Contacts of the helix formed by residues 135 - 155 (chain A) in PDB entry 4G17
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 SER 135 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A THR 4.3 0.2 + - - -
134A PHE* 1.3 76.9 - - - +
136A LEU* 1.3 63.9 + - - +
137A LYS* 3.8 8.3 + - - +
138A THR* 3.2 14.6 + - - -
139A VAL* 3.0 20.5 + - - +
324A ASP* 2.7 32.4 + - - -
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Residues in contact with LEU 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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134A PHE 3.9 0.4 + - - -
135A SER* 1.3 73.1 - - - +
137A LYS* 1.3 64.4 + - - +
139A VAL* 3.1 2.0 + - + -
140A LEU* 2.8 57.0 + - + +
243A LEU* 3.9 27.6 - - + +
280A PHE* 4.3 26.9 - - + -
283A MET* 5.2 2.5 - - + -
311A LEU* 4.4 10.8 - - + -
315A LYS* 3.8 30.5 - - + +
317A TYR* 3.8 17.5 + - + +
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Residues in contact with LYS 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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135A SER* 3.2 8.8 + - - +
136A LEU* 1.3 79.0 - - - +
138A THR* 1.3 63.5 + - - +
140A LEU* 3.2 2.0 + - - +
141A MET* 3.0 42.6 + - + +
312A PHE* 4.0 12.7 - - + -
317A TYR* 3.8 40.1 - - + +
318A MET* 3.2 29.9 + - - +
320A ASP* 3.0 33.6 + - - -
322A GLU* 4.3 11.2 + - - +
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Residues in contact with THR 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A PHE* 3.8 24.9 - - + -
135A SER* 3.2 7.0 + - - -
137A LYS* 1.3 78.9 - - - +
139A VAL* 1.3 63.1 + - - +
141A MET* 3.2 12.2 + - - +
142A ILE* 3.0 28.9 + - + +
322A GLU 4.6 1.0 + - - -
323A TYR* 3.3 11.2 - - + -
324A ASP* 2.9 44.1 + - - +
325A TRP* 3.8 22.7 - - + -
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Residues in contact with VAL 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A PHE* 3.6 20.9 - - + -
135A SER 3.0 13.5 + - - +
136A LEU* 3.7 6.5 - - + +
138A THR* 1.3 77.1 - - - +
140A LEU* 1.3 52.6 + - - +
142A ILE* 3.2 8.7 + - - +
143A ALA* 2.7 31.5 + - - +
239A PHE* 4.1 20.6 - - + +
242A PHE* 3.9 15.0 - - + -
243A LEU* 3.4 45.3 - - + -
283A MET* 4.2 15.0 - - + -
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Residues in contact with LEU 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A LEU* 2.8 53.1 + - + +
137A LYS 3.8 3.1 - - - +
139A VAL* 1.3 69.2 - - - +
141A MET* 1.3 66.9 + - - +
143A ALA* 4.3 2.5 - - - +
144A ILE* 2.9 36.0 + - + +
283A MET* 4.3 10.3 - - + -
308A PHE* 3.9 35.2 - - + +
311A LEU* 4.0 23.8 - - + -
312A PHE* 3.8 33.4 - - + +
317A TYR* 4.2 5.8 - - + -
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Residues in contact with MET 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 LYS* 3.0 46.5 + - + +
138A THR* 3.7 5.4 - - - +
140A LEU* 1.3 77.3 - - - +
142A ILE* 1.3 61.6 + - - +
145A GLN* 2.8 31.2 + - - +
312A PHE* 3.7 18.4 - - + -
319A PHE* 3.8 31.2 - - + -
320A ASP 4.2 5.2 - - - -
321A TYR* 3.6 25.8 - - - -
322A GLU 3.8 26.7 - - - +
323A TYR* 4.0 23.6 - - + +
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Residues in contact with ILE 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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123A LEU* 4.0 25.1 - - + -
134A PHE* 4.1 14.8 - - + -
138A THR* 3.0 34.6 + - + +
139A VAL* 3.4 9.9 - - + +
