Contacts of the helix formed by residues 91 - 114 (chain A) in PDB entry 3S5E
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 ASP 91 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A SER 3.2 6.1 + - - +
90A LEU* 1.3 78.0 - - - +
92A GLU* 1.3 65.8 + - - +
93A THR* 3.6 9.4 + - - +
94A THR* 2.7 42.2 + - - -
95A TYR* 2.9 22.0 + - - +
152A LYS* 4.3 2.2 - - - +
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Residues in contact with GLU 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A ASP* 1.3 77.0 - - - +
93A THR* 1.3 63.7 + - - +
95A TYR* 3.4 8.3 + - + +
96A GLU* 2.9 42.4 + - + +
152A LYS* 4.3 13.6 - - - +
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Residues in contact with THR 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ASP* 3.3 10.5 + - - -
92A GLU* 1.3 80.4 - - - +
94A THR* 1.3 65.1 + - - +
96A GLU* 3.4 5.2 + - - +
97A ARG* 3.1 23.4 + - + +
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Residues in contact with THR 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A LEU* 3.8 21.1 - - + -
91A ASP* 2.7 28.1 + - - -
93A THR* 1.3 74.9 - - - +
95A TYR* 1.3 65.8 + - - +
97A ARG* 3.3 23.2 + - - +
98A LEU* 2.9 35.2 + - + +
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Residues in contact with TYR 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A LEU* 4.1 15.3 - - + +
91A ASP 2.9 18.2 + - - +
92A GLU* 3.7 6.1 - - + +
94A THR* 1.3 78.1 - - - +
96A GLU* 1.3 83.3 + - + +
98A LEU* 4.7 1.3 - - - -
99A ALA* 2.8 42.7 + - + +
147A LYS* 3.4 11.8 - - + +
148A GLN 3.3 16.4 + - - -
149A THR* 4.1 17.0 - - + -
152A LYS* 3.2 54.7 - - + -
153A GLN 2.7 23.3 + - - -
173A TRP* 3.9 18.4 - + - -
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Residues in contact with GLU 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A GLU* 2.9 39.3 + - + +
93A THR* 3.8 5.6 - - - +
95A TYR* 1.3 96.4 - - + +
97A ARG* 1.3 63.1 + - - +
99A ALA* 4.7 2.0 - - - -
100A GLU* 2.9 40.7 + - - +
147A LYS* 2.5 38.9 + - - +
149A THR* 4.2 8.8 - - - +
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Residues in contact with ARG 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A THR* 3.1 18.7 + - + +
94A THR* 3.6 20.5 + - - +
96A GLU* 1.3 76.7 - - - +
98A LEU* 1.3 79.9 + - - +
100A GLU* 3.9 6.4 - - - +
101A GLU* 3.0 56.6 + - + +
205A TYR* 3.4 24.0 + - - -
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Residues in contact with LEU 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A LEU* 3.8 21.8 - - + -
94A THR* 2.9 29.7 + - + +
95A TYR* 3.9 2.9 - - - +
97A ARG* 1.3 96.0 - - - +
99A ALA* 1.3 58.5 + - - +
101A GLU* 3.8 1.4 - - - +
102A THR* 2.7 34.5 + - - -
168A TRP* 3.7 38.6 - - + +
173A TRP* 4.1 11.2 - - + -
205A TYR* 3.5 40.8 - - + +
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Residues in contact with ALA 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A TYR* 2.8 42.9 + - + +
96A GLU* 4.1 2.0 - - - +
98A LEU* 1.3 73.4 - - - +
100A GLU* 1.3 58.0 + - - +
102A THR* 3.3 3.8 + - - -
103A LEU* 2.8 36.8 + - - +
147A LYS* 4.1 21.5 - - + -
154A ILE* 4.4 8.3 - - + -
173A TRP* 4.0 12.9 - - + -
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Residues in contact with GLU 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A GLU* 2.9 30.0 + - - +
97A ARG* 3.9 5.1 - - - +
99A ALA* 1.3 75.6 - - - +
101A GLU* 1.3 58.4 + - + +
103A LEU* 3.3 5.1 + - - +
104A ASP* 2.8 42.4 + - - +
127A PHE* 6.1 0.4 - - - -
147A LYS* 2.8 35.1 + - - +
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Residues in contact with GLU 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A ARG* 3.0 51.9 + - + +
98A LEU* 4.6 0.2 - - - +
100A GLU* 1.3 75.7 - - + +
102A THR* 1.3 61.4 + - - +
104A ASP* 3.8 9.0 - - - +
105A SER* 3.2 24.8 + - - -
204A ALA* 3.9 7.4 - - + +
205A TYR* 2.7 41.2 + - + -
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Residues in contact with THR 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A LEU 2.7 22.3 + - - -
99A ALA 3.5 4.5 - - - -
101A GLU* 1.3 79.6 - - - +
103A LEU* 1.3 62.8 + - - +
105A SER* 3.4 2.9 + - - -
106A LEU* 3.1 30.9 + - + +
154A ILE* 4.0 11.7 - - + -
173A TRP* 2.9 36.9 + - + +
182A LEU* 4.8 1.6 - - + -
183A HIS* 4.1 21.0 + - + -
204A ALA* 4.1 11.5 - - - +
205A TYR* 3.5 12.4 - - - +
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Residues in contact with LEU 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A ALA* 2.8 25.7 + - + +
100A GLU* 3.9 3.4 - - - +
102A THR* 1.3 72.9 - - - +
104A ASP* 1.3 58.8 + - - +
106A LEU* 3.3 11.3 + - + +
107A ALA* 2.8 30.1 + - - +
127A PHE* 3.9 18.6 - - + -
