Contacts of the helix formed by residues 79 - 98 (chain B) in PDB entry 6TOS
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 THR 79 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B HIS 3.9 17.3 - - - +
77B MET* 2.9 7.0 + - - +
78B ARG* 1.3 77.3 - - - +
80B VAL* 1.3 64.1 + - - +
81B THR* 3.8 7.9 + - - -
82B ASN* 3.3 25.6 + - - +
83B TYR* 3.0 27.2 + - - -
158B ALA* 5.2 1.3 - - - -
364B LYS* 6.2 1.6 - - - +
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Residues in contact with VAL 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B THR* 1.3 74.2 - - - +
81B THR* 1.4 63.0 + - - +
83B TYR* 3.3 3.4 + - - +
84B PHE* 3.1 48.5 + - + -
143B ASP* 3.3 33.2 - - - +
144B ARG* 5.8 1.6 - - - +
156B SER* 3.8 21.5 - - - +
157B THR 3.7 31.6 - - - +
158B ALA* 3.8 4.2 - - - +
161B ALA* 4.2 10.9 - - + +
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Residues in contact with THR 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B THR* 3.4 8.1 + - - -
80B VAL* 1.4 77.3 - - - +
82B ASN* 1.4 54.7 + - - +
84B PHE* 3.3 10.5 + - - +
85B LEU* 2.8 41.1 + - + +
140B ILE* 4.1 10.2 - - + +
143B ASP* 4.2 3.7 + - - -
144B ARG* 3.7 26.7 + - - -
296B THR* 4.0 14.9 - - + +
299B MET* 5.3 0.4 - - + -
300B LEU* 3.8 36.6 - - + -
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Residues in contact with ASN 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B VAL* 4.1 10.4 - - + +
77B MET* 2.8 46.5 + - - +
79B THR* 3.3 15.8 + - - +
81B THR* 1.4 81.1 - - - +
83B TYR* 1.4 56.2 + - - +
85B LEU* 3.2 15.2 + - - +
86B VAL* 2.8 37.7 + - - +
299B MET* 5.0 2.6 - - - +
364B LYS* 6.0 1.6 - - - +
365B PHE* 3.5 28.5 - - + -
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Residues in contact with TYR 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B VAL* 3.9 14.8 - - + -
78B ARG* 3.4 48.3 + - + +
79B THR 3.0 17.0 + - - +
80B VAL 3.6 4.7 - - - +
82B ASN* 1.4 71.1 - - - +
84B PHE* 1.4 58.4 + - - +
86B VAL* 3.2 11.1 + - + +
87B ASN 3.0 22.5 + - - -
158B ALA* 3.4 47.9 - - + +
161B ALA* 4.6 4.5 - - + -
162B LEU* 4.7 20.4 - - + +
165B ILE* 3.6 22.1 - - + +
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Residues in contact with PHE 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B VAL* 3.1 43.9 + - + -
81B THR* 3.3 3.1 + - - +
83B TYR* 1.4 74.7 - - - +
85B LEU* 1.4 60.9 + - - +
87B ASN* 3.0 4.3 + - - +
88B LEU 3.0 8.3 + - - -
136B THR* 3.0 34.0 - - + +
139B PHE* 3.7 34.5 - + + -
140B ILE* 3.3 35.4 - - + -
143B ASP* 5.0 1.3 - - + -
161B ALA* 4.1 8.5 - - + -
164B SER* 3.7 27.6 - - - -
165B ILE* 3.7 27.8 - - + -
168B ILE* 4.0 8.5 - - + -
416B SOG 6.1 0.4 - - - -
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Residues in contact with LEU 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B VAL* 4.4 7.1 - - + +
81B THR* 2.8 24.9 + - + +
82B ASN* 3.2 29.3 + - - +
84B PHE* 1.4 70.1 - - - +
86B VAL* 1.4 56.6 - - - +
88B LEU* 3.2 14.7 + - + +
89B SER* 3.0 28.9 + - - -
140B ILE* 3.7 20.0 - - + -
