Contacts of the helix formed by residues 77 - 93 (chain B) in PDB entry 5EWL
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 ASP 77 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A PHE* 4.2 0.7 - - - -
329A CYS 3.1 35.3 - - - +
330A VAL 3.4 2.1 + - - -
331A GLY* 3.1 13.6 + - - -
332A ASN 3.3 17.0 - - - +
333A THR* 3.6 9.9 - - + +
75B GLU* 3.5 4.5 - - - +
76B THR* 1.3 80.3 - - - +
78B PRO* 1.4 70.6 - - + +
79B LYS* 3.2 10.0 + - - +
80B SER* 2.6 42.7 + - - -
81B ILE* 3.2 20.4 + - - +
111B ILE* 4.2 1.1 - - - -
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Residues in contact with PRO 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ALA* 6.3 0.2 - - + -
79A CYS* 4.7 2.0 - - - -
110A THR* 4.6 25.6 - - + +
113A PHE* 3.6 42.6 - - + -
114A TYR* 3.7 9.0 - - + +
329A CYS* 4.8 2.0 - - + -
77B ASP* 1.4 87.4 - - + +
79B LYS* 1.4 56.9 + - - +
81B ILE* 3.5 1.2 + - - +
82B ILE* 2.9 46.7 + - + +
111B ILE* 3.8 19.5 - - + -
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Residues in contact with LYS 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A LEU* 3.8 17.8 - - + +
79A CYS* 4.0 24.2 - - + -
80A GLU* 2.8 37.3 + - + +
329A CYS* 3.8 12.8 - - + +
330A VAL* 3.7 23.6 - - + -
77B ASP* 3.2 9.6 + - - +
78B PRO* 1.4 77.1 - - - +
80B SER* 1.3 58.3 + - - +
82B ILE* 4.0 0.8 - - - +
83B THR* 2.8 54.2 + - - +
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Residues in contact with SER 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A VAL* 3.9 17.0 - - - +
73B MET* 4.4 4.3 - - - -
75B GLU* 3.5 27.9 - - - +
77B ASP* 2.6 32.1 + - - -
79B LYS* 1.3 75.1 - - - +
81B ILE* 1.3 54.0 + - - +
83B THR* 3.7 4.4 - - - +
84B ARG* 2.8 36.6 + - - +
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Residues in contact with ILE 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B MET* 3.7 25.4 - - + -
76B THR* 3.3 37.2 - - + +
77B ASP 3.2 12.8 + - - +
80B SER* 1.3 70.8 - - - +
82B ILE* 1.3 67.8 + - - +
84B ARG* 3.9 0.2 - - - +
85B ILE* 3.1 36.3 + - + +
99B PHE* 4.4 4.7 - - + -
108B ILE* 4.0 26.5 - - + -
111B ILE* 3.8 19.5 - - + -
112B LEU* 4.1 10.5 - - + -
115B ILE* 3.7 18.4 - - + -
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Residues in contact with ILE 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ILE* 3.5 32.8 - - + -
75A ALA* 4.1 26.0 - - + -
76A LEU* 4.0 19.5 - - + -
78B PRO* 2.9 38.4 + - + +
79B LYS* 4.0 2.5 - - - +
81B ILE* 1.3 71.7 - - - +
83B THR* 1.4 57.1 + - - +
85B ILE* 4.0 1.6 - - - +
86B CYS* 3.0 38.4 + - - -
111B ILE* 4.4 5.2 - - + -
114B PHE* 4.2 14.4 - - + -
115B ILE* 3.8 28.4 - - + +
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Residues in contact with THR 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A LEU* 3.7 11.0 - - - +
79B LYS* 2.8 47.1 + - - +
80B SER* 3.8 4.9 - - - +
82B ILE* 1.4 69.4 - - - +
84B ARG* 1.3 66.0 + - - +
86B CYS* 3.4 5.8 + - - -
87B ASP* 3.0 46.3 + - - +
322B TYR* 5.2 5.0 + - - +
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Residues in contact with ARG 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B ILE* 5.1 3.4 - - + -
71B VAL* 3.4 26.8 - - + +
72B ALA 3.3 26.3 + - - +
73B MET* 3.6 29.0 - - + +
80B SER 2.8 21.6 + - - +
81B ILE 3.9 2.0 - - - +
83B THR* 1.3 73.4 - - - +
85B ILE* 1.4 65.1 + - + +
87B ASP* 3.3 10.3 + - - +
88B LEU* 3.1 57.2 + - + +
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Residues in contact with ILE 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B ILE* 3.6 26.5 - - + -
73B MET* 5.7 0.4 - - + -
81B ILE* 3.1 17.1 + - + +
82B ILE 4.1 2.0 - - - +
84B ARG* 1.4 74.8 - - + +
86B CYS* 1.3 57.4 + - - +
