Contacts of the helix formed by residues 115 - 133 (chain R) in PDB entry 1RZZ
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 TYR 115 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105R VAL* 3.9 32.1 - - + -
108R CYS* 3.7 27.4 - - + -
109R ARG* 3.6 25.7 + - + +
113R ILE 4.6 7.4 - - - -
114R GLY* 1.3 73.4 - - - -
116R HIS* 1.3 66.4 + - - +
117R ILE 3.3 2.5 - - - -
118R PRO* 3.0 24.1 - - + +
119R PHE* 3.2 13.1 + - + +
4S GLN* 4.9 18.5 + - - +
228S ARG* 6.2 0.7 - - - -
241T LEU* 5.7 8.1 - - + +
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Residues in contact with HIS 116 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114R GLY* 3.3 12.6 + - - -
115R TYR* 1.3 77.5 - - - +
117R ILE* 1.3 57.4 + - - +
119R PHE* 3.3 10.9 + + - +
120R ALA* 2.8 30.1 + - - +
234R LEU* 4.9 5.8 - - + +
3S TYR 5.6 0.4 - - - -
4S GLN* 2.7 52.3 + - + +
5S ASN* 5.3 0.9 - - + -
6S ILE* 4.3 9.2 - - + -
221S ALA* 3.3 30.6 - - + +
224S LEU* 3.7 38.9 - - + +
225S ALA* 3.5 14.9 - - + -
228S ARG* 5.5 2.7 - - - -
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Residues in contact with ILE 117 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104R GLU* 3.9 1.3 - - - +
108R CYS* 5.5 0.4 - - - -
113R ILE* 5.0 6.5 - - + -
114R GLY 5.1 0.9 + - - +
116R HIS* 1.3 73.6 - - - +
118R PRO* 1.3 71.1 - - + +
120R ALA* 3.0 5.7 + - - +
121R PHE* 2.9 19.1 + - - +
2006R BPH 3.6 18.5 - - + +
218S MET* 4.4 1.1 - - - +
221S ALA* 3.8 22.2 - - + +
222S THR* 3.3 33.7 - - + +
225S ALA* 4.9 2.7 - - + -
251S PHE* 3.3 43.7 - - + -
252S TRP* 3.6 26.9 - - + +
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Residues in contact with PRO 118 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101R ALA* 3.8 25.6 - - + +
104R GLU* 3.4 24.0 - - + +
105R VAL* 4.0 20.4 - - + -
108R CYS* 4.2 13.7 - - - -
115R TYR* 3.0 33.4 - - + +
117R ILE* 1.3 91.1 - - + +
119R PHE* 1.3 59.8 + - - +
121R PHE* 3.2 5.0 + - + +
122R ALA* 2.9 22.9 + - - +
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Residues in contact with PHE 119 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115R TYR* 3.2 15.2 + - + +
116R HIS* 3.4 14.6 - + - +
117R ILE 3.1 0.6 - - - -
118R PRO* 1.3 76.8 - - - +
120R ALA* 1.3 66.5 + - - +
122R ALA* 3.3 21.0 + - + +
123R PHE* 3.4 39.0 - + - -
234R LEU* 6.0 3.4 - - + -
238R LEU* 4.7 10.1 - - + -
4S GLN* 5.5 9.6 - - - +
6S ILE* 6.5 1.8 - - + -
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Residues in contact with ALA 120 (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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116R HIS 2.8 13.6 + - - +
117R ILE* 3.4 11.0 - - - +
119R PHE* 1.3 76.8 - - + +
121R PHE* 1.3 62.1 - - - +
123R PHE* 3.0 23.1 + - - +
234R LEU* 3.7 27.6 - - + -
238R LEU* 3.9 17.7 - - + +
2006R BPH 3.6 21.9 - - + +
217S ALA* 4.5 3.1 - - + +
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Residues in contact with PHE 121 (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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97R PHE* 3.4 28.9 - - + -
100R TRP* 3.8 13.7 - + - -
101R ALA* 3.8 22.2 - - + -
104R GLU* 4.2 7.6 - - - +
117R ILE 2.9 13.4 + - - +
118R PRO 3.6 7.0 - - - +
120R ALA* 1.3 77.2 - - - +
122R ALA* 1.3 62.2 + - - +
124R ALA* 2.9 15.4 + - + +
125R ILE* 3.2 28.0 + - + +
2002R BCL 4.1 15.7 - - + -
2006R BPH 3.4 79.5 - + + +
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Residues in contact with ALA 122 (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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101R ALA* 5.8 2.7 - - + -
118R PRO 2.9 12.0 + - - +
119R PHE* 3.4 17.5 - - + +
120R ALA 3.2 0.4 - - - -
121R PHE* 1.3 76.7 - - - +
123R PHE* 1.3 57.6 + - + +
125R ILE* 3.3 15.9 + - + +
126R LEU* 2.8 41.7 + - + +
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Residues in contact with PHE 123 (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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119R PHE* 3.4 49.1 - + - -
120R ALA 3.0 12.3 + - - +
122R ALA* 1.3 78.3 - - + +
124R ALA* 1.3 66.0 + - - +
126R LEU* 3.2 15.0 + - + +
127R ALA 2.9 18.0 + - - -
238R LEU* 3.8 44.6 - - + -
241R VAL* 3.6 11.9 - - + +
242R PHE* 4.6 22.4 - + + -
2006R BPH 3.6 12.3 - - + -
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Residues in contact with ALA 124 (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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121R PHE* 2.9 22.2 + - + +
123R PHE* 1.3 77.7 - - - +
125R ILE* 1.3 64.6 + - - +
127R ALA* 3.0 6.2 + - - +