140A LEU 3.1 0.2 - - - -
141A MET* 1.3 76.6 - - - +
143A ALA* 1.3 58.4 + - - +
145A GLN* 3.3 8.2 + - - +
146A LEU* 2.9 50.3 + - + +
181A ILE* 4.7 9.4 - - + +
239A PHE* 4.7 6.3 - - + -
242A PHE* 4.6 8.7 - - + -
323A TYR* 4.2 14.4 - - + -
325A TRP* 4.0 13.9 - - + -
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Residues in contact with ALA 143 (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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139A VAL* 2.7 21.9 + - + +
140A LEU* 3.9 5.4 - - - +
142A ILE* 1.3 71.3 - - - +
144A ILE* 1.3 66.3 + - - +
146A LEU* 3.8 0.3 - - - +
147A ILE* 3.0 32.5 + - - +
239A PHE* 3.5 39.3 - - + -
283A MET* 5.1 1.3 - - + -
308A PHE* 3.9 20.9 - - + -
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Residues in contact with ILE 144 (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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140A LEU* 2.9 27.3 + - + +
141A MET 4.1 3.4 - - - +
143A ALA* 1.3 77.8 - - - +
145A GLN* 1.3 64.0 + - + +
147A ILE* 3.6 7.5 + - - +
148A SER* 3.4 20.8 + - - +
305A ARG* 4.2 17.7 - - + +
308A PHE* 4.1 21.8 - - + +
309A THR* 3.8 35.9 - - + -
312A PHE* 4.8 7.2 - - + -
319A PHE* 3.8 31.0 - - + -
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Residues in contact with GLN 145 (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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141A MET 2.8 24.5 + - - +
142A ILE 3.3 5.7 + - - +
143A ALA 3.2 0.4 - - - -
144A ILE* 1.3 79.8 - - + +
146A LEU* 1.3 57.6 + - - +
148A SER* 3.2 7.9 + - - -
149A ARG* 2.9 47.2 + - - +
179A GLN 4.0 2.8 - - - +
180A VAL* 4.0 4.0 - - - +
181A ILE* 3.3 37.6 + - + +
319A PHE* 4.1 12.7 - - + -
321A TYR* 4.0 19.0 + - + +
323A TYR* 2.9 25.9 + - - -
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Residues in contact with LEU 146 (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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123A LEU* 4.6 1.6 - - + -
142A ILE* 2.9 35.5 + - + +
143A ALA 4.1 2.5 - - - +
145A GLN* 1.3 74.4 - - - +
147A ILE* 1.3 59.5 + - - +
149A ARG* 3.5 14.9 - - + +
150A MET* 2.9 32.1 + - + +
168A PHE* 3.7 33.2 - - + -
181A ILE* 3.8 20.6 - - + +
182A HIS 5.8 0.2 - - - -
235A LEU* 3.9 24.6 - - + +
238A MET* 3.6 31.6 - - + -
239A PHE* 4.4 5.6 - - + -
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Residues in contact with ILE 147 (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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143A ALA* 3.0 22.8 + - + +
144A ILE* 4.0 4.3 - - - +
146A LEU* 1.3 76.3 - - - +
148A SER* 1.3 58.4 + - - +
150A MET* 3.4 6.3 + - - +
151A GLU* 3.0 26.9 + - - +
232A LEU* 5.2 4.9 - - + +
235A LEU* 4.7 3.6 - - + -
239A PHE* 5.0 4.9 - - + -
286A TYR* 4.0 23.8 - - + +
301A TYR* 4.1 25.6 - - + +
304A LEU* 4.1 19.5 - - + +
305A ARG* 3.9 23.8 - - + +
308A PHE* 3.6 34.3 - - + -
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Residues in contact with SER 148 (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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144A ILE* 3.4 11.7 + - - +
145A GLN* 3.2 11.6 + - - -
147A ILE* 1.3 77.3 - - - +
149A ARG* 1.3 67.2 + - - +
151A GLU* 3.2 5.6 + - - +
152A TYR* 2.9 29.1 + - - +
305A ARG* 3.1 30.8 + - - +
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Residues in contact with ARG 149 (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 ASP* 3.4 38.9 + - - +
