Contacts of the helix formed by residues 86 - 103 (chain R) in PDB entry 2JA7
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 86 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
852M TYR* 3.5 25.7 + - + +
1059M HIS* 3.2 17.0 - - - +
1060M PRO* 3.8 23.7 + - + +
1441M PHE* 4.5 0.3 - - - -
82R THR* 5.5 2.0 - - + -
84R TYR 3.5 2.9 + - - +
85R MET* 1.3 74.7 - - - +
87R LYS* 1.3 65.1 + - - +
88R TYR* 3.5 6.8 + - - +
89R GLU* 2.6 55.8 + - - +
90R ARG* 3.1 11.1 + - - +
136R ARG* 3.9 5.4 - - - +
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Residues in contact with LYS 87 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452M LYS* 5.9 2.4 - - - +
503M GLN 5.4 4.9 - - - +
504M LEU* 4.8 8.0 - - + +
874M ASP* 3.6 20.2 + - - -
877M HIS* 5.9 1.2 + - - -
1059M HIS* 3.0 35.6 + - + +
1062M GLU* 3.5 27.8 + - - -
85R MET 3.7 0.2 + - - -
86R THR* 1.3 70.9 - - - +
88R TYR* 1.3 81.5 + - + +
90R ARG* 3.6 7.8 - - - +
91R ALA* 3.0 28.1 + - - +
155R LEU* 4.4 18.2 - - + -
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Residues in contact with TYR 88 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504M LEU* 3.8 15.5 - - + -
1059M HIS* 4.1 9.9 - - + -
1060M PRO 5.5 0.4 - - - +
1061M GLY* 4.3 8.7 - - - -
1062M GLU* 2.5 53.6 + - - +
1063M MET 4.4 0.9 + - - -
1437M GLY* 3.1 31.6 - - - -
1438M THR* 3.2 21.0 + - - +
1441M PHE* 3.9 5.6 - - + -
1140N ALA 4.7 2.6 + - - -
1141N HIS 3.6 10.2 + - - -
1142N GLY* 3.6 20.0 - - - -
86R THR* 3.1 7.4 - - - +
87R LYS* 1.3 102.2 - - + +
89R GLU* 1.3 73.0 + - - +
91R ALA* 3.2 6.7 + - - +
92R ARG* 2.7 22.2 + - - +
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Residues in contact with GLU 89 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
852M TYR* 2.5 26.7 + - - +
1441M PHE* 3.3 20.2 - - + -
85R MET* 3.5 7.8 - - + +
86R THR* 2.6 42.2 + - - +
88R TYR* 1.3 75.0 - - - +
90R ARG* 1.3 51.6 + - - +
92R ARG* 2.6 26.7 + - - +
93R ILE* 2.7 20.1 + - - +
134R ILE* 3.0 37.1 - - + +
136R ARG* 2.7 39.0 + - - -
151R LEU* 4.3 0.3 - - - +
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Residues in contact with ARG 90 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503M GLN* 2.7 29.5 + - + +
85R MET* 3.3 31.4 - - + +
86R THR 3.1 4.4 + - - +
87R LYS 3.6 10.1 - - - +
89R GLU* 1.3 78.4 - - - +
91R ALA* 1.3 69.9 + - + +
93R ILE* 4.0 6.5 - - - -
94R LEU* 2.9 52.5 + - - +
122R MET* 4.6 11.7 - - - +
125R LEU* 4.0 16.6 - - + +
153R VAL* 5.2 4.1 - - + +
155R LEU* 3.2 35.3 - - + +
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Residues in contact with ALA 91 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499M ALA* 4.0 10.7 - - - +
500M GLU* 5.4 3.1 - - + -
503M GLN* 4.1 15.7 - - + -
504M LEU* 3.3 33.4 - - + -
1438M THR* 4.9 3.4 - - - +
87R LYS 3.0 17.4 + - - +
88R TYR* 3.3 8.7 - - - +
90R ARG* 1.3 86.3 - - - +
92R ARG* 1.3 61.4 + - - +