88B LEU* 3.2 10.3 + - + +
89B MET* 3.0 55.5 + - + +
97B VAL* 4.4 16.8 - - + -
99B PHE* 4.8 2.0 - - + -
112B LEU* 3.6 30.3 - - + -
115B ILE* 3.8 31.6 - - + -
123B ILE* 4.5 5.6 - - + -
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Residues in contact with CYS 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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72A ILE* 4.2 4.5 - - - -
82B ILE* 3.0 40.2 + - - +
83B THR* 3.8 4.0 - - - +
84B ARG 3.3 0.2 - - - -
85B ILE* 1.3 78.0 - - - +
87B ASP* 1.3 56.9 + - - +
89B MET* 3.5 4.5 + - - +
90B SER* 3.2 26.0 + - - -
115B ILE* 5.5 4.0 - - - -
119B THR* 5.1 0.2 - - - -
319B SER 5.1 0.5 - - - +
320B SER* 5.6 0.7 - - - -
321B CYS* 2.0 53.6 + - + -
322B TYR* 3.7 23.2 - - + +
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Residues in contact with ASP 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B THR* 3.0 37.6 + - - +
84B ARG* 3.3 10.4 + - - +
86B CYS* 1.3 74.5 - - - +
88B LEU* 1.3 65.8 + - + +
90B SER* 3.2 7.2 + - - -
91B ASP* 3.0 35.8 + - - +
322B TYR* 4.4 10.0 + - - -
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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
----------------------------------------------------------
38B ALA* 3.8 15.9 - - + -
40B ILE* 3.8 28.5 - - + -
69B GLU* 5.8 3.4 - - - +
71B VAL* 3.8 30.7 - - + -
84B ARG* 3.1 42.8 + - + +
85B ILE* 3.5 9.6 - - + +
87B ASP* 1.3 79.0 - - + +
89B MET* 1.3 58.9 + - + +
91B ASP* 4.6 7.2 - - - +
92B ARG* 3.2 21.7 + - - +
94B ILE* 3.6 20.9 - - + +
97B VAL* 6.0 1.3 - - + -
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Residues in contact with MET 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ILE* 3.0 37.8 + - + +
86B CYS 3.6 7.6 - - - +
87B ASP 3.2 0.2 - - - -
88B LEU* 1.3 75.2 - - - +
90B SER* 1.4 61.7 + - - +
93B LYS* 3.2 24.2 + - - +
94B ILE* 4.7 17.5 - - + +
97B VAL* 5.2 1.3 - - + -
115B ILE* 4.6 2.0 - - + -
119B THR* 3.4 33.0 - - + +
121B THR* 3.3 35.4 - - + +
123B ILE* 5.8 0.2 - - + -
318B LYS* 3.9 22.1 - - - +
319B SER* 3.8 16.7 - - - -
320B SER 5.0 2.2 - - - +
321B CYS* 3.9 14.1 - - - -
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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 CYS 3.2 11.5 + - - -
87B ASP* 3.4 12.9 - - - -
89B MET* 1.4 78.8 - - - +
91B ASP* 1.4 67.8 + - - +
319B SER* 3.3 26.9 + - - +
320B SER* 5.8 0.4 - - - -
322B TYR* 6.3 2.7 - - - -
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Residues in contact with ASP 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 ASP* 3.0 23.5 + - - +
88B LEU* 4.6 7.5 - - - +
90B SER* 1.4 88.8 + - - +
92B ARG* 1.3 65.8 - - + +
93B LYS* 3.5 2.1 + - - +
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Residues in contact with ARG 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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34B SER* 4.9 9.1 + - - -
35B ILE* 4.4 1.6 - - - +
36B GLY* 3.5 24.4 - - - +
67B ARG* 3.2 26.0 + - - +
69B GLU* 2.9 44.0 + - + +
88B LEU* 3.2 12.3 + - + +
91B ASP* 1.3 78.6 - - + +
93B LYS* 1.3 79.0 + - - +
94B ILE* 3.8 11.7 - - + -
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Residues in contact with LYS 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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36B GLY* 4.0 3.6 + - - -
88B LEU 3.9 0.6 + - - -
89B MET 3.2 18.9 + - - -
91B ASP 3.5 2.1 - - - +
92B ARG* 1.3 101.1 + - - +
94B ILE* 1.3 61.1 + - - +
95B GLN 3.9 1.6 + - - -
317B PRO* 3.7 31.2 - - + +
318B LYS 5.4 0.2 - - - -
319B SER* 5.7 4.5 - - - +
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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