5 + - - +
83B GLU* 3.3 20.8 - - - +
85B ARG* 1.3 74.1 - - - +
87B VAL* 1.3 57.1 + - - +
89B LYS* 3.1 8.0 + - + +
90B LEU* 2.8 45.5 + - + +
152B SER* 4.5 13.7 + - - -
156B LEU* 3.8 25.1 - - + +
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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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71B VAL* 4.5 4.7 - - + -
76B ILE* 4.1 28.3 - - + -
79B LEU* 4.0 12.8 - - + -
83B GLU 2.9 17.2 + - - +
84B GLN 3.2 6.7 + - - +
86B GLU* 1.3 75.4 - - - +
88B ALA* 1.3 58.4 + - - +
90B LEU* 3.3 8.2 + - - +
91B ILE* 3.0 45.7 + - + +
153B LEU* 4.6 11.0 - - + -
156B LEU* 3.6 32.3 - - + -
157B LEU* 4.7 7.0 - - + -
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Residues in contact with ALA 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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64B PHE* 3.7 17.2 - - + -
67B ILE* 3.7 13.2 - - + +
68B GLN* 4.0 26.0 - - + -
71B VAL* 4.0 11.4 - - + +
84B GLN 3.0 15.9 + - - +
85B ARG* 3.6 6.3 - - - +
87B VAL* 1.3 77.2 - - - +
89B LYS* 1.3 52.2 + - - +
91B ILE* 3.3 3.3 + - - +
92B TYR* 2.7 35.3 + - - +
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Residues in contact with LYS 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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64B PHE* 3.7 15.2 - - + -
85B ARG* 2.9 15.7 + - + +
86B GLU* 3.4 12.3 - - + +
88B ALA* 1.3 73.8 - - - +
90B LEU* 1.3 61.3 + - + +
92B TYR* 3.1 7.5 + - + -
93B GLU* 2.6 73.1 + - + +
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Residues in contact with LEU 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 GLU* 2.8 28.8 + - + +
87B VAL* 3.4 8.7 - - - +
89B LYS* 1.3 79.6 - - + +
91B ILE* 1.3 61.6 + - - +
93B GLU* 3.9 11.3 - - - +
94B MET* 3.3 26.3 + - - +
149B ILE* 4.2 25.9 - - + +
152B SER* 3.8 17.3 - - - -
153B LEU* 3.5 52.7 - - + +
156B LEU* 4.2 11.0 - - + -
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Residues in contact with ILE 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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50B ALA* 4.5 16.8 - - + +
53B ILE* 4.2 31.9 - - + -
54B ALA* 4.4 14.6 - - + -
57B VAL* 4.4 14.5 - - + +
67B ILE* 4.0 13.9 - - + -
71B VAL* 4.5 10.1 - - + -
76B ILE* 5.6 0.4 - - + -
87B VAL* 3.0 35.7 + - + +
88B ALA 3.6 6.5 - - - +
90B LEU* 1.3 72.7 - - - +
92B TYR* 1.3 69.2 + - - +
94B MET* 3.4 24.9 - - + +
99B ARG* 3.9 7.8 + - - +
102B PHE* 5.7 3.1 - - + -
153B LEU* 4.8 12.3 - - + -
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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
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57B VAL* 5.4 1.9 - - + +
62B LEU 3.9 11.2 - - - -
63B THR* 4.3 2.7 + - - -
64B PHE* 3.8 37.9 - + + -
67B ILE* 3.7 28.0 - - + +
88B ALA 2.7 21.0 + - - +
89B LYS* 3.1 10.7 + - + +
91B ILE* 1.3 74.3 - - - +
93B GLU* 1.3 67.9 + - + +
94B MET 2.9 7.4 + - - +
99B ARG* 3.7 10.7 + - - -
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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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89B LYS* 2.6 60.4 + - - +
90B LEU* 3.9 10.3 - - - +
92B TYR* 1.3 79.1 - - + +
94B MET* 1.3 60.8 + - - +
95B ASP* 3.7 10.4 + - - +
149B ILE* 4.1 22.0 - - + +
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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