Contacts of the helix formed by residues 85 - 99 (chain B) in PDB entry 1JS6
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 SER 85 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B SER* 1.3 75.2 + - - +
86B TYR* 1.3 66.9 + - - +
87B PRO* 3.4 11.2 - - - +
88B ALA* 3.2 13.2 + - - +
89B MET* 3.1 27.7 + - - +
306B LEU* 2.9 29.2 + - - -
308B ASN* 3.0 8.0 + - - +
365B VAL* 3.8 5.4 - - - +
369B TYR* 3.7 21.2 - - - -
453B ARG* 4.5 6.1 - - - +
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Residues in contact with TYR 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 3.1 43.1 - - + -
2A ASN* 3.4 20.4 - - - -
3A ALA* 3.5 22.2 + - - +
6A PHE* 3.1 43.0 - + + -
18B ALA* 4.9 2.3 - - - -
21B LEU* 3.6 30.1 - - + +
85B SER* 1.3 72.1 - - - +
87B PRO* 1.3 72.2 - - + +
89B MET* 3.1 23.4 + - + +
90B LEU* 2.9 29.0 + - - +
369B TYR* 5.0 1.0 + - - -
453B ARG* 3.5 23.7 + - - -
454B LYS* 3.9 4.9 + - - -
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Residues in contact with PRO 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 4.3 12.6 - - + +
85B SER* 3.4 14.1 - - - +
86B TYR* 1.3 95.5 - - + +
88B ALA* 1.3 61.3 + - - +
90B LEU* 3.3 2.5 + - + +
91B ALA* 3.0 22.5 + - - +
364B PHE* 3.5 32.1 - - - +
365B VAL* 4.0 6.1 - - - -
368B MET* 3.8 34.8 - - + -
369B TYR* 3.6 20.4 - - + +
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Residues in contact with ALA 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B SER* 3.2 11.4 + - - +
87B PRO* 1.3 78.9 - - - +
89B MET* 1.3 51.3 + - - +
91B ALA* 3.1 8.5 + - - +
92B ASP* 2.7 36.8 + - - +
307B VAL* 4.3 1.8 - - - -
308B ASN* 3.1 42.8 - - + +
361B LYS* 3.8 12.2 - - + +
365B VAL* 3.8 16.0 - - + +
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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
----------------------------------------------------------
6A PHE* 4.4 9.0 - - + -
96A GLY* 4.2 15.9 - - - +
97A ALA* 4.2 9.0 - - - -
17B MET* 4.0 26.0 - - + -
21B LEU* 4.9 8.5 - - + -
84B SER* 3.5 24.5 - - - +
85B SER* 3.1 23.4 + - - +
86B TYR* 3.5 33.4 - - + +
88B ALA* 1.3 77.6 - - - +
90B LEU* 1.3 62.8 + - - +
92B ASP* 3.1 8.0 + - - +
93B MET* 3.0 28.6 + - - +
308B ASN* 3.5 15.3 - - - +
453B ARG* 5.8 2.7 - - - +
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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
----------------------------------------------------------
1A MET* 4.4 12.6 - - + -
6A PHE* 4.0 10.1 - - + -
9A ARG* 3.9 11.4 - - + +
10A GLY* 3.6 36.6 - - - +
13A MET* 3.8 21.2 - - + +
53A PHE* 3.9 12.1 - - + -
86B TYR 2.9 20.7 + - - +
87B PRO* 3.6 6.1 - - + +
89B MET* 1.3 74.5 - - - +
91B ALA* 1.3 64.1 + - - +
93B MET* 3.2 14.1 + - - +
94B LEU 3.2 15.9 + - - -
364B PHE* 4.2 10.1 - - + -
368B MET* 3.4 31.4 - - + -
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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 PRO 3.0 14.2 + - - +
88B ALA 3.3 8.1 - - - +
90B LEU* 1.3 74.0 - - - +
92B ASP* 1.3 65.7 + - - +
94B LEU* 3.0 5.5 + - - +
95B CYS* 2.9 23.0 + - - +
360B LEU* 3.5 31.5 - - + +
361B LYS* 3.6 14.8 - - - -
364B PHE* 3.6 19.9 - - + -
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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
----------------------------------------------------------
92A ASP* 2.8 27.9 - - - +
356A ARG* 4.3 3.3 + - - -
88B ALA 2.7 19.0 + - - +
89B MET* 3.6 8.1 - - - +
91B ALA* 1.3 72.8 - - - +
93B MET* 1.3 65.3 + - + +
95B CYS* 3.2 9.6 + - - +
96B GLY* 3.0 20.4 + - - -
308B ASN* 5.6 4.3 - - + +
