Contacts of the helix formed by residues 153 - 167 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152D GLU* 1.3 74.2 - - - +
154D ILE* 1.3 65.0 + - - +
155D TRP* 3.5 7.7 + - - +
156D GLU* 2.8 34.9 + - - +
157D ILE* 2.8 27.8 + - - +
317D MET* 6.4 2.0 - - - -
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Residues in contact with ILE 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D LEU* 3.4 33.2 - - + -
153D SER* 1.3 72.7 - - - +
155D TRP* 1.3 58.7 + - - +
157D ILE* 3.0 7.3 + - + +
158D THR* 2.7 32.9 + - - +
186D PHE* 3.7 35.2 - - + -
310D LEU* 3.9 25.7 - - + +
313D SER* 4.0 9.2 - - - -
314D PHE* 3.8 33.9 - - + +
317D MET* 5.3 11.1 - - + -
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Residues in contact with TRP 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D SER* 3.2 6.8 + - - +
154D ILE* 1.3 79.8 - - + +
156D GLU* 1.3 64.5 + - + +
158D THR* 3.2 15.9 + - + -
159D GLU* 3.0 23.7 + - - +
183D LEU* 4.7 1.6 - - + -
186D PHE* 4.0 23.1 - + - -
187D ILE* 4.3 12.8 - - + -
235D ALA* 5.2 4.0 - - + -
239D ILE* 3.9 36.5 - - + +
241D PRO* 5.9 1.1 - - + -
314D PHE* 3.9 34.7 - + - -
358D VAL* 3.1 34.9 + - + -
360D ARG* 3.4 59.3 - - + +
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Residues in contact with GLU 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151D GLY 4.1 2.3 - - - +
152D GLU* 2.8 36.1 - - + +
153D SER* 2.8 37.2 + - - +
155D TRP* 1.3 76.8 - - + +
157D ILE* 1.3 63.8 + - - +
159D GLU* 3.4 8.9 + - - +
160D LYS* 3.1 27.0 + - - +
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Residues in contact with ILE 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D LEU* 3.6 46.7 - - + +
148D LEU* 3.8 26.9 - - + -
152D GLU* 4.4 11.2 - - + +
153D SER 2.8 24.6 + - - +
154D ILE* 3.3 8.3 - - + +
156D GLU* 1.3 77.2 - - - +
158D THR* 1.3 63.5 + - - +
160D LYS* 3.2 3.6 + - - +
161D ILE* 2.9 40.8 + - + +
293D TYR* 3.6 19.1 - - + +
310D LEU* 4.2 11.9 - - + -
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Residues in contact with THR 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154D ILE* 2.7 36.9 + - - +
155D TRP* 3.4 19.6 - - + -
157D ILE* 1.3 74.0 - - - +
159D GLU* 1.3 59.2 + - - +
161D ILE* 3.3 0.6 + - - -
162D LEU* 2.8 34.5 + - + +
182D PHE* 3.4 32.3 - - + -
183D LEU* 4.5 12.3 - - + -
186D PHE* 3.9 26.9 - - + -
239D ILE* 5.4 0.9 - - + -
310D LEU* 4.6 5.0 - - - +
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Residues in contact with GLU 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D TRP 3.0 9.4 + - - +
156D GLU* 3.7 11.2 - - - +
157D ILE 3.3 0.2 - - - -
158D THR* 1.3 78.5 - - - +
160D LYS* 1.3 59.6 + - - +
162D LEU* 3.4 7.5 - - - +
163D ASN* 2.8 33.3 + - + +
238D ARG* 3.1 47.2 + - - +
239D ILE* 4.0 28.1 - - + +
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Residues in contact with LYS 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152D GLU* 3.0 32.7 + - - +
156D GLU* 3.1 11.4 + - - +
157D ILE 3.3 8.3 - - - +
159D GLU* 1.3 78.8 - - - +
161D ILE* 1.3 67.8 + - - +
163D ASN* 2.9 8.6 + - - +
