Contacts of the helix formed by residues 121 - 142 (chain A) in PDB entry 3F3Z
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 ARG 121 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A LYS* 5.5 1.9 - - + +
119A VAL 4.0 2.5 + - - +
120A PHE* 1.3 74.7 - - - +
122A GLU* 1.3 67.7 + - - +
123A SER* 3.2 9.6 - - - +
124A ASP* 3.1 22.5 + - - +
125A ALA* 3.0 15.6 + - - +
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Residues in contact with GLU 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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120A PHE 3.5 0.8 + - - +
121A ARG* 1.3 72.9 - - - +
123A SER* 1.3 57.3 + - - +
125A ALA 3.3 0.3 + - - -
126A ALA* 2.8 29.8 + - - +
218A LEU* 3.9 24.5 - - + -
250A ASN 4.4 3.1 - - - +
251A VAL* 3.5 15.8 - - + -
252A SER* 2.7 51.6 + - - -
255A ALA* 3.5 2.9 - - - +
281A TRP* 3.0 23.9 + - - +
285A GLN* 3.3 20.6 + - + +
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Residues in contact with SER 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ARG* 4.5 6.8 - - - +
122A GLU* 1.3 76.7 - - - +
124A ASP* 1.3 66.9 + - - +
126A ALA* 3.4 2.9 + - - +
127A ARG* 3.1 23.7 + - - +
285A GLN* 3.2 36.1 + - - -
286A LEU* 3.6 9.1 - - - +
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Residues in contact with ASP 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A LYS* 3.9 16.2 + - - +
120A PHE* 4.4 16.2 - - + -
121A ARG* 3.1 26.3 + - - +
123A SER* 1.3 86.1 + - - +
125A ALA* 1.3 64.7 + - - +
127A ARG* 3.4 15.1 + - - +
128A ILE* 3.1 29.6 + - + +
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Residues in contact with ALA 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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120A PHE* 4.2 7.2 - - + +
121A ARG 3.0 9.4 + - - +
122A GLU 3.6 4.7 - - - +
124A ASP* 1.3 75.3 - - - +
126A ALA* 1.3 58.2 + - - +
128A ILE* 3.4 3.3 + - - +
129A MET* 2.9 34.8 + - + +
214A MET* 6.0 0.2 - - + -
217A LEU* 4.1 25.8 - - + -
218A LEU* 3.5 32.5 - - + -
281A TRP* 3.7 8.1 - - + -
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Residues in contact with ALA 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 GLU 2.8 17.4 + - - +
123A SER 3.6 4.0 - - - +
124A ASP 3.2 0.4 - - - -
125A ALA* 1.3 74.5 - - - +
127A ARG* 1.3 58.4 + - - +
130A LYS* 2.8 29.5 + - - +
281A TRP* 3.4 23.3 - - + -
282A PHE* 3.3 12.6 - - + -
285A GLN* 3.5 25.6 - - + -
286A LEU* 3.9 13.0 - - + -
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Residues in contact with ARG 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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113A ARG* 5.1 7.3 - - - +
123A SER 3.1 13.7 + - - +
124A ASP* 3.4 19.1 + - - +
126A ALA* 1.3 76.6 - - - +
128A ILE* 1.3 68.4 + - - +
130A LYS* 3.5 3.2 + - - +
131A ASP* 3.4 27.2 + - - +
156A PHE* 3.4 31.3 - - - -
160A SER 4.4 1.6 + - - -
161A PRO* 2.7 31.1 + - - +
162A ASP* 4.8 3.4 - - - +
163A SER* 2.5 39.5 + - - +
165A LEU* 5.9 0.4 - - - +
286A LEU* 3.8 16.5 - - + +
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Residues in contact with ILE 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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110A LEU* 3.9 27.4 - - + -
120A PHE* 3.8 32.8 - - + -
124A ASP* 3.1 16.6 + - + +
125A ALA 3.7 5.6 - - - +
127A ARG* 1.3 81.6 - - + +
129A MET* 1.3 64.6 + - - +
131A ASP* 3.1 8.3 + - - +
132A VAL* 3.0 26.3 + - + +
156A PHE* 4.7 15.3 - - + -
