Contacts of the helix formed by residues 110 - 132 (chain C) in PDB entry 3A98
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 LYS 110 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C LEU* 3.1 42.1 + - + +
108C ALA* 3.6 30.9 + - + +
109C SER* 1.3 72.8 - - - +
111C LYS* 1.3 63.5 + - - +
112C GLU 3.5 2.5 - - - -
113C ARG* 3.4 9.0 + - + -
114C PHE* 2.9 23.6 + - - +
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Residues in contact with LYS 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725B ASP* 6.1 0.4 - - - +
109C SER* 2.9 21.1 + - - +
110C LYS* 1.3 68.7 - - - +
112C GLU* 1.3 64.2 + - - +
114C PHE* 3.1 9.6 + - - +
115C LEU* 3.0 33.5 + - + +
555D ARG* 3.9 33.1 - - - +
660D HIS* 4.5 15.8 + - - -
661D GLU* 5.7 0.4 + - - -
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Residues in contact with GLU 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725B ASP* 5.7 3.1 - - - -
110C LYS 3.5 0.8 - - - -
111C LYS* 1.3 79.3 - - - +
113C ARG* 1.3 91.2 + - - +
115C LEU* 3.3 6.2 + - - +
116C GLN* 3.0 28.3 + - + +
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Residues in contact with ARG 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C LEU* 4.0 23.8 - - + -
110C LYS* 3.4 12.1 + - + +
112C GLU* 1.3 102.5 + - - +
114C PHE* 1.3 58.2 + - - +
116C GLN* 3.2 27.0 + - - +
117C VAL* 2.8 36.2 + - - +
154C TYR* 5.7 0.8 + - - -
158C ILE* 4.1 39.8 + - - +
159C LEU* 4.4 17.9 - - - -
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Residues in contact with PHE 114 (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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102C TRP* 2.9 76.5 + + - -
105C LEU* 4.1 11.6 - - + +
106C TYR* 3.5 43.5 - + + -
110C LYS 2.9 19.4 + - - +
111C LYS* 3.1 7.4 + - - +
113C ARG* 1.3 77.4 - - - +
115C LEU* 1.3 71.1 + - + +
118C GLN* 2.9 37.2 + - - +
688D THR* 4.3 10.8 - - + -
689D LEU* 4.3 4.9 - - + -
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Residues in contact with LEU 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725B ASP* 3.2 38.8 - - + +
726B CYS* 3.8 34.1 - - + +
111C LYS* 3.0 26.1 + - + +
112C GLU* 3.9 4.9 - - - +
114C PHE* 1.3 86.9 - - + +
116C GLN* 1.3 65.4 + - - +
118C GLN* 3.3 23.3 + - - +
119C SER* 3.1 25.6 + - - -
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Residues in contact with GLN 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C GLU* 3.0 20.8 + - + +
113C ARG* 3.2 35.1 + - - +
115C LEU* 1.3 78.7 - - - +
117C VAL* 1.3 63.6 + - + +
119C SER* 3.4 5.1 + - - -
120C MSE 3.0 38.3 + - + +
154C TYR* 3.1 36.6 + - - -
158C ILE* 3.9 10.1 - - + -
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Residues in contact with VAL 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C TRP* 4.5 11.0 - - + +
102C TRP* 3.6 28.3 - - + -
105C LEU* 3.8 16.2 - - + -
113C ARG* 2.8 23.5 + - - +
116C GLN* 1.3 74.4 - - + +
118C GLN* 1.3 66.2 + - - +
120C MSE 3.8 21.7 - - + +
121C MSE 2.9 40.4 + - + +
158C ILE* 5.4 0.4 - - + -
159C LEU* 3.9 23.3 - - + -
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Residues in contact with GLN 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ALA* 5.3 1.2 - - - +
25A PRO* 5.5 1.2 - - - +
722B PHE* 6.3 1.8 - - - -
726B CYS* 4.8 7.2 - - - -
102C TRP* 3.6 29.6 - - + +
114C PHE* 2.9 22.8 + - - +
115C LEU* 3.4 28.8 - - - +
117C VAL* 1.3 78.1 - - - +
119C SER* 1.3 57.8 + - - +