94R LEU* 3.8 2.4 - - - +
95R GLY* 3.1 17.2 + - - -
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Residues in contact with ARG 92 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496M GLU* 5.4 6.4 + - - +
500M GLU* 6.2 1.3 - - - -
1433M MET* 4.0 24.5 - - - +
1438M THR* 3.0 42.3 + - + -
1439M GLY* 3.9 7.7 - - - -
1441M PHE* 3.0 36.6 + - + -
1442M ASP* 4.2 10.7 + - - -
1443M VAL* 3.4 29.9 - - + +
1145N SER* 5.4 1.7 + - - +
88R TYR 2.7 11.0 + - - +
89R GLU 2.6 14.0 + - - +
91R ALA* 1.3 72.8 - - - +
93R ILE* 1.3 60.5 + - + +
95R GLY* 4.4 1.1 - - - +
96R THR* 2.7 46.5 + - - +
61S ILE 4.8 2.2 + - - -
62S LEU 4.7 3.8 + - - -
63S PRO* 4.1 12.7 - - - +
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Residues in contact with ILE 93 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1441M PHE* 5.8 0.4 - - + -
1443M VAL* 4.8 9.0 - - + -
85R MET* 3.0 37.0 - - + -
89R GLU* 2.7 21.8 + - - +
90R ARG* 3.2 6.0 + - - +
92R ARG* 1.3 73.3 - - + +
94R LEU* 1.3 55.0 + - - +
96R THR* 3.5 4.6 - - - +
97R ARG* 2.6 37.6 + - - +
125R LEU* 4.7 4.5 - - + -
130R ILE* 4.3 24.9 - - + -
132R LEU* 4.5 10.3 - - + -
134R ILE* 3.2 28.9 - - + -
148R VAL* 3.4 24.9 - - + -
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Residues in contact with LEU 94 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499M ALA* 5.2 1.1 - - + -
503M GLN* 4.4 8.3 - - + +
90R ARG* 2.9 55.5 + - - +
91R ALA* 3.8 3.4 - - - +
93R ILE* 1.3 75.7 - - - +
95R GLY* 1.3 55.2 + - - +
97R ARG* 3.7 1.5 - - - -
98R ALA* 2.7 38.3 + - - +
118R LEU* 4.1 12.6 - - + -
121R ALA* 3.4 15.4 - - + +
122R MET* 3.2 50.5 - - + +
125R LEU* 3.7 22.0 - - + -
130R ILE* 5.4 0.7 - - + -
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Residues in contact with GLY 95 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496M GLU* 3.7 17.8 - - - +
499M ALA* 3.6 25.0 - - - +
91R ALA 3.1 9.7 + - - -
92R ARG* 3.6 2.7 - - - -
94R LEU* 1.3 76.7 - - - +
96R THR* 1.3 65.6 + - - +
98R ALA* 2.8 17.5 + - - +
99R LEU* 2.8 12.6 + - - +
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Residues in contact with THR 96 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496M GLU* 4.0 14.5 + - - +
1443M VAL* 4.7 6.3 - - + +
92R ARG* 2.7 42.1 + - - +
93R ILE* 3.5 4.0 - - - -
95R GLY* 1.3 69.9 - - - +
97R ARG* 1.3 63.9 + - - +
99R LEU* 3.1 9.5 + - - +
100R GLN* 3.0 29.0 + - + +
132R LEU* 3.8 11.0 - - + -
61S ILE* 3.7 40.6 - - + +
62S LEU 5.7 0.9 + - - -
66S GLY* 6.0 0.4 - - - -
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Residues in contact with ARG 97 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93R ILE* 2.6 24.6 + - + +
94R LEU* 3.8 2.9 - - - +
96R THR* 1.3 69.8 - - - +
98R ALA* 1.3 67.2 + - - +
100R GLN* 2.8 48.4 + - - +
101R ILE* 2.8 38.5 + - + +
105R ALA* 4.5 7.0 - - - +
106R PRO* 2.7 30.5 + - - +
108R PHE* 3.2 23.5 - - - -
121R ALA* 4.2 9.2 - - + -
