Contacts of the helix formed by residues 93 - 111 (chain R) in PDB entry 3J9X
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 GLY 93 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92R SER* 1.3 76.7 - - - +
94R PRO* 1.3 68.5 - - - -
95R ALA 3.3 1.8 - - - -
96R LEU* 2.8 29.6 + - - +
97R VAL* 3.2 14.5 + - - +
133R VAL* 4.5 10.1 - - - -
64T THR* 4.5 0.9 - - - -
65T GLN* 5.3 2.2 - - - -
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Residues in contact with PRO 94 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93R GLY* 1.3 82.9 - - - -
95R ALA* 1.3 62.5 + - - +
97R VAL* 3.0 6.2 + - - +
98R ASN* 2.9 25.6 + - - +
133R VAL* 3.8 25.7 - - + -
64T THR* 3.3 15.9 - - + +
65T GLN* 3.4 39.0 - - - +
66T TYR 4.7 0.2 - - - -
67T GLY* 3.9 11.7 - - - -
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Residues in contact with ALA 95 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90R ILE* 3.6 22.0 - - + -
93R GLY 3.1 0.6 + - - -
94R PRO* 1.3 80.4 - - - +
96R LEU* 1.3 57.7 + - - +
98R ASN* 3.3 1.8 + - - +
99R MET* 3.0 24.6 + - - +
64T THR* 3.2 17.7 + - + +
67T GLY* 3.5 15.5 - - - -
68T ILE 3.6 22.0 - - - +
69T THR* 3.4 14.8 - - + +
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Residues in contact with LEU 96 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83R VAL* 4.5 4.0 - - + +
86R ALA* 3.8 33.2 - - + +
87R LEU* 3.6 39.5 - - + +
90R ILE* 4.0 5.5 - - + +
91R GLY 3.4 12.3 - - - +
92R SER* 3.8 11.9 - - - -
93R GLY 2.8 16.0 + - - +
95R ALA* 1.3 71.3 - - - +
97R VAL* 1.3 63.3 + - + +
99R MET* 3.1 6.0 + - + +
100R ILE* 2.8 49.6 + - + +
126R THR* 4.8 11.0 - - + -
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Residues in contact with VAL 97 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93R GLY* 3.9 8.7 - - - +
94R PRO 3.0 8.6 + - - +
96R LEU* 1.3 78.9 - - + +
98R ASN* 1.3 66.7 + - - +
100R ILE* 3.2 5.5 + - + -
101R ASN* 2.9 27.9 + - - +
130R THR* 3.5 21.1 + - - +
131R GLY 3.7 26.5 - - - +
132R TYR* 4.2 6.7 - - - +
133R VAL* 3.8 34.3 - - + +
134R SER 5.2 0.9 - - - +
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Residues in contact with ASN 98 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109Q SER 3.5 22.5 - - - +
110Q ALA* 3.6 3.2 - - - +
112Q ASN* 5.1 10.0 - - - +
94R PRO* 2.9 12.5 + - - +
95R ALA* 3.4 8.3 - - - +
97R VAL* 1.3 80.2 - - - +
99R MET* 1.3 65.4 + - - +
101R ASN* 3.5 8.8 + - - +
102R GLY 3.3 13.9 + - - -
67T GLY* 3.1 35.6 + - - -
69T THR* 4.4 7.9 - - + -
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Residues in contact with MET 99 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2397 A 4.1 13.2 - - - +
106Q TYR* 4.6 13.5 - - - +
110Q ALA* 3.9 21.3 + - - +
111Q PHE* 3.7 30.5 - - + -
82R LYS* 5.9 2.5 - - - -
86R ALA* 3.8 24.0 - - + -
90R ILE* 3.8 23.6 - - + -
95R ALA 3.0 13.6 + - - +
96R LEU* 3.1 12.3 + - + +
98R ASN* 1.3 78.6 - - - +
100R ILE* 1.3 59.7 + - + +
102R GLY* 3.2 3.8 + - - -
103R LEU* 2.9 33.9 + - + +
69T THR* 4.7 5.8 - - + -
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Residues in contact with ILE 100 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79R PHE* 5.1 1.1 - - + -
83R VAL* 4.3 22.7 - - + -
96R LEU* 2.8 48.6 + - + +
97R VAL* 4.7 3.4 - - + -
99R MET* 1.3 73.8 - - + +
101R ASN* 1.3 58.2 + - - +
103R LEU* 4.1 6.5 - - + -
104R LYS* 2.7 34.2 + - + +
122R VAL* 4.3 20.2 - - + -
126R THR* 4.1 23.6 - - + -
130R THR* 3.6 34.8 - - + +
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Residues in contact with ASN 101 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109Q SER* 4.2 7.6 + - - +
97R VAL* 2.9 23.5 + - - +
98R ASN* 3.7 10.2 + - - +
100R ILE* 1.3 76.5 - - - +
102R GLY* 1.3 61.1 + - - +
104R LYS* 3.8 3.3 - - - +
105R GLY* 3.2 18.7 + - - -
130R THR* 2.5 31.2 + - - +
131R GLY* 2.9 33.6 + - - -
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Residues in contact with GLY 102 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105Q GLY 4.2 2.8 - - - +
106Q TYR* 3.7 11.6 + - - -
109Q SER* 2.9 25.0 + - - -
110Q ALA* 4.1 10.3 - - - -
98R ASN 3.3 4.6 + - - -
99R MET 3.2 6.2 + - - -
101R ASN* 1.3 75.6 - - - +
103R LEU* 1.3 59.9 + - - +
105R GLY* 3.4 1.5 + - - -