121C MSE 3.3 5.7 + - - +
122C TYR* 2.9 70.9 + - + -
688D THR* 3.5 21.7 + - - +
692D MSE 5.9 0.7 - - - -
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Residues in contact with SER 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720B TYR 2.7 27.6 + - - -
721B ASP* 4.2 11.5 - - - -
722B PHE* 4.1 13.5 + - - -
115C LEU 3.1 13.1 + - - -
116C GLN* 3.8 4.9 - - - -
118C GLN* 1.3 78.5 - - - +
120C MSE 1.3 60.2 + - - +
122C TYR* 3.2 9.3 + - - +
123C ASP* 2.9 34.7 + - - +
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Residues in contact with MSE 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721B ASP* 5.5 0.7 - - - +
98C TRP* 3.7 27.8 - - + -
116C GLN* 3.0 20.8 + - + +
117C VAL* 3.3 29.6 + - + +
119C SER* 1.3 75.2 - - - +
121C MSE 1.3 57.3 + - - +
123C ASP* 3.3 9.8 + - - +
124C LEU* 3.0 32.7 + - - +
151C LYS* 4.1 21.6 - - + +
154C TYR* 4.0 32.3 - - - -
155C GLY* 3.9 18.8 - - - -
158C ILE* 4.2 10.1 - - + -
159C LEU* 4.4 5.6 - - + -
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Residues in contact with MSE 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C LEU* 3.7 31.1 - - + +
98C TRP* 4.0 15.3 - - + -
99C GLY* 3.6 34.3 - - - -
102C TRP* 4.1 17.0 - - - -
117C VAL* 2.9 34.1 + - + +
118C GLN 3.5 4.9 - - - +
120C MSE 1.3 74.3 - - - +
122C TYR* 1.3 65.5 + - - +
124C LEU* 3.3 2.4 + - - +
125C MSE 3.0 29.4 + - - +
692D MSE 3.7 35.0 - - + +
696D LEU* 3.9 14.4 - - + -
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Residues in contact with TYR 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ALA* 3.7 8.4 + - - +
25A PRO* 3.5 46.0 - - + +
720B TYR* 3.6 41.6 - + + -
722B PHE* 5.0 6.3 - + - -
102C TRP* 5.4 0.5 - - - -
118C GLN* 2.9 57.0 + - + +
119C SER* 3.6 8.7 - - - +
121C MSE 1.3 77.0 - - - +
123C ASP* 1.3 61.9 + - - +
125C MSE 3.3 7.9 + - - +
126C GLU* 3.0 26.0 + - - +
688D THR* 4.6 6.1 + - - +
692D MSE 3.6 36.3 - - + -
695D LYS* 4.5 3.8 - - + -
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Residues in contact with ASP 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
719B ASN* 3.6 4.9 - - - -
720B TYR* 2.8 29.7 + - - -
721B ASP* 2.5 33.1 - - - +
119C SER 2.9 18.6 + - - +
120C MSE 3.5 6.0 - - - +
122C TYR* 1.3 78.2 - - - +
124C LEU* 1.3 57.4 + - - +
126C GLU* 3.3 3.5 + - - -
127C TRP* 2.8 63.5 + - + +
151C LYS* 3.8 14.9 - - - -
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Residues in contact with LEU 124 (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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91C VAL* 3.9 19.1 - - + +
94C THR* 4.1 13.0 - - + -
95C LEU* 4.1 14.4 - - + -
98C TRP* 3.3 36.6 - - + -
120C MSE 3.0 17.9 + - - +
121C MSE 3.3 4.0 + - - +
123C ASP* 1.3 75.2 - - - +
125C MSE 1.3 58.8 + - - +
127C TRP* 4.0 7.8 - - + +
128C ARG* 2.8 33.3 + - - +
148C VAL* 4.1 32.1 - - + +
151C LYS* 4.1 16.4 - - + -
152C ILE* 4.2 11.0 - - + -
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Residues in contact with MSE 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C LEU* 3.6 20.4 - - + -
121C MSE 3.0 19.1 + - - +
122C TYR* 3.7 7.6 - - - +
124C LEU* 1.3 75.1 - - - +
126C GLU* 1.3 58.9 + - - +
128C ARG* 3.3 5.2 + - - +
129C SER* 2.9 30.5 + - - -
692D MSE 3.2 33.7 - - + +
695D LYS* 3.4 38.6 - - + +
696D LEU* 3.4 37.2 - - + +
699D LEU* 4.5 12.4 - - + +
