Contacts of the helix formed by residues 118 - 140 (chain A) in PDB entry 5HVO
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 118 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A GLY* 4.5 7.9 - - - +
103A ILE* 4.1 16.0 - - + +
114A GLU* 6.2 1.1 - - + -
116A VAL* 3.4 5.8 + - - +
117A PHE* 1.3 78.7 - - - +
119A GLU* 1.3 61.2 + - - +
120A GLY* 3.3 7.1 + - - -
121A ALA* 3.1 39.5 + - + +
122A TRP* 3.3 11.8 + - - +
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Residues in contact with GLU 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A PHE* 3.3 36.5 + - - +
118A ASP* 1.3 72.1 + - - +
120A GLY* 1.3 57.1 + - - +
122A TRP* 3.2 15.3 + - - +
123A ASP* 3.0 34.7 + - - +
428B ASN* 4.4 6.2 - - - +
430B GLU* 3.3 41.5 + - + +
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Residues in contact with GLY 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ARG* 3.3 24.6 + - - -
118A ASP* 3.3 7.0 + - - -
119A GLU* 1.3 79.8 - - - +
121A ALA* 1.3 61.1 + - - +
123A ASP* 3.5 9.8 + - - +
124A ALA* 3.1 16.6 + - - +
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Residues in contact with ALA 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ARG* 3.9 6.7 - - + +
98A GLY* 3.4 38.8 - - - +
99A PHE* 3.7 12.3 - - + +
103A ILE* 4.7 0.2 - - + -
118A ASP* 3.1 26.6 + - + +
120A GLY* 1.3 75.3 - - - +
122A TRP* 1.3 52.0 + - - +
124A ALA* 3.1 11.0 + - - +
125A TYR* 2.8 33.6 + - - +
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Residues in contact with TRP 122 (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 PHE* 3.6 24.5 - + + -
117A PHE* 4.0 11.7 - + + -
118A ASP 3.3 9.5 + - - +
119A GLU* 3.2 23.3 + - - +
121A ALA* 1.3 75.3 - - - +
123A ASP* 1.3 64.4 + - - +
125A TYR* 3.2 26.5 + + - -
126A ARG* 3.0 59.0 + - - +
155A LEU* 3.7 16.8 - - + -
193A VAL* 3.4 30.0 - - + +
196A GLN* 3.9 26.7 - - + +
197A LEU* 3.6 28.9 - - + -
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Residues in contact with ASP 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ARG* 4.6 6.1 - - - +
119A GLU* 3.0 20.0 + - - +
120A GLY* 3.7 12.8 - - - +
122A TRP* 1.3 75.9 - - - +
124A ALA* 1.3 57.6 + - - +
126A ARG* 2.3 43.6 + - - +
127A GLU* 2.8 35.8 + - - +
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Residues in contact with ALA 124 (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 LEU* 3.8 14.6 - - + +
94A ARG* 3.4 48.9 - - + +
95A HIS* 4.0 3.6 - - - +
120A GLY 3.1 11.0 + - - +
121A ALA 3.1 11.3 + - - +
123A ASP* 1.3 78.2 - - - +
125A TYR* 1.3 57.1 + - - +
127A GLU* 3.6 1.9 - - - +
128A ALA* 2.8 33.5 + - - +
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Residues in contact with TYR 125 (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 HIS* 3.4 23.7 + + - +
99A PHE* 3.2 36.1 - + + -
100A SER* 3.7 12.3 - - - -
104A LEU* 3.9 3.7 - - + +
121A ALA 2.8 15.7 + - - +
122A TRP* 3.2 30.9 + + + +
124A ALA* 1.3 71.5 - - - +
126A ARG* 1.3 56.6 + - - +
128A ALA* 3.3 0.7 + - - +
129A ASN* 2.7 46.3 + - - -
151A TYR 2.6 24.5 + - - -
152A HIS 3.1 22.6 + - - -
154A MET* 3.0 22.0 + - - +
155A LEU* 4.0 20.6 - - + -
197A LEU* 4.3 4.7 - - + -
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Residues in contact with ARG 126 (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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122A TRP* 3.0 54.3 + - + +
123A ASP* 2.3 38.3 + - - +
125A TYR* 1.3 73.9 - - - +
