Contacts of the helix formed by residues 78 - 94 (chain B) in PDB entry 1S0V
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 LEU 78 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B ILE* 3.0 16.9 + - + +
75B THR* 5.0 0.9 - - - +
77B LEU* 1.3 74.1 - - - +
79B PRO* 1.3 61.6 - - + +
80B LYS 2.9 4.3 - - - -
81B MET* 2.5 28.9 + - - +
82B ILE* 3.0 22.0 + - + +
112B GLU* 4.9 3.1 - - + +
115B ALA* 3.6 13.0 - - + -
116B TYR* 3.2 62.4 - - + +
119B ILE* 4.1 9.2 - - + -
746B ARG* 4.6 13.7 - - - -
755B PHE* 4.3 17.5 - - + +
756B ARG* 6.0 3.8 - - - -
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Residues in contact with PRO 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B THR 3.3 24.0 - - - +
76B THR* 3.7 11.7 - - - +
78B LEU* 1.3 92.4 - - + +
80B LYS* 1.3 60.1 + - - +
81B MET 3.1 0.7 + - - -
82B ILE* 4.0 17.1 - - + +
83B ALA* 3.4 24.3 + - - +
756B ARG 6.5 0.9 - - - -
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Residues in contact with LYS 80 (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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76B THR 4.0 12.1 - - - +
77B LEU 3.9 6.1 - - - +
78B LEU 2.7 2.8 + - - -
79B PRO* 1.3 77.0 - - + +
81B MET* 1.3 54.2 + - - +
83B ALA* 4.6 3.8 - - - +
84B ARG* 4.0 6.8 + - - +
223B SER* 2.8 54.7 - - - +
224B THR* 3.3 32.7 - - + +
250B TYR* 4.7 3.0 + - - -
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Residues in contact with MET 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B LEU 3.8 9.8 + - - +
78B LEU* 2.5 19.6 + - - +
80B LYS* 1.3 72.7 - - - +
82B ILE* 1.3 59.1 + - - +
83B ALA 3.2 1.3 - - - -
84B ARG* 3.0 18.9 + - - +
85B ILE* 3.2 20.3 + - + +
115B ALA* 3.3 27.6 - - + -
118B THR* 4.0 22.7 - - + +
119B ILE* 4.0 12.3 - - + -
216B CYS* 3.9 10.8 - - - +
219B MET* 3.7 20.0 - - + +
220B LEU* 3.7 29.6 - - + +
223B SER* 3.5 17.0 - - - +
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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
----------------------------------------------------------
78B LEU* 3.0 19.2 + - + +
79B PRO* 4.1 21.1 - - + +
81B MET* 1.3 76.4 - - - +
83B ALA* 1.3 64.6 + - + +
85B ILE* 3.5 6.5 + - - +
86B ASN* 3.1 34.7 + - - +
111B PRO* 5.0 3.5 - - + +
112B GLU* 2.8 60.3 - - + +
115B ALA* 4.2 9.2 - - + -
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Residues in contact with ALA 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B PRO 3.4 14.6 + - - +
80B LYS* 5.0 3.8 - - - +
81B MET 3.2 0.6 - - - -
82B ILE* 1.3 79.6 - - + +
84B ARG* 1.3 57.4 - - - +
86B ASN* 3.6 3.8 + - - +
87B ASP* 2.4 46.1 + - - +
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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
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80B LYS 4.0 2.9 + - - +
81B MET* 3.0 12.6 + - - +
83B ALA* 1.3 77.2 - - - +
85B ILE* 1.3 60.0 + - + +
87B ASP* 3.3 21.4 + - - +
88B TRP* 2.8 24.4 + - - +
91B GLU* 3.6 22.5 + - - -
215B ARG* 4.0 5.1 - - - +
219B MET* 3.2 40.8 - - + +
222B GLU* 2.9 36.0 + - + +
223B SER* 3.9 24.2 - - - +
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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
----------------------------------------------------------
81B MET* 3.2 27.5 + - + +
82B ILE* 3.9 6.5 - - - +
84B ARG* 1.3 74.3 - - - +
86B ASN* 1.3 62.0 + - - +
87B ASP 3.1 0.4 - - - -
88B TRP* 3.4 1.3 - - - +
89B PHE* 2.9 58.8 + - + -
106B LEU* 5.8 0.9 - - + -
111B PRO* 4.3 9.6 - - + +
114B VAL* 4.1 19.5 - - + -
115B ALA* 4.0 25.8 - - + +
219B MET* 3.0 36.8 - - + -