165A LEU* 3.6 24.6 - - + +
213A MET* 5.1 0.7 - - + -
217A LEU* 3.8 23.6 - - + -
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Residues in contact with MET 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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125A ALA 2.9 22.0 + - - +
126A ALA 4.0 2.5 - - - +
128A ILE* 1.3 77.1 - - - +
130A LYS* 1.3 58.5 + - - +
132A VAL* 4.1 18.6 - - + -
133A LEU* 2.9 45.6 + - + +
210A ALA* 3.3 38.8 - - + +
213A MET* 4.3 6.7 - - + -
214A MET* 3.8 34.3 - - + -
217A LEU* 3.7 23.6 - - + -
262A LEU* 5.2 1.3 - - + -
281A TRP* 4.1 14.1 - - + -
282A PHE* 4.1 7.4 - - + -
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Residues in contact with LYS 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 ALA 2.8 22.0 + - - +
127A ARG* 3.8 5.6 - - - +
128A ILE 3.2 0.2 - - - -
129A MET* 1.3 72.4 - - - +
131A ASP* 1.3 60.2 + - - +
134A SER* 2.7 42.9 + - - +
277A LEU* 3.6 19.9 - - + +
282A PHE* 3.6 16.7 - - + -
286A LEU* 3.7 23.8 - - + +
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Residues in contact with ASP 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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84A ASN* 3.2 38.6 + - - +
127A ARG* 3.4 17.5 + - - +
128A ILE 3.1 8.8 + - - +
130A LYS* 1.3 81.3 - - - +
132A VAL* 1.3 64.8 + - - +
134A SER* 3.5 0.3 + - - -
135A ALA* 3.0 19.9 + - - +
154A PHE* 5.2 1.5 - - - -
163A SER 4.4 1.9 - - - +
164A PRO* 3.4 8.3 - - - +
165A LEU* 2.8 39.7 + - + +
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Residues in contact with VAL 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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128A ILE* 3.0 18.9 + - + +
129A MET* 3.7 23.6 - - + +
131A ASP* 1.3 76.1 - - - +
133A LEU* 1.3 59.2 + - - +
135A ALA* 3.2 4.9 + - - +
136A VAL* 3.0 36.7 + - + +
149A LEU* 4.9 2.5 - - + -
154A PHE* 3.9 35.8 - - + -
165A LEU* 4.1 11.2 - - + -
210A ALA* 4.4 12.6 - - + -
213A MET* 4.0 27.8 - - + -
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Residues in contact with LEU 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 MET* 2.9 36.1 + - + +
132A VAL* 1.3 71.7 - - + +
134A SER* 1.3 61.5 + - - +
136A VAL* 4.3 3.1 - - + -
137A ALA* 2.8 32.2 + - - +
207A GLU* 5.3 0.2 - - + -
210A ALA* 3.8 26.2 - - + -
214A MET* 6.2 0.2 - - - -
258A LEU* 4.9 4.7 - - + -
262A LEU* 4.5 11.4 - - + -
273A SER* 3.5 29.5 - - - +
276A ALA* 3.7 25.4 - - + -
277A LEU* 3.9 15.5 - - + -
282A PHE* 3.8 23.6 - - + -
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Residues in contact with SER 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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82A HIS* 3.5 5.4 + - - -
84A ASN* 3.8 15.0 - - - -
130A LYS* 2.7 32.2 + - - +
131A ASP* 3.7 4.3 - - - -
133A LEU* 1.3 76.5 - - - +
135A ALA* 1.3 62.7 + - - +
138A TYR* 3.1 23.9 + - - +
277A LEU* 3.7 12.5 - - - +
295A GOL 3.3 32.6 + - - -
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Residues in contact with ALA 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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82A HIS* 3.9 10.0 - - - -
84A ASN* 3.7 23.8 - - + +
85A ILE* 3.8 13.5 - - + +
131A ASP 3.0 17.9 + - - +
132A VAL* 3.6 6.3 - - - +
134A SER* 1.3 75.4 - - - +
136A VAL* 1.3 57.1 + - + +
138A TYR* 3.4 2.6 + - - +
139A CYS* 3.0 33.9 + - - -
154A PHE* 5.0 1.6 - - + -
167A LEU* 4.3 15.3 - - + -
