Contacts of the helix formed by residues 85 - 98 (chain A) in PDB entry 6B0B
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 CYS 85 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A HIS* 3.7 11.4 - - + +
83A SER 3.7 0.8 + - - -
84A PRO* 1.3 79.1 - - - +
86A SER* 1.3 67.1 + - - +
87A SER* 3.6 21.5 - - - -
88A CYS* 3.8 0.4 - - - -
89A ALA* 3.2 19.4 + - - +
112A TYR* 4.7 11.3 - - + +
119A GLN* 3.2 32.5 - - - +
122A GLY* 4.9 1.7 - - - +
123A LEU* 6.2 0.2 - - - -
200A ZN 2.3 37.3 - - - -
85E CYS* 6.1 0.9 - - - -
87E SER* 4.7 6.3 - - - +
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Residues in contact with SER 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A CYS* 1.3 78.1 - - - +
87A SER* 1.3 66.1 + - - -
89A ALA* 3.2 4.3 + - - +
90A TRP* 3.0 28.0 + - - -
118A PRO* 3.8 31.8 - - - +
119A GLN* 3.7 11.1 - - - +
122A GLY* 4.4 11.2 - - - -
86E SER* 2.4 30.8 + - - -
87E SER* 4.2 6.2 + - - -
118E PRO* 4.5 8.5 - - - -
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Residues in contact with SER 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A HIS* 5.4 0.7 - - - -
85A CYS* 3.6 12.3 - - - -
86A SER* 1.3 83.4 + - - +
88A CYS* 1.3 59.4 + - - +
90A TRP* 3.1 6.1 + - - +
91A GLU 2.9 22.3 + - - -
85E CYS* 4.8 6.8 - - - -
86E SER* 4.3 2.1 + - - -
114E HIS* 3.3 23.0 + - - -
116E CYS* 4.2 1.3 - - - -
118E PRO* 4.1 11.0 - - - -
119E GLN* 3.2 39.5 + - - -
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Residues in contact with CYS 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A HIS* 3.1 21.1 - - - -
56A GLU* 4.1 24.2 - - + +
57A ILE* 4.0 11.8 - - + +
60A ILE* 5.2 0.5 - - - +
85A CYS* 3.8 4.1 - - - +
86A SER 3.4 0.4 - - - -
87A SER* 1.3 73.3 - - - +
89A ALA* 1.3 59.6 + - - +
91A GLU* 3.3 9.6 + - - +
92A LEU* 2.8 31.7 + - - +
200A ZN 2.3 35.2 - - - -
114E HIS* 4.0 17.3 - - - -
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Residues in contact with ALA 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A PRO* 4.8 12.4 - - + +
85A CYS 3.2 21.7 + - - +
86A SER 3.2 2.6 + - - +
87A SER 3.2 0.4 - - - -
88A CYS* 1.3 79.3 - - - +
90A TRP* 1.3 56.9 + - - +
92A LEU* 3.3 9.2 + - - +
93A VAL* 2.9 28.2 + - - +
122A GLY 3.2 26.2 - - - +
123A LEU* 4.9 1.3 - - - +
126A LEU* 3.8 19.9 - - + +
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Residues in contact with TRP 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A SER 3.0 24.2 + - - -
87A SER 3.1 8.1 + - - +
89A ALA* 1.3 77.5 - - - +
91A GLU* 1.3 60.0 + - - +
93A VAL* 3.1 14.4 - - + +
94A ASP* 2.9 39.2 + - - +
121A ASP* 5.0 10.2 + - + -
122A GLY* 4.0 22.3 - - - -
125A LEU* 3.5 37.7 - - + -
116E CYS* 3.6 23.6 - - + -
117E LYS* 3.5 44.6 - - + -
118E PRO* 3.3 33.6 - - + +
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Residues in contact with GLU 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A ILE* 4.9 15.7 - - + +
60A ILE* 3.9 18.4 - - + +
87A SER 2.9 8.6 + - - +
88A CYS* 3.3 11.6 + - - +
90A TRP* 1.3 76.4 - - - +
92A LEU* 1.3 57.3 + - - +
94A ASP* 3.4 11.8 + - - +
95A PHE* 2.9 31.7 + - - +
114E HIS* 3.7 46.9 - - + +