128R TYR* 2.9 21.3 + - - +
241R VAL* 4.4 5.2 - - - -
2002R BCL 4.0 21.8 - - + +
2006R BPH 3.3 40.7 - - + +
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Residues in contact with ILE 125 (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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94R THR* 5.4 1.8 - - + +
97R PHE* 3.9 32.8 - - + +
98R VAL* 4.0 18.8 - - + +
101R ALA* 4.3 5.4 - - + -
121R PHE* 3.2 50.6 + - + +
122R ALA* 3.5 14.1 - - + +
124R ALA* 1.3 75.7 - - - +
126R LEU* 1.3 59.8 + - + +
128R TYR* 3.1 6.1 + - + +
129R LEU* 2.8 48.7 + - + +
2002R BCL 4.1 7.9 - - + -
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Residues in contact with LEU 126 (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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122R ALA* 2.8 30.2 + - + +
123R PHE* 3.5 15.0 - - + +
124R ALA 3.2 0.2 - - - -
125R ILE* 1.3 79.9 - - + +
127R ALA* 1.3 51.5 + - - +
129R LEU* 3.8 19.1 - - + +
130R THR* 2.5 37.4 + - - -
134R PHE* 4.1 16.3 - - + -
245R ALA* 5.3 0.9 - - - -
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Residues in contact with ALA 127 (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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123R PHE 2.9 5.5 + - - -
124R ALA 3.0 8.7 + - - +
126R LEU* 1.3 74.1 - - - +
128R TYR* 1.3 66.3 + - - +
130R THR* 3.2 15.8 + - - -
131R LEU* 3.2 19.2 + - - +
241R VAL* 3.5 33.7 - - + +
245R ALA* 4.3 8.3 - - + -
2002R BCL 3.7 27.1 - - - +
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Residues in contact with TYR 128 (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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90R THR* 3.6 12.0 - - + +
93R ALA* 3.6 14.6 - - + +
94R THR* 3.8 21.1 - - - -
97R PHE* 3.8 26.5 - + - -
124R ALA 2.9 11.1 + - - +
125R ILE* 3.2 11.7 - - + +
127R ALA* 1.3 77.3 - - - +
129R LEU* 1.3 71.3 + - + +
131R LEU* 3.2 7.3 + - - +
132R VAL* 3.0 48.8 + - + +
146R PHE* 4.2 7.4 - + - -
148R TYR* 2.8 24.0 + - - -
2002R BCL 4.1 19.2 - - + +
2006R BPH 4.2 2.9 - - + -
2004S BCL 3.7 33.7 - - + -
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Residues in contact with LEU 129 (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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90R THR* 5.9 1.1 - - + -
94R THR* 3.6 34.8 - - + +
98R VAL* 5.7 1.6 - - + -
125R ILE* 2.8 39.9 + - + +
126R LEU* 3.8 13.9 - - + +
128R TYR* 1.3 90.0 - - + +
130R THR* 1.3 55.9 + - - +
132R VAL* 4.9 2.5 - - + -
133R LEU* 2.7 49.0 + - + +
134R PHE* 3.0 35.3 + - + -
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Residues in contact with THR 130 (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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126R LEU 2.5 21.7 + - - -
127R ALA 3.3 9.9 - - - -
128R TYR 3.1 0.4 - - - -
129R LEU* 1.3 78.1 - - - +
131R LEU* 1.3 61.1 + - + +
134R PHE* 3.4 14.8 - - + -
135R ARG* 2.9 34.7 + - + +
245R ALA* 3.6 39.9 - - + +
248R MET* 4.9 5.2 - - + -
249R ILE* 4.1 26.2 - - + +
2002R BCL 5.5 0.2 - - - -
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Residues in contact with LEU 131 (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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127R ALA 3.2 11.0 + - - +
128R TYR 3.2 6.8 + - - +
130R THR* 1.3 82.2 - - - +
132R VAL* 1.3 58.0 + - - +
133R LEU 3.7 0.2 - - - -
135R ARG* 4.5 7.3 + - - +
136R PRO* 3.4 17.8 - - - +
144R TYR 4.6 1.6 - - - +
145R ALA* 3.7 11.6 - - - -
146R PHE* 4.0 15.6 + - + -
156R TRP* 3.8 18.0 - - + -
248R MET* 3.9 23.3 - - + -
2002R BCL 3.4 34.5 - - + +
2004S BCL 3.6 48.5 - - + -
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Residues in contact with VAL 132 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86R TRP* 3.4 26.2 - - + -
90R THR* 3.2 35.4 - - + -
128R TYR* 3.0 31.3 + - + +
129R LEU* 4.9 2.0 - - + -
131R LEU* 1.3 78.8 - - - +
133R LEU* 1.3 59.8 + - + +
136R PRO* 3.5 11.0 - - - +
142R TRP* 3.9 9.1 - - + -
145R ALA* 4.0 3.8 - - + -
146R PHE* 3.4 33.4 - - + -
148R TYR* 3.8 7.2 - - + +
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Residues in contact with LEU 133 (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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129R LEU* 2.7 40.9 + - + +
132R VAL* 1.3 77.4 - - + +
134R PHE* 1.3 85.6 + - + +
135R ARG 3.3 1.3 - - - -
136R PRO* 3.1 3.3 - - - +
137R VAL* 2.8 52.6 + - + +
142R TRP* 4.5 13.7 - - + -
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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