Contacts of the helix formed by residues 76 - 96 (chain D) in PDB entry 5BOU
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 76 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C GLN* 3.1 25.0 - - - +
119C THR* 4.5 0.3 + - - -
120C GLN* 4.3 3.3 + - - +
151C SER 5.1 1.0 - - - +
73D LEU* 3.1 23.8 + - - +
75D ALA* 1.3 78.0 - - - +
77D ALA* 1.3 60.7 + - - +
78D ARG 3.3 0.7 + - - -
79D SER* 3.8 8.9 + - - -
80D MET* 3.7 14.7 - - - +
128D ARG* 2.7 38.7 + - - -
130D PHE* 3.8 13.7 - - + -
131D GLY* 3.0 19.7 + - - +
132D VAL* 4.1 12.6 - - + -
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Residues in contact with ALA 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D MET* 3.7 28.5 - - + -
74D THR 3.2 15.3 + - - +
75D ALA 3.1 0.8 - - - -
76D ASP* 1.3 77.4 - - - +
78D ARG* 1.3 57.9 + - - +
79D SER 3.4 0.2 - - - -
80D MET* 3.1 7.9 + - - +
81D ILE* 2.8 33.4 + - + +
132D VAL* 3.9 21.4 - - + +
134D LEU* 4.3 10.1 - - + -
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Residues in contact with ARG 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C ARG* 6.1 4.5 - - + +
113C GLY* 6.5 2.2 - - - -
116C GLN* 6.1 1.3 - - + +
154C TYR* 4.9 23.6 - - + -
57D GLU* 3.1 40.4 + - - +
58D LYS* 5.8 0.4 - - - +
60D VAL* 4.1 13.5 - - - +
70D MET* 3.9 24.3 - - - +
74D THR* 3.8 19.5 + - - -
75D ALA* 3.5 21.4 - - - +
76D ASP 3.3 1.6 - - - -
77D ALA* 1.3 77.0 - - - +
79D SER* 1.3 57.9 + - - +
81D ILE* 3.4 10.8 + - - +
82D GLU* 3.0 27.9 + - - +
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Residues in contact with SER 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C GLN* 5.2 9.9 + - - +
120C GLN* 4.5 5.4 + - - -
75D ALA 4.8 0.4 + - - -
76D ASP 3.8 4.8 + - - -
78D ARG* 1.3 75.8 - - - +
80D MET* 1.3 62.5 + - - +
82D GLU* 3.6 7.8 - - - +
83D HIS* 3.0 28.6 + - - +
111D LEU* 4.7 3.2 - - - +
130D PHE* 3.7 23.0 - - - -
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Residues in contact with MET 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D ASP 3.7 10.3 - - - +
77D ALA* 3.4 8.1 - - - +
79D SER* 1.3 75.9 + - - +
81D ILE* 1.3 60.2 + - - +
83D HIS* 3.5 2.8 + - - +
84D ALA* 3.0 28.4 + - - +
108D VAL* 3.8 24.8 - - + +
111D LEU* 4.5 9.9 - - + -
112D ALA* 6.4 1.3 - - + -
130D PHE* 3.7 45.1 - - + -
132D VAL* 3.6 33.9 - - + +
134D LEU* 3.7 31.6 - - + -
150D ALA* 5.7 4.7 - - + +
151D GLU 5.9 5.4 - - - +
152D PRO* 6.4 0.9 - - + -
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Residues in contact with ILE 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60D VAL* 3.5 35.7 - - + -
61D GLU 4.7 0.2 - - - +
62D ILE* 4.7 7.4 - - + -
68D CYS* 3.7 32.5 - - + -
70D MET* 4.5 13.0 - - + -
77D ALA 2.8 24.0 + - - +
78D ARG* 3.6 11.0 - - - +
79D SER 3.4 0.2 - - - -
80D MET* 1.3 74.7 - - - +
82D GLU* 1.3 59.6 + - - +
84D ALA* 3.2 5.1 + - + +
85D ARG* 2.8 55.4 + - + +
134D LEU* 4.9 8.3 - - + -
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Residues in contact with GLU 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D ARG 3.0 18.1 + - - +
79D SER* 3.6 9.6 - - - +
81D ILE* 1.3 77.9 - - - +
83D HIS* 1.3 53.2 + - - +
85D ARG* 3.5 14.9 + - - +
86D THR* 2.8 54.0 + - - +
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Residues in contact with HIS 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D SER 3.0 18.7 + - - +
80D MET 3.7 4.3 - - - +
82D GLU* 1.3 76.3 - - - +
84D ALA* 1.3 60.7 + - - +
86D THR* 3.4 7.0 + - - -
87D ALA* 2.8 30.8 + - + +
107D SER* 2.9 45.9 + - - -
108D VAL* 4.2 6.7 - - + -
111D LEU* 3.7 38.2 - - + +
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Residues in contact with ALA 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D ILE* 3.8 30.3 - - + -
80D MET 3.0 18.1 + - - +
81D ILE* 3.2 6.9 + - + +
83D HIS* 1.3 77.5 - - - +
85D ARG* 1.3 57.8 + - - +
87D ALA* 3.3 1.2 + - - -
88D ALA* 2.9 27.4 + - - +
104D LEU* 3.3 17.4 - - + +
108D VAL* 3.8 22.0 - - + -
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Residues in contact with ARG 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57D GLU* 4.9 5.5 + - - -
