Contacts of the helix formed by residues 153 - 167 (chain A) in PDB entry 1M6X
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 153 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152A GLU* 1.3 73.5 - - - +
154A ILE* 1.3 67.0 + - - +
155A TRP* 3.5 7.4 + - - +
156A GLU* 2.8 38.5 + - - +
157A ILE* 2.8 25.7 + - - +
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Residues in contact with ILE 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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148A LEU* 3.8 38.4 - - + -
153A SER* 1.3 73.3 - - - +
155A TRP* 1.3 60.0 + - + +
157A ILE* 3.0 8.4 + - + +
158A THR* 2.8 31.6 + - - +
186A PHE* 3.7 35.2 - - + -
310A LEU* 3.9 26.5 - - + +
313A SER* 4.7 2.2 - - - -
314A PHE* 4.4 30.5 - - + -
317A MET* 5.6 8.5 - - + -
346D GLN* 5.9 1.6 - - - +
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Residues in contact with TRP 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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153A SER* 3.3 7.2 + - - +
154A ILE* 1.3 79.2 - - + +
156A GLU* 1.3 64.0 + - + +
158A THR* 3.1 15.7 + - + -
159A GLU* 3.0 23.6 + - - +
183A LEU* 4.6 0.9 - - + -
186A PHE* 4.0 25.2 - + - -
187A ILE* 4.2 12.1 - - + -
235A ALA* 5.3 4.3 - - + -
239A ILE* 3.9 36.5 - - + +
241A PRO* 6.0 0.9 - - + -
314A PHE* 4.7 25.7 - + - -
357A LEU 5.2 0.6 + - - -
358A VAL* 3.1 36.3 + - + +
360A ARG* 3.3 59.3 - - - +
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Residues in contact with GLU 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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151A GLY 4.8 0.5 - - - -
152A GLU* 3.2 23.1 - - + -
153A SER* 2.8 43.7 + - - +
155A TRP* 1.3 77.4 - - + +
157A ILE* 1.3 63.0 + - - +
159A GLU* 3.4 8.4 + - - +
160A LYS* 3.1 27.7 + - - +
293A TYR* 4.9 0.4 - - - -
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Residues in contact with ILE 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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147A LEU* 3.9 38.8 - - + +
148A LEU* 4.0 17.3 - - + -
152A GLU* 3.8 27.8 - - + +
153A SER 2.8 21.3 + - - +
154A ILE* 3.3 11.4 - - + +
156A GLU* 1.3 74.7 - - - +
158A THR* 1.3 63.7 + - - +
160A LYS* 3.2 2.8 + - - +
161A ILE* 3.0 36.4 + - + +
293A TYR* 3.6 26.2 - - + -
310A LEU* 4.5 11.2 - - + -
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Residues in contact with THR 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 ILE* 2.8 34.0 + - - +
155A TRP* 3.1 20.2 + - + -
157A ILE* 1.3 77.6 - - - +
159A GLU* 1.3 57.8 + - - +
161A ILE* 3.3 0.6 + - - -
162A LEU* 2.8 34.2 + - + +
182A PHE* 3.4 33.3 - - + -
183A LEU* 4.5 12.3 - - + -
186A PHE* 4.0 27.7 - - + -
239A ILE* 5.4 0.9 - - + -
310A LEU* 4.6 4.1 - - - +
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Residues in contact with GLU 159 (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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155A TRP 3.0 12.4 + - - +
156A GLU* 3.7 11.3 - - - +
158A THR* 1.3 75.6 - - - +
160A LYS* 1.3 61.2 + - - +
162A LEU* 3.3 6.4 + - - +
163A ASN* 2.8 52.7 + - - +
238A ARG* 2.8 52.7 + - - +
239A ILE* 4.0 25.4 - - + +
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Residues in contact with LYS 160 (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 GLU* 2.6 30.9 + - - +
156A GLU* 3.1 15.5 + - - +
157A ILE 3.2 8.3 + - - +
159A GLU* 1.3 76.2 - - - +
161A ILE* 1.3 66.7 + - - +
163A ASN* 3.0 8.2 + - - +
164A SER* 2.9 21.8 + - - -
292A PRO* 4.7 9.4 - - + +