98A GLY* 3.5 15.5 - - - -
99A ILE* 4.4 4.9 - - + -
145A GLN* 2.9 49.4 + - - +
146A LEU* 3.5 17.6 - - + +
148A SER* 1.3 83.8 - - - +
150A MET* 1.3 62.6 + - + +
152A TYR* 3.1 9.3 + - - +
153A VAL* 3.0 26.2 + - - +
168A PHE* 6.1 0.2 - - + -
180A VAL* 4.1 10.9 - - - +
181A ILE* 3.1 28.0 + - - +
183A ILE* 4.0 29.6 - - + -
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Residues in contact with MET 150 (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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146A LEU 2.9 19.9 + - - +
147A ILE 3.7 3.8 - - - +
149A ARG* 1.3 73.4 - - + +
151A GLU* 1.3 60.0 + - - +
153A VAL* 3.3 7.0 + - - +
154A HIS* 2.8 57.1 + - + +
160A TYR* 3.9 24.2 - - + -
163A VAL* 4.1 22.2 - - + -
168A PHE* 4.4 5.2 - - + -
183A ILE* 4.2 23.1 - - + -
231A ASP* 3.9 15.3 - - + +
232A LEU* 4.2 15.0 - - + -
235A LEU* 3.9 26.5 - - + -
301A TYR* 4.7 0.4 - - + -
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Residues in contact with GLU 151 (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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147A ILE 3.0 14.9 + - - +
148A SER* 3.2 9.0 + - - +
150A MET* 1.3 72.9 - - - +
152A TYR* 1.3 61.5 + - - +
154A HIS* 3.4 1.8 + - - +
155A SER* 2.9 31.0 + - - -
298A LYS* 5.5 3.3 + - - -
301A TYR* 3.5 50.3 - - + +
302A ASP* 5.2 2.4 - - - +
305A ARG* 2.9 33.2 + - - -
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Residues in contact with TYR 152 (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 LEU* 2.6 33.5 + - + -
94A GLY 4.2 0.2 - - - -
95A SER 3.5 15.0 + - - -
96A GLY* 3.9 13.4 - - - -
97A ASP* 5.4 6.1 - - + +
99A ILE* 4.1 32.8 - - + -
148A SER 2.9 13.7 + - - +
149A ARG* 3.3 13.7 - - - +
151A GLU* 1.3 77.4 - - - +
153A VAL* 1.3 66.5 + - + +
155A SER* 2.6 26.4 + - - -
156A LYS* 3.3 35.2 + - + +
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Residues in contact with VAL 153 (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 LEU* 4.3 11.9 - - + -
99A ILE* 4.6 10.3 - - + -
149A ARG 3.0 14.5 + - - +
150A MET* 3.6 11.4 - - - +
152A TYR* 1.3 80.4 - - + +
154A HIS* 1.3 66.1 + - + +
156A LYS* 3.0 15.1 + - - +
158A LEU* 3.3 37.0 + - + +
159A ILE 4.7 0.2 - - - -
160A TYR* 4.5 12.8 - - + +
183A ILE* 4.8 10.3 - - + -
186A PHE* 4.1 34.1 - - + -
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Residues in contact with HIS 154 (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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150A MET* 2.8 37.7 + - + +
151A GLU 3.8 3.8 - - - +
153A VAL* 1.3 74.4 - - + +
155A SER* 1.3 57.4 + - - +
156A LYS 3.0 5.6 - - - -
157A ASN* 3.0 13.5 + - - +
158A LEU 3.3 19.3 - - - -
159A ILE* 4.2 1.6 - - - -
192A TYR* 2.6 30.0 + - - +
228A ARG* 3.5 44.5 - - + +
231A ASP* 2.9 25.8 + - + -
232A LEU* 4.7 2.9 - - + -
301A TYR* 2.7 34.0 + + + +
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Residues in contact with SER 155 (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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151A GLU* 2.9 19.3 + - - -
152A TYR* 2.6 26.0 + - - -
154A HIS* 1.3 74.8 - - - +
156A LYS* 1.3 72.3 + - - +
157A ASN* 3.3 7.2 + - - +
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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