164D SER* 2.9 21.9 + - - -
292D PRO* 4.9 9.0 - - + +
293D TYR* 3.2 29.8 - - + +
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Residues in contact with ILE 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D LEU* 5.7 1.3 - - + -
157D ILE* 2.9 32.9 + - + +
158D THR 3.7 5.8 - - - +
160D LYS* 1.3 74.8 - - - +
162D LEU* 1.3 65.0 + - - +
164D SER* 2.6 27.7 + - - +
165D PHE* 3.4 14.4 - - + -
182D PHE* 3.7 39.7 - - + -
287D LEU* 4.2 15.7 - - + -
292D PRO* 4.1 6.5 - - + -
293D TYR* 3.9 17.9 - - + -
296D PHE* 3.8 25.4 - - + -
306D ILE* 4.4 1.6 - - + -
310D LEU* 4.0 9.6 - - + -
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Residues in contact with LEU 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158D THR* 2.8 19.3 + - + +
159D GLU* 3.4 5.6 - - - +
161D ILE* 1.3 79.9 - - - +
163D ASN* 1.3 61.7 + - - +
164D SER 3.4 0.2 + - - -
165D PHE* 3.4 14.0 + - + -
179D GLN* 3.0 64.9 + - + +
182D PHE* 3.8 17.5 - - + -
183D LEU* 4.5 9.0 - - + -
239D ILE* 3.8 30.7 - - + -
244D TYR* 3.4 36.1 - - + +
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Residues in contact with ASN 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159D GLU* 2.8 24.3 + - + +
160D LYS* 2.9 6.5 + - - +
162D LEU* 1.3 68.8 - - - +
164D SER* 1.3 58.6 + - - +
165D PHE 2.9 11.8 + - - -
166D GLU* 2.9 49.2 + - - +
167D TYR* 4.2 17.3 + - - -
179D GLN* 4.5 1.9 - - - +
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Residues in contact with SER 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160D LYS 2.9 8.0 + - - -
161D ILE 2.6 20.4 + - - -
163D ASN* 1.3 74.6 - - - +
165D PHE* 1.3 66.0 + - - +
167D TYR 4.9 0.4 - - - -
168D THR* 3.1 29.6 + - - +
287D LEU* 4.9 0.2 - - - +
290D ASN* 3.6 13.5 - - - +
292D PRO* 3.6 39.6 - - - +
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Residues in contact with PHE 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161D ILE* 3.4 37.7 - - + -
162D LEU* 3.4 13.0 + - - +
163D ASN 2.9 1.2 - - - -
164D SER* 1.3 79.6 - - - +
166D GLU* 1.3 67.4 + - - +
167D TYR 3.0 4.9 + - - -
168D THR* 3.6 3.4 - - - -
169D SER* 2.9 33.7 + - - +
175D LYS* 3.6 2.9 - - + +
178D TYR* 3.5 37.9 - + + -
179D GLN* 4.0 17.0 - - + -
182D PHE* 4.7 5.8 - - + -
283D TYR* 3.6 29.2 - + - -
286D ALA* 4.2 14.6 - - + -
287D LEU* 3.9 26.2 - - + -
290D ASN* 3.9 12.8 - - - -
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Residues in contact with GLU 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163D ASN* 2.9 35.2 + - - +
165D PHE* 1.3 78.1 - - - +
167D TYR* 1.3 90.2 + - + +
169D SER* 5.2 0.7 + - - -
175D LYS* 3.1 41.2 + - - +
179D GLN* 3.7 17.8 + - - +
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Residues in contact with TYR 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163D ASN* 4.2 20.3 + - - -
164D SER 4.8 0.4 + - - -
165D PHE 3.2 0.2 - - - -
166D GLU* 1.3 107.3 - - + +
168D THR* 1.3 68.8 + - + +
169D SER 3.5 7.6 - - - +
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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