Contacts of the helix formed by residues 84 - 108 (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 GLU 84 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C PRO* 2.9 13.1 + - - +
83C ALA* 1.3 71.4 - - - +
85C ILE* 1.3 69.8 + - + +
86C PRO* 3.2 3.4 - - - +
87C LEU* 3.5 2.2 + - - +
88C ALA* 3.2 22.0 + - - +
131C LEU* 5.4 8.6 - - - +
132C LEU* 4.9 3.0 - - - +
138C LYS* 5.4 4.5 - - - -
141C LEU* 4.0 17.4 - - - +
145C LYS* 2.8 37.7 + - - +
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Residues in contact with ILE 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C GLU* 5.6 12.1 - - + +
70C THR 6.1 0.4 - - - +
84C GLU* 1.3 78.2 - - + +
86C PRO* 1.3 78.7 - - + +
88C ALA* 3.5 7.6 + - - +
89C GLN* 3.2 21.6 + - + +
132C LEU* 4.9 10.5 - - + -
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Residues in contact with PRO 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C THR 6.0 1.8 - - - +
82C PRO 5.0 0.2 - - - +
83C ALA* 3.3 25.8 - - + -
84C GLU 3.2 8.3 - - - +
85C ILE* 1.3 101.7 - - + +
87C LEU* 1.3 59.3 + - - +
89C GLN* 3.1 16.9 + - + +
90C GLU* 2.8 27.1 + - - +
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Residues in contact with LEU 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C ALA* 2.7 28.7 + - + +
84C GLU* 3.9 2.5 - - - +
85C ILE 3.4 0.4 - - - -
86C PRO* 1.3 78.7 - - - +
88C ALA* 1.3 55.6 - - - +
90C GLU* 2.9 25.8 + - - +
91C VAL* 2.7 38.0 + - + +
131C LEU* 4.0 17.9 - - + -
145C LYS* 4.1 17.3 - - + -
148C VAL* 3.8 24.7 - - + -
149C THR* 3.7 28.7 - - + -
152C ILE* 4.0 12.1 - - + -
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Residues in contact with ALA 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C GLU 3.2 11.3 + - - +
85C ILE* 3.6 10.3 - - + +
87C LEU* 1.3 78.8 - - - +
89C GLN* 1.3 57.1 + - - +
91C VAL* 3.4 7.4 + - - +
92C THR* 3.1 21.3 + - - -
128C ARG* 3.2 26.4 + - + +
131C LEU* 5.4 6.2 - - + +
132C LEU* 3.8 36.6 - - + -
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Residues in contact with GLN 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C VAL* 3.6 18.6 + - - +
70C THR 3.5 26.6 + - - +
85C ILE* 3.2 13.8 + - + +
86C PRO* 3.1 19.6 + - + +
87C LEU 3.0 0.4 - - - -
88C ALA* 1.3 78.4 - - - +
90C GLU* 1.3 63.3 + - - +
92C THR* 3.2 9.5 + - - +
93C THR* 3.1 27.7 + - - +
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Residues in contact with GLU 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C PRO 2.8 12.7 + - - +
87C LEU* 2.9 24.5 + - + +
89C GLN* 1.3 74.1 - - - +
91C VAL* 1.3 56.3 + - - +
93C THR* 3.3 7.6 + - - +
94C THR* 2.6 44.6 + - - +
149C THR* 5.6 0.9 - - - +
152C ILE* 3.7 28.0 - - + +
153C ASP* 5.1 2.9 - - - +
156C ASN* 5.3 1.4 + - - -
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Residues in contact with VAL 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C LEU* 2.7 19.7 + - + +
88C ALA* 3.4 11.0 - - - +
89C GLN 3.2 0.2 - - - -
90C GLU* 1.3 76.5 - - - +
92C THR* 1.3 56.6 + - - +
94C THR* 3.2 6.5 + - - -
95C LEU* 2.8 49.8 + - + +
124C LEU* 3.9 27.1 - - + +
128C ARG* 3.6 22.0 - - + -
131C LEU* 5.6 1.3 - - + -
148C VAL* 3.7 29.8 - - + -
152C ILE* 4.1 7.2 - - + -
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Residues in contact with THR 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C LYS* 5.4 2.2 - - - +
88C ALA 3.1 5.0 + - - -
89C GLN* 3.2 11.5 + - - -
91C VAL* 1.3 78.7 - - - +