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Residues in contact with GLU 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
715B LYS* 5.8 4.3 - - - +
716B GLU* 2.8 37.5 - - - +
717B PRO 3.3 24.3 - - - +
718B SER* 3.6 13.4 - - - +
720B TYR* 4.0 11.7 + - + -
122C TYR 3.0 16.0 + - - +
123C ASP* 3.7 3.6 - - - +
125C MSE 1.3 76.7 - - - +
127C TRP* 1.3 57.8 + - + +
129C SER* 3.3 7.2 + - - -
130C GLN* 2.8 58.0 + - - +
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Residues in contact with TRP 127 (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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1A MSE 3.8 11.9 - - + -
718B SER 2.9 26.5 + - - -
719B ASN* 4.5 4.0 - - + +
721B ASP* 4.6 3.4 - - - -
123C ASP* 2.8 48.5 + - + +
124C LEU* 4.0 6.5 - - + +
126C GLU* 1.3 70.6 - - + +
128C ARG* 1.3 61.7 + - - +
130C GLN* 3.1 18.6 + - - +
131C LEU* 2.8 35.2 + - - +
144C LEU* 3.6 16.1 - - + +
147C LYS* 3.5 52.3 - - + -
148C VAL* 3.7 32.1 - - + -
151C LYS* 3.8 33.0 - - + -
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Residues in contact with ARG 128 (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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88C ALA* 3.2 35.2 + - + +
91C VAL* 3.6 21.3 - - + -
92C THR* 3.2 17.9 + - - -
124C LEU 2.8 22.6 + - - +
125C MSE 3.6 4.9 + - - +
127C TRP* 1.3 71.4 - - - +
129C SER* 1.3 65.3 + - - +
131C LEU* 3.0 14.3 + - - +
132C LEU* 2.9 46.7 + - + +
148C VAL* 5.1 0.6 - - - +
699D LEU* 3.0 53.3 + - - +
700D ASP* 4.1 10.1 + - - +
702D GLU* 3.4 18.4 - - - +
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Residues in contact with SER 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
716B GLU* 4.4 10.3 + - - -
125C MSE 2.9 14.3 + - - -
126C GLU* 3.4 15.2 + - - -
128C ARG* 1.3 78.3 - - - +
130C GLN* 1.3 57.0 + - - +
132C LEU* 3.3 2.9 + - - +
133C SER* 3.0 30.4 + - - -
702D GLU* 3.6 33.5 + - - +
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Residues in contact with GLN 130 (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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1A MSE 5.0 5.4 - - - +
715B LYS* 6.4 2.0 - - - -
718B SER* 3.8 17.7 + - - +
126C GLU* 2.8 50.0 + - - +
127C TRP* 3.1 20.4 + - - +
129C SER* 1.3 78.4 - - - +
131C LEU* 1.3 62.3 + - - +
133C SER* 2.8 24.6 + - - -
134C GLY 4.2 1.4 + - - -
136C LEU* 3.7 30.8 - - + +
141C LEU* 5.0 0.5 - - - +
144C LEU* 3.5 21.9 - - + +
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Residues in contact with LEU 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C GLU* 5.4 10.4 - - - +
87C LEU* 4.0 23.8 - - + -
88C ALA* 5.4 5.8 - - + +
91C VAL* 5.6 0.9 - - + -
127C TRP 2.8 22.8 + - - +
128C ARG* 3.0 11.0 + - - +
130C GLN* 1.3 73.7 - - - +
132C LEU* 1.3 66.1 + - + +
133C SER 3.6 0.3 + - - -
134C GLY* 4.3 5.0 + - - -
141C LEU* 3.4 35.1 - - + +
144C LEU* 3.7 21.1 - - + -
145C LYS* 3.9 20.2 - - + +
148C VAL* 3.9 23.6 - - + -
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Residues in contact with LEU 132 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C GLU 4.9 2.9 - - - +
85C ILE* 4.9 14.1 - - + -
88C ALA* 3.8 26.0 - - + -
128C ARG* 2.9 53.6 + - + +
129C SER* 3.6 4.3 - - - +
131C LEU* 1.3 76.7 - - + +
133C SER* 1.3 62.2 + - - +
134C GLY 3.3 2.4 + - - -
702D GLU* 4.3 14.6 - - + +
703D ASN* 2.9 30.6 + - - +
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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