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Residues in contact with VAL 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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132A VAL* 3.0 20.9 + - + +
133A LEU* 3.8 4.5 - - + +
135A ALA* 1.3 74.5 - - + +
137A ALA* 1.3 64.3 + - - +
139A CYS* 3.3 6.9 + - + +
140A HIS* 3.0 52.7 + - + +
146A HIS* 5.8 1.6 - - + -
149A LEU* 3.4 37.7 - - + -
167A LEU* 5.7 0.7 - - + -
206A ASP* 3.7 14.1 - - + +
207A GLU* 4.1 0.2 - - - +
210A ALA* 5.5 0.2 - - + -
273A SER* 3.3 22.2 - - - +
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Residues in contact with ALA 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 LEU 2.8 22.0 + - - +
134A SER 3.9 3.4 - - - +
136A VAL* 1.3 73.5 - - - +
138A TYR* 1.3 61.8 + - - +
140A HIS* 3.4 5.8 + - - +
141A LYS* 3.1 28.5 + - - +
273A SER* 3.8 15.7 - - - -
274A LEU* 4.0 28.5 - - + +
277A LEU* 4.4 1.3 - - + -
295A GOL 4.0 15.7 - - - +
296A GOL 5.6 0.9 - - - -
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Residues in contact with TYR 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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79A SER 4.2 1.0 + - - -
80A LEU* 3.7 21.8 - - + -
81A ASP* 3.0 48.6 + - - +
82A HIS* 3.4 34.5 - + + -
85A ILE* 3.7 16.8 - - + -
134A SER 3.1 7.6 + - - +
135A ALA 3.5 7.9 - - - +
137A ALA* 1.3 73.0 - - - +
139A CYS* 1.3 68.0 + - - +
141A LYS* 3.2 17.9 + - + +
142A LEU* 3.4 31.9 + - + +
295A GOL 3.6 16.3 - - - -
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Residues in contact with CYS 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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80A LEU* 4.2 10.3 - - - -
85A ILE* 3.7 19.7 - - - -
135A ALA 3.0 20.6 + - - +
136A VAL* 3.6 9.2 - - + +
138A TYR* 1.3 77.3 - - - +
140A HIS* 1.3 60.5 + - + +
142A LEU* 3.0 14.4 + - - -
144A VAL* 2.9 46.9 + - + +
146A HIS* 5.4 7.6 - - + +
167A LEU* 4.8 5.2 - - - -
170A PHE* 4.0 22.7 - - - -
206A ASP* 5.7 0.2 - - - +
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Residues in contact with HIS 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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136A VAL* 3.0 30.4 + - + +
137A ALA* 3.9 4.9 - - - +
139A CYS* 1.3 78.3 - - + +
141A LYS* 1.3 62.0 + - - +
143A ASN* 3.1 19.6 + - - +
144A VAL 3.2 21.3 - - - +
176A PHE* 4.2 5.7 - - + -
203A PRO* 3.0 36.0 + - + +
206A ASP* 2.7 25.4 + - + +
207A GLU* 3.3 18.9 + - - -
296A GOL 2.6 43.3 + - - +
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Residues in contact with LYS 141 (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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137A ALA* 3.1 18.0 + - - +
138A TYR* 3.2 11.6 + - + +
140A HIS* 1.3 75.0 - - - +
142A LEU* 1.3 66.2 + - + +
143A ASN* 3.4 5.7 + - - +
274A LEU* 3.8 40.1 - - + +
295A GOL 3.1 31.5 + - - +
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Residues in contact with LEU 142 (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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79A SER* 3.7 19.3 - - - +
80A LEU* 4.1 4.7 - - + -
138A TYR* 3.4 45.5 + - + +
139A CYS 3.0 9.0 + - - +
141A LYS* 1.3 82.8 - - + +
143A ASN* 1.3 72.7 + - - +
144A VAL* 3.3 15.7 + - + +
175A ARG* 5.1 4.6 + - - +
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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
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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