106R TYR* 2.9 30.7 + - - +
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Residues in contact with LEU 103 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106Q TYR* 4.0 11.5 - - + -
79R PHE* 3.7 11.0 - - + -
82R LYS* 3.5 51.4 - - + +
83R VAL* 3.7 33.4 - - + +
99R MET* 2.9 24.9 + - + +
100R ILE* 3.6 8.1 - - + +
102R GLY* 1.3 74.1 - - - +
104R LYS* 1.3 65.3 + - - +
106R TYR* 3.2 9.3 - - + +
107R TYR* 3.0 38.0 + - + -
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Residues in contact with LYS 104 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79R PHE* 3.8 17.7 - - + -
100R ILE* 2.7 23.3 + - + +
101R ASN* 3.8 5.8 - - - +
103R LEU* 1.3 73.7 - - - +
105R GLY* 1.3 63.1 + - - +
107R TYR* 3.1 5.0 + - - +
108R ILE* 3.0 46.5 + - + +
115R PRO* 4.4 13.1 - - - +
118R LEU* 4.0 13.5 - - + +
119R ASP* 2.7 39.8 + - - +
122R VAL* 6.0 1.3 - - + -
130R THR* 4.3 18.9 - - + +
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Residues in contact with GLY 105 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102Q GLY* 5.0 0.9 - - - -
105Q GLY* 5.9 3.4 - - - -
106Q TYR 5.7 0.2 - - - -
101R ASN 3.2 12.4 + - - -
102R GLY* 3.8 2.5 - - - -
104R LYS* 1.3 78.9 - - - +
106R TYR* 1.3 62.0 + - - +
108R ILE* 3.2 12.8 + - - +
109R SER* 3.0 28.6 + - - -
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Residues in contact with TYR 106 (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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1018 A 3.3 16.5 + - - -
82Q LYS* 2.7 34.8 + - - -
99Q MET* 4.7 3.9 - - - -
102Q GLY 3.5 26.0 + - - -
103Q LEU* 3.9 13.9 - - + -
105Q GLY 5.3 0.2 - - - -
106Q TYR* 3.7 26.1 - + + +
82R LYS* 5.0 5.8 - - - -
102R GLY 2.9 18.9 + - - +
103R LEU* 3.2 13.9 - - + +
105R GLY* 1.3 74.3 - - - +
107R TYR* 1.3 81.2 + + - +
110R ALA* 2.8 46.1 + - + +
111R PHE* 3.7 27.6 - + - -
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Residues in contact with TYR 107 (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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1008 T 4.4 6.5 - - + +
1018 A 3.4 25.3 + - - -
71O PRO* 6.5 0.9 - - + -
75R ILE* 3.5 37.7 - - + -
78R GLY* 3.5 4.9 - - - -
79R PHE* 3.5 39.7 + + + -
82R LYS* 4.6 4.9 - - + -
103R LEU* 3.0 29.2 + - + +
104R LYS 3.8 6.3 - - - +
106R TYR* 1.3 95.5 - + - +
108R ILE* 1.3 65.6 + - - +
111R PHE* 3.0 45.9 + + - -
113R ALA* 3.1 22.6 + - + +
118R LEU* 4.4 2.7 - - + -
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Residues in contact with ILE 108 (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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104R LYS* 3.0 45.7 + - + +
105R GLY* 3.6 10.5 - - - +
107R TYR* 1.3 76.8 - - - +
109R SER* 1.3 62.9 + - - +
112R ASN* 3.0 25.6 - - - +
113R ALA 3.5 16.4 - - - +
115R PRO* 3.9 25.4 - - + -
118R LEU* 3.3 16.6 - - + -
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Residues in contact with SER 109 (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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98Q ASN* 3.5 17.9 - - - +
101Q ASN* 4.2 6.9 + - - -
102Q GLY* 3.0 28.4 - - - -
105R GLY 3.0 11.0 + - - -
108R ILE* 1.3 83.2 - - - +
110R ALA* 1.3 64.7 + - - +
111R PHE 3.4 0.2 - - - -
112R ASN* 4.0 10.8 - - - +
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Residues in contact with ALA 110 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69O THR* 2.6 33.6 + - - +
98Q ASN* 3.7 13.9 - - - +
99Q MET* 4.2 14.7 - - - +
102Q GLY* 4.1 11.7 - - - -
106R TYR* 2.8 35.9 + - + +
109R SER* 1.3 75.6 + - - +
111R PHE* 1.3 70.2 + - + +
112R ASN* 5.2 1.3 - - - -
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Residues in contact with PHE 111 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1008 T 3.6 39.3 - - - -
69O THR* 3.4 17.5 - - - +
70O GLY* 3.6 18.6 - - - -
71O PRO* 4.6 3.4 - - + -
72O ASN* 3.2 18.6 + - - +
82Q LYS* 6.1 0.2 - - - -
99Q MET* 3.8 24.0 - - + -
75R ILE* 4.6 13.4 - - + +
106R TYR* 3.7 37.7 - + - -
107R TYR* 3.0 46.1 + + + +
110R ALA* 1.3 80.1 - - + +
112R ASN* 1.3 74.5 + - - +
113R ALA* 3.2 2.4 + - - +
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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