60D VAL* 3.5 17.0 - - - +
61D GLU* 2.8 29.1 + - - +
62D ILE* 3.5 28.7 - - - +
81D ILE* 2.8 39.9 + - + +
82D GLU* 3.8 14.6 + - - +
84D ALA* 1.3 72.1 - - - +
86D THR* 1.3 58.4 + - - +
88D ALA* 3.4 1.8 + - - +
89D VAL* 3.0 37.4 + - + +
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Residues in contact with THR 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82D GLU* 2.8 38.5 + - - +
83D HIS* 3.7 7.2 - - - -
85D ARG* 1.3 76.6 - - - +
87D ALA* 1.3 55.7 + - - +
89D VAL* 4.1 3.4 - - - +
90D THR* 2.5 48.2 + - - +
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Residues in contact with ALA 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D HIS* 2.8 24.9 + - + +
84D ALA* 3.7 3.8 - - - +
86D THR* 1.3 74.1 - - - +
88D ALA* 1.3 63.5 + - - +
90D THR* 4.0 4.3 - - - -
91D HIS* 3.1 26.0 + - - +
99D ILE* 4.2 1.8 - - - +
104D LEU* 4.2 11.4 - - + -
107D SER* 3.8 23.8 - - - +
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Residues in contact with ALA 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D ILE* 4.3 9.0 - - + +
63D ASP* 3.8 29.0 - - + +
84D ALA 2.9 17.7 + - - +
85D ARG 3.7 4.3 - - - +
87D ALA* 1.3 77.2 - - - +
89D VAL* 1.3 61.2 + - + +
92D ASN* 3.3 13.7 + - - +
99D ILE* 3.3 45.6 - - + +
104D LEU* 4.3 0.8 - - + +
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Residues in contact with VAL 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D ILE 5.6 2.0 - - - +
63D ASP* 5.4 8.1 - - - +
85D ARG* 3.0 22.9 + - + +
86D THR* 4.1 3.8 - - - +
88D ALA* 1.3 75.5 - - + +
90D THR* 1.3 61.8 + - - +
92D ASN* 3.3 8.9 + - + +
93D LEU* 3.0 29.1 + - + +
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Residues in contact with THR 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D THR* 2.5 41.3 + - - +
87D ALA* 4.0 5.4 - - - -
89D VAL* 1.3 75.5 - - - +
91D HIS* 1.3 57.5 + - - +
93D LEU* 3.1 12.0 + - + +
94D TYR* 2.9 62.6 + - + +
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Residues in contact with HIS 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87D ALA 3.1 12.6 + - - +
90D THR* 1.3 76.8 - - - +
92D ASN* 1.3 58.5 + - - +
94D TYR* 4.6 3.1 - - - -
95D TYR* 2.8 56.6 + + - +
97D GLU* 3.0 37.5 + - + +
98D ASP 4.0 0.4 + - - -
99D ILE* 3.3 46.0 - - + +
100D ASN 5.5 1.6 - - - -
103D SER* 6.2 3.5 - - - -
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Residues in contact with ASN 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D ASP* 5.7 2.9 - - - +
88D ALA 3.3 11.1 + - - +
89D VAL* 3.3 12.8 + - - +
90D THR 3.3 0.4 - - - -
91D HIS* 1.3 78.8 - - - +
93D LEU* 1.3 59.4 + - - +
96D ASP* 2.8 30.4 + - - +
97D GLU* 3.2 38.8 + - - +
98D ASP* 4.8 5.4 + - - +
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Residues in contact with LEU 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D VAL* 3.0 16.3 + - + +
90D THR* 3.1 13.9 + - + +
92D ASN* 1.3 81.7 + - - +
94D TYR* 1.3 75.6 + - + +
96D ASP* 4.4 1.9 + - - +
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Residues in contact with TYR 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90D THR* 2.9 43.6 + - + +
91D HIS* 4.9 1.3 - - - -
93D LEU* 1.3 92.8 - - + +
95D TYR* 1.3 89.6 - + + +
96D ASP 3.9 0.2 - - - -
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Residues in contact with TYR 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D HIS* 2.8 52.9 + + - +
94D TYR* 1.3 99.1 - + + +
96D ASP* 1.3 74.4 + - - +
97D GLU* 3.3 27.0 + - + +
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Residues in contact with ASP 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92D ASN* 2.8 28.5 + - - +
93D LEU 4.4 2.1 + - - +
94D TYR 3.9 0.6 - - - -
95D TYR* 1.3 75.6 - - - +
97D GLU* 1.3 57.2 + - - +
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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
------------------------------------------------------------
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