299B MET* 3.7 25.4 - - + -
300B LEU* 4.2 10.5 - - + -
303B VAL* 5.2 3.8 - - + -
358B TYR* 3.3 38.7 + - + +
365B PHE* 4.1 7.6 - - + -
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Residues in contact with VAL 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B VAL* 4.2 11.2 - - + +
68B CYS* 3.7 26.5 - - + +
71B VAL* 3.6 34.8 - - + -
82B ASN 2.8 22.3 + - - +
83B TYR* 3.2 12.3 + - + +
85B LEU* 1.4 71.1 - - - +
87B ASN* 1.3 57.1 + - - +
89B SER* 3.1 10.7 + - - -
90B LEU* 3.0 35.4 + - + +
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Residues in contact with ASN 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B TYR 3.0 12.5 + - - +
84B PHE* 3.0 9.8 + - - +
86B VAL* 1.3 75.7 - - - +
88B LEU* 1.4 54.7 - - - +
90B LEU* 3.2 15.8 + - - +
91B ALA* 3.1 27.5 + - - +
132B VAL* 3.5 16.2 - - - +
136B THR* 2.9 24.9 + - - +
165B ILE* 3.4 35.9 - - + +
168B ILE* 4.2 9.1 - - - +
169B TRP* 2.8 25.5 + - - +
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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
----------------------------------------------------------
84B PHE 3.0 11.9 + - - +
85B LEU* 3.2 14.1 + - + +
87B ASN* 1.4 74.0 - - - +
89B SER* 1.4 57.4 + - - +
91B ALA* 3.5 4.8 + - - +
92B ASP* 3.0 40.8 + - - +
133B ALA* 3.7 41.7 - - + +
136B THR* 3.9 10.4 - - + +
137B LEU* 4.0 28.5 - - + -
303B VAL* 4.2 5.8 - - + -
307B PHE* 5.4 2.9 - - + -
350B ASN* 5.7 0.4 - - - +
354B ASN* 3.9 22.0 - - + +
358B TYR* 3.5 23.1 - - - +
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Residues in contact with SER 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ASN* 2.7 43.4 + - - +
67B VAL* 3.5 26.3 - - - +
68B CYS* 4.3 5.8 - - - -
85B LEU 3.0 10.4 + - - -
86B VAL 3.1 10.1 + - - -
88B LEU* 1.4 74.0 - - - +
90B LEU* 1.4 59.7 + - - +
92B ASP* 3.8 1.5 - - - +
93B VAL* 2.9 33.7 + - - +
354B ASN* 6.0 0.2 - - - +
358B TYR* 4.7 3.8 + - - -
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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
----------------------------------------------------------
68B CYS* 4.4 15.7 - - - -
86B VAL* 3.0 26.8 + - + +
87B ASN* 3.2 23.3 + - - +
89B SER* 1.4 72.3 - - - +
91B ALA* 1.3 59.0 + - - +
93B VAL* 3.2 11.1 + - + +
94B LEU* 3.0 27.4 + - - +
165B ILE* 5.9 2.0 - - + -
169B TRP* 4.4 15.8 - - + +
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Residues in contact with ALA 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ASN 3.1 7.2 + - - +
88B LEU* 3.5 10.5 + - - +
90B LEU* 1.3 75.4 - - - +
92B ASP* 1.3 62.4 + - - +
94B LEU* 3.5 4.0 + - - +
95B ALA 3.3 10.9 + - - -
129B SER* 2.7 41.4 + - - +
132B VAL* 3.7 28.7 - - + -
133B ALA* 4.1 5.6 - - - +
169B TRP* 4.2 11.7 - - - -
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Residues in contact with ASP 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ASN* 4.1 14.1 - - - +
88B LEU* 3.0 27.8 + - - +
89B SER 3.8 4.7 - - - +
90B LEU 3.3 0.2 - - - -
91B ALA* 1.3 78.8 - - - +
93B VAL* 1.4 58.9 + - - +
