Contacts of the helix formed by residues 136 - 158 (chain A) in PDB entry 6AH0
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 ILE 136 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A VAL* 1.3 71.2 - - - +
137A GLU* 1.3 58.2 + - - +
138A PRO 3.1 3.6 - - - -
139A VAL* 3.7 5.1 - - - +
140A TYR* 2.7 33.7 + - - +
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Residues in contact with GLU 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A VAL 3.1 6.8 + - - -
136A ILE* 1.3 72.1 - - - +
138A PRO* 1.3 57.9 - - - +
140A TYR* 5.2 0.4 - - - +
141A ILE* 3.1 24.0 + - - +
410A PRO* 5.5 9.0 - - - -
419A ARG 5.7 1.0 - - - +
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Residues in contact with PRO 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ILE* 3.1 1.0 - - - -
137A GLU* 1.3 78.2 - - - +
139A VAL* 1.3 62.5 + - - +
141A ILE* 4.3 0.4 - - - -
142A SER* 3.3 17.8 + - - -
238A LEU* 5.2 9.0 - - - +
410A PRO 4.8 15.1 - - - +
411A PHE* 5.7 2.5 - - - +
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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
----------------------------------------------------------
136A ILE* 3.2 8.5 + - - +
138A PRO* 1.3 75.9 - - - +
140A TYR* 1.3 54.1 + - - +
142A SER* 3.1 3.2 + - - +
143A GLN* 2.8 31.4 + - - -
207A PHE 5.5 4.8 - - - +
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Residues in contact with TYR 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A VAL* 5.8 2.2 - - - +
136A ILE 2.7 21.9 + - - +
137A GLU* 4.7 0.4 - - - +
139A VAL* 1.3 71.1 - - - +
141A ILE* 1.3 62.1 - - - +
143A GLN* 3.2 2.6 + - - +
144A TRP* 3.0 19.6 + - - -
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Residues in contact with ILE 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A GLU 3.1 17.8 + - - -
138A PRO 4.3 0.2 - - - -
140A TYR* 1.3 76.7 - - - +
142A SER* 1.3 57.8 + - - +
144A TRP* 3.2 2.3 + - - +
145A GLY* 2.9 26.2 + - - -
242A ALA* 5.0 4.0 - - - -
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Residues in contact with SER 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A PRO 3.3 12.9 + - - -
139A VAL* 3.1 7.4 + - - +
141A ILE* 1.3 76.3 - - - +
143A GLN* 1.3 55.0 + - - +
145A GLY* 3.2 1.9 + - - -
146A SER* 2.9 25.3 + - - -
238A LEU* 4.4 18.4 - - - +
241A LEU 4.9 3.9 - - - +
242A ALA* 4.7 8.3 - - - +
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Residues in contact with GLN 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 2.8 14.8 + - - -
140A TYR* 3.2 4.4 + - - +
142A SER* 1.3 76.8 - - - +
144A TRP* 1.3 61.1 + - - +
146A SER* 3.2 3.8 + - - +
147A MET* 3.0 17.8 + - - -
207A PHE 5.9 2.5 - - - -
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Residues in contact with TRP 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 TYR 3.0 13.7 + - - -
141A ILE 3.7 2.2 - - - -
143A GLN* 1.3 74.1 - - - +
145A GLY* 1.3 61.0 + - - +
147A MET* 3.2 2.9 + - - +
148A TRP* 2.9 24.8 + - - -
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Residues in contact with GLY 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 ILE 2.9 14.1 + - - -
142A SER 3.2 4.2 + - - -
144A TRP* 1.3 77.4 - - - +
146A SER* 1.3 60.8 + - - +
148A TRP* 3.2 2.8 + - - -
149A ILE* 3.2 17.5 + - - -
241A LEU 4.3 16.8 - - - +
242A ALA* 4.7 7.0 - - - -
245A LEU* 5.8 6.3 - - - -
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Residues in contact with SER 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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142A SER 2.9 13.2 + - - -
143A GLN* 3.6 4.9 - - - +
144A TRP 3.2 0.4 - - - -
145A GLY* 1.3 75.0 - - - +
147A MET* 1.3 62.1 + - - +
149A ILE* 3.2 4.0 + - - -
150A MET* 3.0 19.1 + - - -
192A GLN 5.5 6.3 - - - +
241A LEU 4.6 2.8 + - - -
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Residues in contact with MET 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 GLN 3.0 13.2 + - - -
144A TRP* 3.2 5.1 + - - +
146A SER* 1.3 76.3 - - - +
148A TRP* 1.3 61.3 + - - +
150A MET* 3.2 2.0 + - - +
151A MET* 2.9 22.5 + - - -
628A GLY 5.0 4.0 - - - +
629A PHE* 6.4 0.9 - - - -