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Residues in contact with ASN 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 ILE* 3.1 25.9 + - - +
83B ALA* 3.6 3.6 + - - +
84B ARG 3.5 0.2 - - - -
85B ILE* 1.3 77.0 - - - +
87B ASP* 1.3 64.2 + - - +
89B PHE* 3.6 12.7 + - - +
90B GLU* 3.1 33.3 + - - +
111B PRO* 3.7 30.7 - - - +
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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
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83B ALA* 2.4 32.6 + - - +
84B ARG* 3.3 17.8 + - - +
86B ASN* 1.3 79.8 - - - +
88B TRP* 1.3 58.2 + - - +
89B PHE 3.3 0.4 - - - -
90B GLU* 3.6 5.9 + - - +
91B GLU* 2.5 44.7 + - - +
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Residues in contact with TRP 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ARG* 2.8 27.9 + - - +
85B ILE* 3.4 6.7 - - - +
87B ASP* 1.3 77.5 - - - +
89B PHE* 1.3 82.7 + + - +
91B GLU* 3.7 12.4 + - + +
92B VAL* 3.0 38.6 + - + +
100B PRO* 3.9 27.1 - - + -
103B PHE* 4.7 9.9 - - - +
106B LEU* 5.7 0.8 - - - +
215B ARG* 3.1 61.0 - - + +
219B MET* 3.6 23.7 - - + +
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Residues in contact with PHE 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ILE* 2.9 35.5 + - + +
86B ASN* 3.6 13.7 + - - +
88B TRP* 1.3 102.3 - + - +
90B GLU* 1.3 64.1 + - - +
91B GLU 3.3 0.4 - - - -
92B VAL* 3.5 1.9 + - - +
93B LYS* 3.1 36.0 + - - +
103B PHE* 3.2 37.5 - + + -
106B LEU* 2.6 46.7 - - + -
107B GLN* 4.1 11.7 - - + +
109B ILE 5.6 0.9 - - - -
111B PRO* 5.2 11.0 - - + -
114B VAL* 5.9 0.9 - - + -
219B MET* 5.2 0.7 - - + -
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Residues in contact with GLU 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 ASN 3.1 19.5 + - - +
87B ASP* 3.9 7.4 - - - +
88B TRP 3.4 0.4 - - - -
89B PHE* 1.3 81.3 - - - +
91B GLU* 1.3 60.5 + - + +
93B LYS* 3.6 30.1 + - - +
94B ALA* 3.4 25.5 + - - +
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Residues in contact with GLU 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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84B ARG* 3.6 20.3 + - - -
87B ASP* 2.5 39.5 + - - +
88B TRP* 4.3 12.1 - - + +
89B PHE 3.3 0.2 - - - -
90B GLU* 1.3 75.8 - - + +
92B VAL* 1.3 62.1 + - + +
94B ALA* 4.4 3.7 - - - +
95B LYS* 3.4 42.9 + - - +
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Residues in contact with VAL 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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88B TRP* 3.0 48.2 - - + +
89B PHE 3.5 4.3 + - - +
90B GLU 3.3 0.6 - - - -
91B GLU* 1.3 79.7 - - + +
93B LYS* 1.3 59.5 + - - +
94B ALA 3.4 0.7 - - - -
95B LYS* 3.1 25.4 - - - +
99B ARG* 3.8 13.9 + - + +
100B PRO* 3.3 30.7 - - + -
103B PHE* 3.6 23.1 - - + -
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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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89B PHE* 3.1 22.0 + - - +
90B GLU* 3.8 31.6 + - - +
92B VAL* 1.3 78.3 - - - +
94B ALA* 1.3 56.6 + - - +
95B LYS 3.2 6.5 + - - +
99B ARG* 5.0 15.9 + - - +
103B PHE* 4.5 11.7 - - + -
107B GLN* 4.0 17.9 - - - +
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Residues in contact with ALA 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 GLU 3.4 13.6 + - - +
91B GLU* 4.4 3.6 - - - +
92B VAL 3.4 0.4 - - - -
93B LYS* 1.3 77.5 - - + +
95B LYS* 1.3 65.6 + - + +
96B ARG* 4.3 3.3 + - - -
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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