Contacts of the helix formed by residues 91 - 111 (chain C) in PDB entry 2J3W
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 GLN 91 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C PHE* 4.1 15.5 - - + -
87C HIS* 4.1 1.0 + - - -
89C VAL* 2.8 21.2 + - - +
90C ARG* 1.3 74.3 + - - +
92C GLU* 1.3 57.4 + - - +
93C ASP 3.3 2.2 - - - -
94C GLY* 3.6 19.6 + - - -
95C ILE* 2.8 52.4 + - + +
137C HIS 3.4 18.2 - - - +
138C LEU* 4.3 8.3 + - + -
140C SER 3.7 18.8 + - - +
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Residues in contact with GLU 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C TYR* 2.6 41.0 + - + +
62C LYS* 3.7 33.8 + - + +
87C HIS* 5.7 0.6 - - - -
90C ARG* 3.5 9.0 + - + +
91C GLN* 1.3 74.2 - - - +
93C ASP* 1.3 67.4 + - - +
95C ILE* 4.8 1.1 - - - -
96C LYS* 3.1 14.0 + - - +
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Residues in contact with ASP 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C TYR* 5.9 0.2 - - - -
91C GLN 3.3 0.2 - - - -
92C GLU* 1.3 91.8 - - - +
94C GLY* 1.3 68.2 + - - +
95C ILE 3.2 0.2 - - - -
96C LYS* 3.2 11.3 + - - +
97C ASN* 3.0 39.1 + - - +
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Residues in contact with GLY 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C GLN* 3.3 17.5 + - - +
93C ASP* 1.3 77.1 - - - +
95C ILE* 1.3 58.1 + - - +
97C ASN* 3.8 3.9 - - - -
98C PHE* 2.8 29.3 + - - +
137C HIS* 3.4 31.3 - - - +
138C LEU* 4.3 1.6 - - - -
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Residues in contact with ILE 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C PHE* 4.5 2.7 - - + -
60C TYR* 3.8 11.0 - - - +
73C SER* 4.2 9.0 - - - +
85C MET* 4.5 10.8 - - + -
87C HIS* 3.2 46.2 - - + +
91C GLN* 2.8 39.8 + - + +
92C GLU* 4.3 1.1 - - - +
94C GLY* 1.3 74.1 - - - +
96C LYS* 1.3 59.2 + - - +
98C PHE* 3.3 6.0 + - - +
99C PHE* 2.9 61.2 + - + -
138C LEU* 4.2 11.4 - - + -
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Residues in contact with LYS 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C TYR* 3.4 54.1 + - + +
75C PHE* 5.5 1.6 - - + -
92C GLU 3.1 12.7 + - - +
93C ASP* 3.2 13.2 + - - +
95C ILE* 1.3 76.9 - - - +
97C ASN* 1.3 68.2 + - - +
99C PHE* 3.4 3.9 + - - +
100C THR* 3.0 43.8 + - + +
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Residues in contact with ASN 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C ASP* 3.0 28.2 + - - +
94C GLY* 3.9 1.6 - - - +
96C LYS* 1.3 85.4 - - - +
98C PHE* 1.3 67.7 + - - +
100C THR* 3.2 9.9 + - - +
101C ASP* 3.0 28.0 + - - +
137C HIS* 3.7 25.5 + - + +
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Residues in contact with PHE 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C PHE* 3.7 31.6 - + - -
22C PHE* 4.0 11.7 - + - -
85C MET* 3.5 27.8 - - + -
94C GLY 2.8 18.1 + - - +
95C ILE 3.5 4.0 - - - +
97C ASN* 1.3 78.2 - - - +
99C PHE* 1.3 64.5 + + - +
101C ASP* 3.2 1.4 + - - +
102C VAL* 2.9 54.7 + - + +
130C VAL* 3.8 11.0 - - + -
133C LEU* 3.8 23.8 - - + -
134C GLY* 3.7 26.0 - - - -
137C HIS* 3.7 14.7 - - + -
138C LEU* 3.9 14.1 - - + -
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Residues in contact with PHE 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C PHE* 3.8 25.6 - + - -
60C TYR* 3.7 23.3 - + - -
73C SER 4.0 3.4 - - - -
74C ALA* 3.8 10.5 - - - -
75C PHE* 3.4 36.3 - - + -
83C PHE* 3.5 35.9 - + + -
85C MET* 3.7 27.6 - - + -
95C ILE* 2.9 33.5 + - + -
96C LYS 3.4 7.9 - - - +
98C PHE* 1.3 84.5 - + - +
100C THR* 1.3 51.5 + - - +
102C VAL* 3.3 1.8 + - - -
103C TYR* 2.7 35.8 + - - +
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Residues in contact with THR 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C PHE* 4.0 23.8 - - + -
96C LYS* 3.0 29.6 + - + +
97C ASN* 3.2 16.2 + - - +
99C PHE* 1.3 73.0 - - - +
101C ASP* 1.3 71.4 + - - +
103C TYR* 3.6 10.4 - - + +
104C ASP* 3.2 26.0 + - - +
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Residues in contact with ASP 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C ASN* 3.0 16.6 + - - +
98C PHE 3.6 3.4 - - - +
100C THR* 1.3 80.6 + - - +
102C VAL* 1.3 62.9 + - - +
104C ASP* 3.3 8.8 + - - +
105C LEU* 3.1 20.3 + - - +
133C LEU* 3.6 29.0 - - + +
136C LYS* 4.7 4.2 + - - -
137C HIS* 2.6 31.6 + - - +