124R GLU* 2.6 33.5 + - - +
130R ILE* 3.9 28.7 - - + -
131R PRO* 4.5 10.8 - - - +
132R LEU* 5.0 4.0 - - + +
18S PHE* 4.9 8.3 - - - +
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Residues in contact with ALA 98 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495M GLU* 3.5 22.2 - - + +
94R LEU 2.7 23.9 + - - +
95R GLY* 2.8 8.1 + - - +
97R ARG* 1.3 69.5 - - - +
99R LEU* 1.3 64.7 + - - +
101R ILE* 2.8 7.3 + - - +
102R SER* 2.7 22.0 + - - -
117R PRO* 3.7 12.5 - - - +
118R LEU* 3.7 27.1 - - + +
121R ALA* 4.0 2.4 - - + +
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Residues in contact with LEU 99 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494M SER* 3.3 26.7 - - - +
495M GLU* 3.7 13.1 - - + +
496M GLU* 3.6 21.8 - - + +
95R GLY 2.8 12.9 + - - +
96R THR* 3.1 12.8 - - - +
98R ALA* 1.3 71.4 - - - +
100R GLN* 1.3 61.1 + - - +
102R SER* 2.3 30.5 + - - +
103R MET* 2.8 39.9 - - + +
64S THR 3.5 20.2 - - - +
65S ASP* 4.3 2.0 - - - -
66S GLY* 4.1 11.9 - - - +
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Residues in contact with GLN 100 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96R THR* 3.0 16.0 + - + +
97R ARG* 2.8 45.5 + - - +
99R LEU* 1.3 75.5 - - - +
101R ILE* 1.3 57.1 + - - +
103R MET* 2.7 36.4 + - - +
105R ALA* 3.2 14.4 - - + +
132R LEU* 4.3 5.0 - - - +
15S PRO* 3.9 10.4 - - + +
18S PHE* 3.4 24.6 - - - -
61S ILE* 3.5 23.9 - - - +
66S GLY* 3.3 34.8 + - - -
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Residues in contact with ILE 101 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381M THR* 4.8 0.7 + - - -
383M TYR* 4.3 14.9 + - + -
97R ARG* 2.8 37.8 + - + +
98R ALA* 2.8 11.1 + - - +
100R GLN* 1.3 72.5 - - - +
102R SER* 1.3 62.4 + - - +
104R ASN* 3.2 14.0 + - - -
105R ALA* 3.9 9.5 + - + +
106R PRO 5.3 0.2 - - - +
107R VAL* 4.2 22.2 - - + -
117R PRO* 4.2 12.1 - - + +
120R ILE* 3.6 37.9 - - + -
121R ALA* 4.0 10.1 - - - +
124R GLU* 3.1 29.8 - - - +
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Residues in contact with SER 102 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379M VAL* 3.8 33.6 - - - +
381M THR* 3.9 14.6 + - - -
383M TYR* 5.8 1.8 - - - -
495M GLU* 4.0 11.4 - - - +
98R ALA 2.7 13.0 + - - -
99R LEU* 2.3 39.3 + - - +
101R ILE* 1.3 73.1 - - - +
103R MET* 1.3 58.5 + - - +
104R ASN* 3.2 2.6 + - - -
117R PRO* 4.1 20.8 - - - +
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Residues in contact with MET 103 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379M VAL* 5.4 12.3 - - - -
99R LEU* 2.8 36.6 - - + +
100R GLN* 2.7 13.8 + - - +
102R SER* 1.3 80.5 - - - +
104R ASN* 1.3 73.4 + - - +
14S HIS* 3.7 34.8 + - + +
15S PRO* 4.1 14.6 - - + -
16S SER 4.8 0.7 + - - -
65S ASP* 3.3 22.9 - - + -
66S GLY* 3.0 31.9 - - - +
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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