127A GLU* 1.3 59.0 + - - +
129A ASN* 3.3 2.6 + - - +
130A LEU* 2.9 29.8 + - - +
155A LEU* 3.3 29.4 - - + -
159A LEU* 4.3 3.2 - - - +
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Residues in contact with GLU 127 (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 LEU* 3.7 29.7 - - + +
94A ARG* 4.0 13.2 + - - -
123A ASP* 2.8 24.1 + - - +
124A ALA* 3.6 4.5 - - - +
126A ARG* 1.3 73.0 - - - +
128A ALA* 1.3 61.4 - - - +
130A LEU* 3.4 8.8 + - - +
131A LEU* 3.2 30.5 + - + +
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Residues in contact with ALA 128 (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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87A MET* 3.8 23.1 - - + -
91A LEU* 4.4 5.6 - - + +
95A HIS* 3.6 36.1 - - + +
124A ALA 2.8 21.5 + - - +
125A TYR 3.6 0.2 - - - +
127A GLU* 1.3 72.4 - - - +
129A ASN* 1.3 65.6 + - - +
131A LEU* 3.1 13.1 + - - +
132A PHE* 3.3 22.7 + - + -
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Residues in contact with ASN 129 (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 HIS* 3.8 4.2 - - - -
125A TYR* 2.7 40.6 + - - +
126A ARG 3.3 4.2 + - - +
128A ALA* 1.3 76.0 - - - +
130A LEU* 1.3 62.1 + - - +
132A PHE* 3.4 7.1 + - - +
133A ALA 3.2 15.2 + - - -
152A HIS 3.2 20.5 + - - -
153A LEU* 3.1 35.2 - - - +
155A LEU* 3.4 16.3 + - + -
156A LEU* 3.3 23.9 + - - +
159A LEU* 3.4 14.8 - - + +
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Residues in contact with LEU 130 (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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126A ARG 2.9 17.8 + - - +
127A GLU* 3.6 9.4 - - - +
128A ALA 3.2 0.2 - - - -
129A ASN* 1.3 76.8 - - - +
131A LEU* 1.3 58.8 + - + +
133A ALA* 2.9 23.2 + - + +
134A LYS* 2.9 35.1 + - + +
159A LEU* 3.3 25.2 - - + +
163A GLU* 4.0 21.1 - - - +
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Residues in contact with LEU 131 (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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85A VAL* 4.0 11.9 - - + -
86A PHE 3.8 20.0 - - - +
87A MET* 3.9 7.4 - - + -
91A LEU* 3.7 28.9 - - + -
127A GLU* 3.2 17.2 + - + +
128A ALA 3.1 7.7 + - - +
130A LEU* 1.3 80.7 - - + +
132A PHE* 1.3 61.3 + - - +
134A LYS* 4.1 12.2 - - + +
135A THR* 2.9 30.1 + - - -
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Residues in contact with PHE 132 (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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16A VAL* 3.8 19.7 - - + -
17A SER 3.4 21.5 - - - -
18A ASN* 3.7 25.4 - - - -
57A TYR* 5.2 0.4 - - + -
58A GLY* 3.9 10.5 - - - -
59A TRP* 3.8 9.6 - - + -
85A VAL* 3.8 28.5 - - + -
87A MET* 4.4 18.8 - - + -
95A HIS* 5.5 1.6 - - - -
128A ALA* 3.3 22.7 + - + -
129A ASN 3.6 8.5 - - - +
130A LEU 3.2 0.4 - - - -
131A LEU* 1.3 77.6 - - + +
133A ALA* 1.3 64.2 + - - +
135A THR* 3.3 1.0 + - - -
136A ILE* 2.9 32.8 + - + +
153A LEU* 3.9 24.5 - - + -
156A LEU* 3.8 12.8 - - + -
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Residues in contact with ALA 133 (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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129A ASN 3.2 6.0 + - - +
130A LEU* 2.9 11.5 + - + +
132A PHE* 1.3 79.7 - - - +
134A LYS* 1.3 57.7 + - - +
136A ILE 3.4 0.2 + - - -
137A VAL* 3.1 30.8 + - - +
156A LEU* 3.5 11.6 - - + +
159A LEU* 3.7 33.9 - - + -
160A LEU* 3.9 10.8 - - + +
163A GLU* 3.9 16.3 - - + +