130A GLY* 3.8 29.2 - - - +
132A LEU* 4.3 6.9 - - + +
145A ILE* 3.6 43.3 - - + +
146A ASN 4.4 0.7 - - - +
147A LYS* 3.9 25.6 - - + +
154A ILE* 4.6 12.1 - - + -
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Residues in contact with ASP 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A GLU* 2.8 29.9 + - - +
101A GLU* 3.8 7.8 - - - +
103A LEU* 1.3 71.2 - - - +
105A SER* 1.3 57.6 + - - +
107A ALA* 3.3 3.2 + - - +
108A GLU* 3.0 27.5 + - - +
127A PHE* 3.2 29.0 - - - -
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Residues in contact with SER 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A GLU 3.2 15.4 + - - -
102A THR 3.7 3.1 - - - -
104A ASP* 1.3 78.0 - - - +
106A LEU* 1.3 65.7 + - - +
108A GLU* 3.3 7.5 + - - +
109A PHE* 3.1 21.8 + - - +
203A LEU* 3.4 18.4 - - - +
204A ALA* 2.9 37.4 + - - +
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Residues in contact with LEU 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A THR* 3.1 29.9 + - + +
103A LEU* 3.6 10.8 - - + +
105A SER* 1.3 77.5 - - - +
107A ALA* 1.3 61.9 + - - +
109A PHE* 3.2 2.4 + - - +
110A PHE* 2.9 38.0 + - + -
132A LEU* 3.7 12.1 - - + -
145A ILE* 4.3 15.7 - - + -
182A LEU* 4.0 25.4 - - + -
183A HIS* 4.0 13.0 - - - +
186A LEU* 3.8 24.7 - - + -
200A LEU* 3.9 7.9 - - + -
203A LEU* 3.7 22.4 - - + +
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Residues in contact with ALA 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A LEU 2.8 20.5 + - - +
104A ASP 3.5 5.4 - - - +
105A SER 3.2 0.2 - - - -
106A LEU* 1.3 72.6 - - - +
108A GLU* 1.3 58.3 + - - +
110A PHE* 3.3 2.1 + - - +
111A GLU* 2.8 44.8 + - - +
127A PHE* 3.7 33.0 - - + -
132A LEU* 3.8 17.9 - - + +
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Residues in contact with GLU 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A ASP 3.0 14.0 + - - +
105A SER* 3.7 9.9 - - - +
106A LEU 3.2 0.2 - - - -
107A ALA* 1.3 76.4 - - - +
109A PHE* 1.3 64.3 + - - +
111A GLU* 3.2 12.7 + - - +
112A ASP* 2.9 36.9 + - + +
203A LEU* 6.5 0.4 - - + -
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Residues in contact with PHE 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A SER 3.1 13.0 + - - +
106A LEU 3.2 6.9 + - - +
108A GLU* 1.3 79.0 - - - +
110A PHE* 1.3 86.1 + + - +
112A ASP* 3.4 7.3 + - - +
113A LEU* 3.1 57.0 + - + +
190A LEU* 4.1 4.3 - - + -
198A LEU* 4.5 14.4 - - + -
199A ASP 4.5 9.2 - - - -
200A LEU* 3.5 41.5 - - + -
203A LEU* 3.6 29.6 - - + +
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Residues in contact with PHE 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A LEU* 2.9 42.3 + - + +
107A ALA* 3.9 3.4 - - - +
109A PHE* 1.3 92.0 - + - +
111A GLU* 1.3 62.2 + - - +
113A LEU* 3.2 11.7 + - + -
123A TYR* 2.7 41.4 + + - +
125A VAL* 3.8 15.3 - - + -
132A LEU* 4.0 4.5 - - + -
134A VAL* 3.6 33.2 - - + -
136A LEU* 5.3 0.4 - - + -
143A TYR* 5.6 4.3 - + + -
145A ILE* 4.2 19.3 - - + -
186A LEU* 4.5 15.3 - - + -
190A LEU* 3.6 39.9 - - + -
200A LEU* 5.0 0.4 - - + -
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Residues in contact with GLU 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A ALA* 2.8 32.9 + - - +
108A GLU* 3.9 13.4 - - - +
110A PHE* 1.3 77.9 - - - +
112A ASP* 1.3 60.5 + - - +
114A ALA* 3.1 21.5 + - - +
115A ASP* 4.3 4.0 + - - +
125A VAL* 3.8 29.7 - - + +
127A PHE* 4.5 9.9 - - - +
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Residues in contact with ASP 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A GLU* 2.9 29.4 + - + +
109A PHE* 3.7 7.2 - - - +
111A GLU* 1.3 76.8 - - - +
113A LEU* 1.3 65.3 + - - +
115A ASP* 3.1 31.5 + - - +
116A LYS* 3.6 27.9 + - - +
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Residues in contact with LEU 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A PHE* 3.1 49.3 + - + +
110A PHE* 3.4 16.4 - - + +
111A GLU 3.2 0.6 - - - -
112A ASP* 1.3 76.8 + - - +
114A ALA* 1.3 64.5 + - - +
116A LYS* 3.0 22.8 + - + +
118A TYR* 3.6 29.6 - - + +
119A THR* 2.9 17.9 + - + +
123A TYR* 3.5 15.9 - - + +
190A LEU* 5.3 0.7 - - + -
194A LEU* 3.8 28.0 - - + -
198A LEU* 4.2 9.2 - - + -
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Residues in contact with ALA 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A PHE 3.5 3.0 + - - +
111A GLU* 3.1 17.0 + - - +
113A LEU* 1.3 77.4 - - - +
115A ASP* 1.4 60.0 + - - +
119A THR* 3.7 2.9 - - - -
123A TYR* 3.6 27.3 - - + +
125A VAL* 5.7 0.9 - - + -
1165A MG 2.6 21.5 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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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