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Residues in contact with VAL 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C PHE* 3.9 24.7 - - + -
9C ILE* 4.3 11.2 - - + -
83C PHE* 4.2 8.3 - - + -
98C PHE* 2.9 49.9 + - + +
99C PHE 3.8 4.3 - - - +
101C ASP* 1.3 73.5 - - - +
103C TYR* 1.3 55.9 + - - +
105C LEU* 3.1 7.3 + - - +
106C TYR* 2.7 33.1 + - - +
126C PHE* 4.4 12.8 - - + -
130C VAL* 4.2 9.4 - - + -
133C LEU* 3.8 16.8 - - + -
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Residues in contact with TYR 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C MET* 3.6 12.8 - - - -
75C PHE* 3.7 19.1 - + + -
77C THR* 3.4 27.1 - - + -
78C ALA* 3.1 11.3 + - - +
83C PHE* 3.8 13.2 - + + -
99C PHE 2.7 19.0 + - - +
100C THR* 3.6 10.8 - - + +
102C VAL* 1.3 77.1 - - - +
104C ASP* 1.3 58.3 + - - +
106C TYR* 3.3 9.4 + + - +
107C ILE* 2.9 53.1 + - + +
67F ASP* 2.7 29.4 + - - -
71F MET* 3.1 44.8 - - + +
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Residues in contact with ASP 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C THR 3.2 14.4 + - - +
101C ASP* 3.4 12.6 - - - +
103C TYR* 1.3 79.7 - - - +
105C LEU* 1.3 65.1 + - - +
107C ILE* 3.3 14.5 + - - +
108C LYS* 3.1 49.1 + - + +
71F MET* 5.4 7.4 - - - +
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Residues in contact with LEU 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C ASP 3.1 9.2 + - - +
102C VAL* 3.3 9.2 - - - +
104C ASP* 1.3 80.6 - - - +
106C TYR* 1.3 57.2 + - - +
108C LYS* 3.3 13.3 + - + +
109C PHE* 3.0 26.7 + - + +
126C PHE* 3.3 28.9 - - + +
129C LYS* 3.5 50.9 - - + +
130C VAL* 3.6 28.3 - - + +
133C LEU* 4.3 10.5 - - + -
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Residues in contact with TYR 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C ILE* 5.0 9.0 - - + -
77C THR* 5.3 0.7 - - + -
81C MET* 3.4 47.5 - - + +
83C PHE* 4.6 10.8 - + + -
102C VAL* 2.7 20.2 + - + +
103C TYR* 3.4 21.1 - + - +
105C LEU* 1.3 74.4 - - - +
107C ILE* 1.3 57.8 + - + +
109C PHE* 3.1 4.9 + + - +
110C ALA* 2.7 54.9 + - + +
115C TYR* 4.3 12.3 - + - -
117C PRO 4.2 10.2 + - - -
121C ILE* 3.9 28.7 - - + -
126C PHE* 4.0 13.3 - - + -
67F ASP* 5.0 13.0 - - - -
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Residues in contact with ILE 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C TYR* 2.9 63.8 + - + +
104C ASP* 3.6 14.1 - - - +
106C TYR* 1.3 76.3 - - + +
108C LYS* 1.3 63.7 + - + +
110C ALA* 3.4 4.0 + - - +
111C MET* 3.0 50.0 + - + +
64F SER 5.3 1.3 - - - +
67F ASP* 3.8 30.5 - - + +
68F VAL* 4.6 9.0 - - + +
71F MET* 4.8 9.4 - - + -
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Residues in contact with LYS 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C ASP* 3.1 36.1 + - - +
105C LEU* 3.5 13.5 - - + +
107C ILE* 1.3 79.5 - - + +
109C PHE* 1.3 63.0 + - - +
111C MET* 3.3 16.9 + - + +
112C ASN* 3.9 3.8 + - - +
115D PHE* 4.0 40.5 - - + +
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Residues in contact with PHE 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C LEU* 3.0 15.5 + - + +
106C TYR* 3.3 13.5 - + - +
108C LYS* 1.3 77.9 - - - +
110C ALA* 1.3 60.9 + - + +
112C ASN* 3.3 26.6 + - - +
115C TYR* 3.4 42.5 - + - +
121C ILE* 3.6 36.1 - - + -
122C ARG 4.5 5.2 - - - -
123C SER* 3.8 26.9 - - - -
126C PHE* 4.1 17.9 - + + -
117D GLU* 5.0 15.5 - - - -
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Residues in contact with ALA 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C TYR* 2.7 39.3 + - + +
107C ILE* 3.7 4.5 - - - +
109C PHE* 1.3 69.6 - - - +
111C MET* 1.3 63.7 + - + +
112C ASN 3.1 10.0 + - - +
115C TYR* 3.6 33.9 - - + +
64F SER* 3.9 11.7 + - - -
67F ASP* 6.2 0.2 - - - +
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Residues in contact with MET 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C ILE* 3.0 44.2 + - + +
108C LYS* 3.8 9.0 - - + +
109C PHE 3.2 1.0 - - - -
110C ALA* 1.3 75.5 - - - +
112C ASN* 1.3 65.0 + - - +
113C PRO* 3.0 11.6 - - - +
17D GLU* 4.6 9.4 - - - +
21D LEU* 4.1 25.8 - - + +
114D ASP 5.3 0.2 - - - +
115D PHE* 4.1 45.5 - - + +
64F SER* 3.8 30.8 + - - +
68F VAL* 4.0 23.8 - - + -
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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