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Residues in contact with TRP 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 TRP 2.9 13.0 + - - -
145A GLY* 3.7 4.7 - - - -
146A SER 3.2 0.4 - - - -
147A MET* 1.3 75.9 - - - +
149A ILE* 1.3 61.9 + - - +
151A MET* 4.0 0.7 - - - +
152A ARG* 3.1 20.8 + - - -
628A GLY 5.4 5.4 - - - -
629A PHE* 6.4 1.1 - - - +
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Residues in contact with ILE 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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145A GLY 3.2 8.1 + - - -
146A SER* 3.2 7.1 + - - +
148A TRP* 1.3 76.0 - - - +
150A MET* 1.3 58.8 + - - +
152A ARG* 3.4 1.1 + - - +
153A ARG* 2.9 26.7 + - - -
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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
----------------------------------------------------------
146A SER 3.0 13.0 + - - -
147A MET* 3.2 3.1 + - - +
149A ILE* 1.3 77.1 - - - +
151A MET* 1.3 61.6 + - - +
153A ARG* 3.4 1.3 + - - +
154A GLU* 3.0 19.9 + - - -
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Residues in contact with MET 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 MET 2.9 14.8 + - - -
148A TRP 4.0 0.4 - - - -
150A MET* 1.3 76.3 - - - +
152A ARG* 1.3 56.6 + - - +
154A GLU* 3.2 1.6 + - - +
155A LYS* 2.9 25.5 + - - -
572A PHE* 6.5 1.3 - - - +
626A GLY 4.0 8.8 - - - +
627A CYS* 5.8 0.9 - - - -
628A GLY* 4.8 18.2 - - - +
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Residues in contact with ARG 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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148A TRP 3.1 14.5 + - - -
149A ILE 3.9 2.2 - - - -
151A MET* 1.3 76.6 - - - +
153A ARG* 1.3 60.4 + - - +
155A LYS* 4.0 1.0 - - - +
156A ARG* 3.2 18.2 + - - -
616A PHE* 4.9 13.5 - - - +
621A VAL* 5.5 3.1 - - - -
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Residues in contact with ARG 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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149A ILE 2.9 16.6 + - - -
150A MET* 3.9 1.3 - - - +
152A ARG* 1.3 75.7 - - - +
154A GLU* 1.3 57.6 + - - +
156A ARG* 3.2 2.1 + - - +
157A ASP* 2.9 26.9 + - - -
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Residues in contact with GLU 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 3.0 14.8 + - - -
151A MET* 3.2 3.6 + - - +
153A ARG* 1.3 77.0 - - - +
155A LYS* 1.3 61.2 + - - +
157A ASP* 3.2 9.6 + - - +
158A ARG* 3.3 12.0 + - - +
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Residues in contact with LYS 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 MET 2.9 13.3 + - - -
152A ARG* 4.0 1.3 - - - +
154A GLU* 1.3 77.2 - - - +
156A ARG* 1.3 62.1 - - - +
158A ARG 3.2 18.6 - - - +
621A VAL* 5.2 3.9 - - - -
626A GLY* 3.7 26.8 + - - +
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Residues in contact with ARG 156 (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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152A ARG 3.2 14.7 + - - -
153A ARG* 3.7 2.7 - - - +
155A LYS* 1.3 78.8 - - - +
157A ASP* 1.3 60.6 + - - +
158A ARG 3.5 3.6 + - - +
159A ARG* 5.4 0.7 - - - -
620A PRO 4.4 8.6 - - - +
621A VAL* 4.3 20.5 - - - +
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Residues in contact with ASP 157 (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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153A ARG 2.9 16.1 + - - -
154A GLU* 3.2 3.5 + - - +
156A ARG* 1.3 77.5 - - - +
158A ARG* 1.3 57.4 + - - +
159A ARG 3.9 1.6 + - - -
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Residues in contact with ARG 158 (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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154A GLU 3.3 11.2 + - - +
155A LYS* 3.2 16.4 - - - +
156A ARG 4.2 2.4 - - - +
157A ASP* 1.3 76.2 - - - +
159A ARG* 1.3 66.6 + - - +
160A HIS 3.2 13.4 + - - +
161A PHE* 4.4 4.4 + - - +
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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
------------------------------------------------------------
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