116E CYS* 4.9 1.5 - - - -
1G U 4.5 22.4 + - - +
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Residues in contact with LEU 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A LEU* 6.2 0.2 - - + -
56A GLU* 4.2 24.0 - - + -
59A PHE* 3.6 24.5 - - + -
60A ILE* 3.6 24.8 - - + +
84A PRO* 5.7 4.7 - - + -
88A CYS 2.8 14.5 + - - +
89A ALA* 3.4 9.0 - - - +
90A TRP 3.2 0.2 - - - -
91A GLU* 1.3 75.5 - - - +
93A VAL* 1.3 57.3 + - - +
95A PHE* 3.2 5.3 + - + +
96A ILE* 2.9 30.2 + - + +
104A LEU* 3.8 28.0 - - + -
106A ILE* 4.5 10.8 - - + -
126A LEU* 4.3 20.6 - - + -
131A VAL* 5.6 1.6 - - + -
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Residues in contact with VAL 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A ALA 2.9 15.6 + - - +
90A TRP* 3.1 33.4 - - + +
92A LEU* 1.3 77.0 - - - +
94A ASP* 1.3 65.9 + - - +
96A ILE* 3.2 15.4 - - + +
97A LYS* 2.9 42.5 + - + +
125A LEU* 4.5 14.4 - - + -
126A LEU* 4.3 16.1 - - + +
129A SER* 4.2 19.5 - - - +
130A GLN* 4.3 10.3 - - + +
131A VAL* 6.4 1.3 - - + -
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Residues in contact with ASP 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A TRP* 2.9 25.9 + - - +
91A GLU* 3.8 13.9 - - - +
93A VAL* 1.3 87.2 - - - +
95A PHE* 1.3 60.3 + - - +
97A LYS* 3.5 15.2 + - - +
98A ALA* 3.5 20.1 + - - +
114E HIS 5.4 1.7 - - - +
115E TRP 5.4 1.4 - - - +
116E CYS* 4.5 16.2 - - - +
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Residues in contact with PHE 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A PHE* 5.7 5.4 - + - -
60A ILE* 3.9 42.8 - - + -
63A ILE* 3.9 33.4 - - + -
64A LYS* 4.5 24.9 - - + -
68A LEU* 4.8 1.8 - - + -
91A GLU* 2.9 19.0 + - - +
92A LEU* 3.2 6.0 + - + +
94A ASP* 1.3 77.0 - - - +
96A ILE* 1.3 71.1 + - + +
98A ALA* 3.7 4.5 + - + -
99A HIS* 3.2 56.0 + + + +
102A LEU* 5.6 5.2 - - + -
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Residues in contact with ILE 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A VAL* 5.8 0.9 - - + -
92A LEU* 2.9 15.0 + - + +
93A VAL* 3.2 21.8 - - + +
94A ASP 3.2 0.2 - - - -
95A PHE* 1.3 86.7 - - + +
97A LYS* 1.3 65.8 + - - +
98A ALA 3.2 0.7 - - - -
99A HIS* 3.0 23.8 - - + +
100A ASP* 4.7 1.0 - - - -
102A LEU* 3.8 38.5 - - + +
103A ASN* 5.6 0.2 - - - -
104A LEU* 4.5 22.7 - - + +
130A GLN* 3.8 33.6 - - + +
131A VAL* 4.8 15.0 - - + -
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Residues in contact with LYS 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A VAL* 2.9 30.8 + - + +
94A ASP* 3.9 17.6 + - - +
95A PHE 3.4 0.4 - - - -
96A ILE* 1.3 82.5 - - + +
98A ALA* 1.3 61.6 + - - +
99A HIS 3.6 2.1 + - - -
100A ASP* 4.7 4.7 + - - +
130A GLN* 4.7 16.6 - - - +
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Residues in contact with ALA 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A ASP 3.5 13.3 + - - +
95A PHE* 4.1 2.9 - - - +
96A ILE 3.2 0.8 - - - -
97A LYS* 1.3 78.1 - - - +
99A HIS* 1.3 79.3 + - + +
100A ASP 3.9 1.4 + - - -
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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