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Residues in contact with LYS 134 (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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130A LEU* 2.9 38.7 + - + +
131A LEU* 4.2 12.6 - - + +
133A ALA* 1.3 76.9 - - - +
135A THR* 1.3 59.6 + - - +
137A VAL* 3.1 23.7 - - + +
138A LYS* 3.2 22.2 - - - +
163A GLU* 4.0 27.9 + - - +
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Residues in contact with THR 135 (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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57A TYR* 4.3 5.2 - - + -
83A THR* 3.9 18.4 - - + -
84A PRO 3.8 21.5 - - - +
85A VAL* 4.0 22.5 - - + +
86A PHE 5.3 0.5 + - - -
131A LEU 2.9 20.1 + - - -
132A PHE 3.8 2.9 - - - -
134A LYS* 1.3 76.5 - - - +
136A ILE* 1.3 64.2 + - - +
138A LYS* 3.7 15.1 + - - +
139A GLU* 4.0 10.4 - - - +
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Residues in contact with ILE 136 (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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14A LEU* 4.3 13.7 - - + -
16A VAL* 3.8 35.0 - - + -
57A TYR* 3.9 31.2 + - + -
85A VAL* 5.9 0.7 - - + -
132A PHE* 2.9 25.9 + - + +
133A ALA 4.0 2.7 - - - +
135A THR* 1.3 76.1 - - - +
137A VAL* 1.3 65.7 + - - +
139A GLU* 3.2 5.5 + - - +
140A ALA* 3.0 20.6 + - + +
146A ILE* 4.1 20.6 - - + -
156A LEU* 3.9 15.0 - - + -
160A LEU* 4.0 22.0 - - + -
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Residues in contact with VAL 137 (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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133A ALA 3.1 16.1 + - - +
134A LYS* 3.1 21.5 - - + +
136A ILE* 1.3 77.2 - - - +
138A LYS* 1.3 70.6 + - + +
139A GLU 3.4 0.2 + - - -
140A ALA* 3.4 9.9 + - - +
160A LEU* 5.1 2.2 - - + -
163A GLU* 3.3 46.9 - - + +
164A LEU* 4.1 11.7 - - + +
167A ALA* 3.8 15.9 - - + -
169A LYS* 3.1 19.5 + - + -
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Residues in contact with LYS 138 (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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134A LYS* 3.2 25.3 - - - +
135A THR* 3.9 9.4 - - - +
136A ILE 3.2 0.4 - - - -
137A VAL* 1.3 84.4 - - + +
139A GLU* 1.3 64.1 + - + +
141A GLN* 4.6 2.3 - - - +
169A LYS* 3.5 10.5 + - - +
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Residues in contact with GLU 139 (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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14A LEU* 5.5 1.1 - - - +
55A GLN* 4.2 4.7 + - - +
57A TYR* 3.1 23.4 + - - +
73A LYS* 3.9 18.7 + - - -
77A LYS* 6.0 1.7 - - - +
83A THR* 2.7 41.6 + - - +
135A THR 4.0 12.1 - - - +
136A ILE 3.2 3.6 + - - +
138A LYS* 1.3 80.7 - - + +
140A ALA* 1.3 64.7 + - - +
141A GLN* 3.5 14.7 + - - +
144A ASP* 4.5 1.7 - - - +
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Residues in contact with ALA 140 (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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14A LEU* 4.1 18.4 - - + -
57A TYR* 4.9 0.2 + - - -
136A ILE* 3.0 19.2 + - + +
137A VAL* 3.4 10.5 + - - +
138A LYS 3.4 1.4 - - - -
139A GLU* 1.3 77.7 - - - +
141A GLN* 1.3 66.4 + - - +
144A ASP* 4.0 5.6 - - + +
146A ILE* 5.0 3.6 - - + -
164A LEU* 4.3 18.6 - - + -
169A LYS* 2.5 34.6 + - + +
172A ASN* 5.2 1.3 - - - +
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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