293A TYR* 3.3 29.6 - - + +
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Residues in contact with ILE 161 (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 LEU* 5.8 0.9 - - + -
157A ILE* 3.0 33.1 + - + +
158A THR 3.6 6.3 - - - +
160A LYS* 1.3 74.8 - - - +
162A LEU* 1.3 64.7 + - - +
164A SER* 2.6 27.1 + - - +
165A PHE* 3.4 15.4 - - + -
182A PHE* 3.7 40.2 - - + -
287A LEU* 4.2 16.4 - - + -
292A PRO* 4.1 5.6 - - + -
293A TYR* 3.9 16.8 - - + -
296A PHE* 3.9 25.8 - - + -
306A ILE* 4.4 1.6 - - + -
310A LEU* 4.3 8.7 - - + -
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Residues in contact with LEU 162 (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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158A THR* 2.8 19.1 + - + +
159A GLU* 3.4 5.4 - - - +
161A ILE* 1.3 79.6 - - - +
163A ASN* 1.3 63.4 + - - +
164A SER 3.4 0.2 + - - -
165A PHE* 3.4 14.2 + - - -
179A GLN* 3.0 65.2 + - + +
182A PHE* 3.8 17.5 - - + -
183A LEU* 4.5 8.1 - - + -
239A ILE* 3.7 31.4 - - + -
244A TYR* 3.3 36.6 - - + +
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Residues in contact with ASN 163 (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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159A GLU* 2.8 46.4 + - - +
160A LYS* 3.6 5.7 - - - +
162A LEU* 1.3 75.1 - - - +
164A SER* 1.3 57.2 + - - +
165A PHE 2.9 11.0 + - - -
166A GLU* 2.9 31.8 + - + +
167A TYR* 4.3 4.9 + - + -
179A GLN* 4.6 4.4 - - - +
239A ILE* 5.4 1.6 - - - +
244A TYR* 4.5 11.3 + - - -
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Residues in contact with SER 164 (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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160A LYS 2.9 7.4 + - - -
161A ILE 2.6 20.5 + - - -
163A ASN* 1.3 75.1 - - - +
165A PHE* 1.3 65.8 + - - +
167A TYR 4.9 0.4 - - - -
168A THR* 3.0 30.5 + - - +
287A LEU* 4.9 0.2 - - - +
290A ASN* 3.6 12.8 - - - +
292A PRO* 3.6 40.6 - - - +
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Residues in contact with PHE 165 (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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161A ILE* 3.4 37.2 - - + -
162A LEU* 3.4 13.2 - - - +
163A ASN 2.9 0.8 - - - -
164A SER* 1.3 78.1 - - - +
166A GLU* 1.3 67.5 + - - +
167A TYR 2.9 5.4 + - - -
168A THR* 3.6 4.0 - - - -
169A SER* 2.9 33.1 + - - +
175A LYS* 3.6 3.1 - - + +
178A TYR* 3.5 37.2 - + + -
179A GLN* 4.0 16.4 - - + -
182A PHE* 4.7 5.6 - - + -
283A TYR* 3.6 27.8 - + - -
286A ALA* 4.1 3.4 - - + -
287A LEU* 3.9 38.6 - - + -
290A ASN* 3.9 13.0 - - - -
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Residues in contact with GLU 166 (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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163A ASN* 2.9 29.4 + - + +
165A PHE* 1.3 78.2 - - - +
167A TYR* 1.3 99.6 + - + +
169A SER* 5.2 1.0 + - - +
175A LYS* 3.1 41.0 + - - +
179A GLN* 3.7 18.0 + - - +
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Residues in contact with TYR 167 (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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163A ASN* 4.3 4.9 + - + -
164A SER 4.8 0.6 + - - -
165A PHE 2.9 0.8 + - - -
166A GLU* 1.3 116.0 - - + +
168A THR* 1.3 65.8 + - + +
169A SER 3.5 6.7 - - - +
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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
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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