356B ARG* 3.4 24.5 + - - -
361B LYS* 3.1 30.2 + - + +
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Residues in contact with MET 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A PHE* 4.9 12.6 - - - -
10A GLY 3.8 8.5 - - - +
13A MET* 3.9 14.1 - - + -
14A VAL* 3.5 25.8 - - + -
17A MET* 3.5 37.5 - - + +
93A MET* 3.5 50.7 - - + -
17B MET* 5.4 2.5 - - + -
89B MET 3.0 19.3 + - - +
90B LEU* 3.2 14.8 + - - +
92B ASP* 1.3 77.4 - - - +
94B LEU* 1.3 64.1 + - - +
96B GLY* 3.2 2.1 + - - -
97B ALA 3.0 16.3 + - - -
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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
----------------------------------------------------------
13A MET* 4.3 13.8 - - + -
16A TYR* 3.6 34.8 - - + -
17A MET* 4.8 0.7 - - + -
20A TYR* 6.5 0.7 - - + -
57A LEU* 5.3 0.4 - - + -
60A VAL* 3.8 32.5 - - + -
65A MET* 5.3 0.7 - - + -
90B LEU 3.2 7.8 + - - +
91B ALA* 3.0 9.9 + - - +
93B MET* 1.3 79.1 - - - +
95B CYS* 1.3 55.8 + - - +
97B ALA* 2.7 31.2 + - + +
98B ILE* 2.9 35.8 + - + +
360B LEU* 4.1 15.9 - - + -
364B PHE* 3.8 17.5 - - + -
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Residues in contact with CYS 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ALA 2.9 11.5 + - - +
92B ASP* 3.3 15.0 - - - +
94B LEU* 1.3 75.8 - - - +
96B GLY* 1.3 58.0 + - - +
98B ILE* 3.7 3.1 + - - +
99B GLY* 2.9 25.5 + - - -
100B CYS* 4.6 1.2 + - - -
356B ARG* 3.9 26.7 - - - -
357B PHE* 3.5 43.9 - - - +
358B ARG* 4.3 1.8 - - - -
360B LEU* 3.7 19.2 - - + +
361B LYS* 6.0 1.8 - - + -
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Residues in contact with GLY 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A SER* 4.2 4.9 + - - -
89A MET* 4.2 8.0 - - - +
308A ASN* 3.6 26.6 + - - -
92B ASP 3.0 13.6 + - - -
93B MET 3.7 4.0 - - - -
95B CYS* 1.3 76.2 - - - +
97B ALA* 1.3 64.0 + - - +
99B GLY* 3.4 11.7 + - - -
356B ARG* 6.0 0.9 - - - +
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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
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17A MET* 3.8 28.5 - - + -
20A TYR* 3.6 16.1 - - + -
21A LEU* 3.9 27.2 - - + +
72A HIS* 4.3 5.0 - - - -
84A SER* 4.7 1.9 + - - -
89A MET* 4.2 9.4 - - - -
93B MET 3.0 11.2 + - - +
94B LEU* 2.7 19.9 + - + +
96B GLY* 1.3 69.5 - - - +
98B ILE* 1.3 65.6 + - - +
99B GLY* 3.1 1.6 + - - -
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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
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20A TYR* 3.9 16.9 + - + +
60A VAL* 5.2 1.1 - - + -
64A ILE* 4.7 10.1 - - + -
65A MET* 4.3 21.8 - - + -
68A VAL* 3.8 30.8 - - + +
69A THR 5.4 0.5 - - - +
71A TRP 5.1 3.6 + - - -
72A HIS* 3.5 10.9 - - - -
94B LEU* 2.9 43.1 + - + +
95B CYS* 4.1 4.0 - - - +
97B ALA* 1.3 75.8 - - + +
99B GLY* 1.3 64.4 + - - +
100B CYS* 3.3 21.1 + - + +
357B PHE* 4.4 22.0 - - + -
360B LEU* 4.5 3.6 - - + -
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Residues in contact with GLY 99 (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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71A TRP* 4.0 1.6 - - - +
72A HIS* 2.9 26.3 + - - -
82A THR* 3.4 15.2 - - - +
83A ALA 5.2 1.5 - - - +
84A SER* 5.7 1.1 - - - -
308A ASN* 6.0 0.4 - - - -
95B CYS 2.9 18.0 + - - -
96B GLY* 3.6 11.7 - - - -
97B ALA 3.1 1.6 - - - -
98B ILE* 1.3 76.6 - - - +
100B CYS* 1.3 60.6 + - - +
101B ILE* 5.6 0.9 - - - -
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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