95B ALA* 3.5 2.2 + - - +
96B THR* 2.9 35.2 + - - -
129B SER* 4.7 3.3 + - - -
133B ALA* 4.5 6.2 - - - +
311B TYR* 5.1 4.5 + - - -
350B ASN* 4.3 4.8 + - - -
351B SER* 3.2 36.4 + - - +
354B ASN* 3.2 27.0 + - - -
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Residues in contact with VAL 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B ALA 4.6 5.4 - - - +
61B LEU* 4.8 13.2 - - + +
64B ASN* 3.8 21.3 - - + -
65B THR* 4.8 16.2 - - + -
89B SER 2.9 20.9 + - - +
90B LEU* 3.2 11.2 + - + +
92B ASP* 1.4 72.4 - - - +
94B LEU* 1.3 61.3 + - - +
96B THR* 4.4 4.5 - - - +
97B ALA* 2.9 38.5 + - + +
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Residues in contact with LEU 94 (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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90B LEU 3.0 12.7 + - - +
91B ALA* 3.6 9.6 - - - +
92B ASP 3.4 0.2 - - - -
93B VAL* 1.3 76.3 - - - +
95B ALA* 1.4 60.6 + - - +
97B ALA* 5.1 1.6 - - - -
98B ILE* 3.3 50.7 + - + +
99B CYS* 3.9 1.7 + - - -
125B LEU* 3.7 50.7 - - + +
128B VAL* 4.4 5.6 - - + -
129B SER* 4.5 6.1 - - - +
169B TRP* 4.2 28.0 - - + -
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Residues in contact with ALA 95 (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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91B ALA 3.3 5.3 + - - +
92B ASP* 3.9 6.1 - - - +
93B VAL 3.4 0.2 - - - -
94B LEU* 1.4 76.6 - - - +
96B THR* 1.3 61.1 + - - +
99B CYS* 3.2 15.7 + - - +
100B LEU 2.8 26.3 + - - -
126B GLN* 4.3 10.1 - - - +
129B SER* 3.3 27.8 + - - +
347B VAL* 6.0 1.3 - - + -
348B TYR* 3.5 19.5 - - + -
351B SER* 5.0 3.8 - - - +
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Residues in contact with THR 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B PHE* 3.4 45.7 - - + +
60B ALA* 3.5 25.2 - - + +
61B LEU* 3.7 16.8 - - + -
92B ASP 2.9 19.6 + - - -
93B VAL* 4.0 3.4 - - - -
95B ALA* 1.3 75.7 - - - +
97B ALA* 1.3 62.0 + - - +
100B LEU* 3.3 30.8 - - + +
101B PRO* 3.4 1.2 - - - +
348B TYR* 4.9 3.4 + - - -
351B SER* 3.6 9.5 + - - -
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Residues in contact with ALA 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B PHE* 4.1 11.2 - - - -
61B LEU* 4.3 12.9 - - + +
93B VAL* 2.9 23.3 + - + +
94B LEU* 4.4 1.8 - - - +
96B THR* 1.3 77.8 - - - +
98B ILE* 1.3 65.0 + - + +
101B PRO* 3.4 19.9 - - - +
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Residues in contact with ILE 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B LEU* 3.3 35.6 + - + +
97B ALA* 1.3 85.2 - - + +
99B CYS* 1.3 69.5 + - - +
100B LEU 3.6 0.4 - - - -
101B PRO* 3.5 8.3 - - - +
102B ALA* 3.9 12.5 + - - +
121B VAL* 5.8 0.7 - - + -
122B ILE* 4.0 26.0 - - + +
125B LEU* 4.3 20.4 - - + -
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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
------------------------------------------------------------
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