93C THR* 1.3 64.6 + - - +
95C LEU* 3.3 2.9 + - - +
96C TRP* 3.1 41.3 + - + +
128C ARG* 3.2 31.7 + - - -
699D LEU* 4.0 20.6 - - + +
700D ASP* 4.3 20.3 + - - +
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Residues in contact with THR 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C GLN* 3.1 16.6 + - - +
90C GLU* 3.8 9.4 - - - -
92C THR* 1.3 79.8 - - - +
94C THR* 1.3 64.2 + - - +
96C TRP* 3.4 7.1 + - - +
97C GLU* 3.1 39.9 + - + +
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Residues in contact with THR 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C GLU* 2.6 30.1 + - - +
91C VAL* 3.5 7.6 - - - -
93C THR* 1.3 78.6 - - - +
95C LEU* 1.3 56.9 + - - +
97C GLU* 3.0 8.8 + - - +
98C TRP* 2.8 71.7 + - + +
124C LEU* 4.1 7.9 - - + -
152C ILE* 3.9 19.6 - - + +
156C ASN* 4.1 8.7 + - - +
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Residues in contact with LEU 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C VAL* 2.8 43.2 + - + +
92C THR 3.6 4.5 - - - +
94C THR* 1.3 73.3 - - - +
96C TRP* 1.3 57.4 + - - +
98C TRP* 3.3 2.4 + - + -
99C GLY* 2.8 28.9 + - - -
121C MSE 3.7 51.9 - - + +
124C LEU* 4.1 13.9 - - + -
125C MSE 3.6 27.4 - - + +
696D LEU* 3.7 14.4 - - + +
699D LEU* 3.9 21.8 - - + -
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Residues in contact with TRP 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C LYS* 3.2 49.2 - - + +
92C THR* 3.1 42.5 + - + +
93C THR* 3.9 7.4 - - - +
94C THR 3.3 0.2 - - - -
95C LEU* 1.3 78.1 - - - +
97C GLU* 1.3 63.0 + - + +
99C GLY* 3.5 0.9 + - - -
100C SER* 3.4 19.1 + - - -
693D GLU* 3.8 17.7 - - - -
696D LEU* 3.6 51.3 + - + -
697D ARG* 3.7 29.8 - - + -
699D LEU* 4.3 3.9 - - + +
700D ASP* 5.6 1.0 + - - -
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Residues in contact with GLU 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C THR* 3.1 27.3 + - + +
94C THR* 3.0 10.4 + - - +
96C TRP* 1.3 75.8 - - + +
98C TRP* 1.3 66.5 + - + +
100C SER* 3.4 14.0 + - - -
101C ILE* 3.5 16.7 + - - +
161C LEU* 4.3 26.6 - - + +
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Residues in contact with TRP 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C THR* 2.8 36.4 + - + +
95C LEU* 3.9 4.7 - - + +
97C GLU* 1.3 74.3 - - + +
99C GLY* 1.3 52.4 + - - +
101C ILE* 3.1 5.3 + - - +
102C TRP* 2.7 35.9 + - - +
117C VAL* 4.5 3.4 - - + +
120C MSE 3.7 30.5 - - + -
121C MSE 4.0 28.0 - - + -
124C LEU* 3.3 33.4 - - + -
151C LYS* 3.5 21.5 - - + -
152C ILE* 3.6 12.3 - - - -
155C GLY* 3.4 25.8 - - - -
156C ASN* 3.0 21.6 + - - +
159C LEU* 3.7 21.3 - - + +
161C LEU* 3.7 19.5 - - + +
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Residues in contact with GLY 99 (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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95C LEU 2.8 17.2 + - - -
96C TRP 3.5 2.2 + - - -
97C GLU 3.2 0.2 - - - -
98C TRP* 1.3 77.1 - - - +
100C SER* 1.3 59.7 + - - +
102C TRP* 3.3 8.5 + - - +
103C LYS* 3.2 33.2 + - - +
121C MSE 3.6 18.1 - - - +
696D LEU* 4.6 10.1 - - - -
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Residues in contact with SER 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C TRP 3.4 12.1 + - - -
97C GLU* 3.7 9.6 - - - -
98C TRP 3.2 0.4 - - - -
99C GLY* 1.3 75.4 - - - +
101C ILE* 1.3 65.4 + - - +
103C LYS* 3.5 12.8 + - - +
104C GLN* 3.4 31.9 + - - +
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Residues in contact with ILE 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C GLU 3.5 9.6 + - - +
98C TRP* 3.1 8.4 + - - +
100C SER* 1.3 75.8 - - - +
102C TRP* 1.3 65.0 + - - +
104C GLN* 3.0 23.6 + - + +
105C LEU* 2.9 37.9 + - + +
159C LEU* 4.1 30.5 - - + +
161C LEU* 3.5 42.2 - - + -
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Residues in contact with TRP 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C TRP 2.7 20.3 + - - +
99C GLY* 3.4 12.1 - - - +
100C SER 3.3 0.2 - - - -
101C ILE* 1.3 73.5 - - - +
103C LYS* 1.3 61.2 + - + +
105C LEU* 3.1 11.3 + - + +
106C TYR* 2.9 23.6 + - - +
114C PHE* 2.9 67.6 + + - -
117C VAL* 3.6 20.4 - - + +
118C GLN* 3.6 29.8 - - + +
121C MSE 4.1 10.5 - - + -
122C TYR* 5.4 0.9 - - - -
688D THR* 3.5 27.6 - - + -
689D LEU* 3.7 23.3 - - + -
692D MSE 3.4 37.5 - - + -
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Residues in contact with LYS 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C GLY* 3.2 17.1 + - - +
100C SER* 3.8 12.2 - - - +
101C ILE 3.3 0.2 - - - -
102C TRP* 1.3 81.2 - - + +
104C GLN* 1.3 57.6 + - + +
106C TYR* 3.2 8.0 + - - +
107C VAL* 2.9 36.1 + - - +
543D GLU* 3.9 15.1 + - - -
544D ILE* 5.2 4.5 - - - -
547D LEU* 3.8 33.9 - - + -
689D LEU* 4.9 11.4 - - + -
693D GLU* 2.9 36.3 + - - -
696D LEU* 6.1 1.8 - - - -
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Residues in contact with GLN 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C SER* 3.4 28.5 + - - +
101C ILE* 3.0 28.8 + - + +
103C LYS* 1.3 74.4 - - + +
105C LEU* 1.3 67.6 + - + +
107C VAL* 3.6 5.5 + - - +
108C ALA* 3.1 25.6 + - - +
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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
----------------------------------------------------------
101C ILE* 2.9 32.0 + - + +
102C TRP* 3.1 13.7 + - - +
104C GLN* 1.3 75.4 - - + +
106C TYR* 1.3 68.1 + - - +
108C ALA 3.3 1.2 + - - -
109C SER 3.0 14.7 + - - -
110C LYS* 3.1 37.6 + - + -
113C ARG* 4.0 24.7 - - + +
114C PHE* 4.1 16.3 - - + +
117C VAL* 3.8 29.2 - - + -
159C LEU* 4.6 4.5 - - + -
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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
----------------------------------------------------------
102C TRP 2.9 8.4 + - - +
103C LYS* 3.4 10.8 - - - +
105C LEU* 1.3 75.5 - - - +
107C VAL* 1.3 74.6 + - + +
109C SER* 2.7 27.2 + - - +
114C PHE* 3.5 40.5 - + + -
547D LEU* 3.8 5.8 - - + -
548D ILE* 3.4 27.8 - - - +
551D GLN* 3.4 39.9 + - + +
552D ARG* 3.7 4.0 + - - -
685D ASP* 2.6 42.7 + - + +
689D LEU* 3.5 30.3 - - + -
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Residues in contact with VAL 107 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C LYS 2.9 19.6 + - - +
104C GLN* 4.1 5.6 - - - +
106C TYR* 1.3 74.4 - - + +
108C ALA* 1.3 58.0 + - - +
109C SER* 3.3 0.9 + - - -
547D LEU* 3.7 40.8 - - + +
550D GLN* 3.8 27.4 - - + +
551D GLN* 3.6 18.7 - - - +
554D ASN* 2.9 41.2 + - - +
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Residues in contact with ALA 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C GLN 3.1 17.3 + - - +
105C LEU 3.3 0.2 + - - -
106C TYR 2.9 1.0 + - - -
107C VAL* 1.3 77.0 - - - +
109C SER* 1.3 69.6 + - - +
110C LYS* 3.3 28.8 + - + -
554D ASN* 4.7 6.1 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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