Contacts of the helix formed by residues 183 - 196 (chain e) in PDB entry 5OOM
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 THR 183 (chain e).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1578 LEU* 6.0 0.7 - - - -
1608 GLU* 3.6 22.4 - - + +
181e GLY 3.7 3.3 + - - -
182e GLU* 1.3 72.0 - - - +
184e LEU* 1.3 57.8 - - - +
185e ARG* 3.9 15.5 - - + +
186e GLY* 3.0 14.1 + - - +
187e THR* 2.4 37.9 + - - -
207e ASN* 4.4 2.5 - - - +
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Residues in contact with LEU 184 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1508 LEU* 3.9 25.6 - - + -
1578 LEU* 3.8 35.7 - - + +
1608 GLU* 3.4 22.7 + - - +
1618 ALA* 5.7 1.1 - - + -
178e TRP* 4.2 31.4 - - + +
182e GLU 3.8 1.3 + - - +
183e THR* 1.3 71.9 - - - +
185e ARG* 1.3 60.5 + - - +
187e THR* 3.2 9.7 + - - +
188e ALA 3.0 22.0 + - - -
207e ASN* 4.0 8.3 - - - +
232e PHE* 4.7 9.4 - - + -
234e PHE* 3.1 31.3 - - + -
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Residues in contact with ARG 185 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1658 ASP* 2.6 44.3 + - - +
1678 ASN* 4.4 16.2 - - - +
1688 LEU* 6.4 0.2 - - - +
183e THR* 3.3 10.6 - - + +
184e LEU* 1.3 78.6 - - - +
186e GLY* 1.3 56.1 + - - +
188e ALA* 3.2 6.1 + - - +
189e GLU* 2.9 49.5 + - + +
203e LYS* 4.8 8.3 - - - +
204e PHE* 3.4 50.4 + - + +
205e LEU 3.7 0.8 + - - -
206e GLY 3.6 20.8 + - - +
207e ASN* 3.9 19.3 + - + +
234e PHE* 3.9 9.2 - - - -
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Residues in contact with GLY 186 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182e GLU* 5.4 2.9 - - - -
183e THR* 3.0 20.0 + - - -
185e ARG* 1.3 76.0 - - - +
187e THR* 1.3 60.0 + - - +
189e GLU* 3.7 17.6 + - - +
190e ARG* 2.9 28.8 + - - +
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Residues in contact with THR 187 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49e GLY* 4.5 15.3 - - - -
50e ALA 5.3 1.1 - - - +
176e ALA* 4.3 7.2 - - + -
178e TRP* 3.3 30.0 - - + +
182e GLU* 3.2 20.1 + - - +
183e THR 2.4 34.4 + - - -
184e LEU* 3.2 16.1 + - + +
186e GLY* 1.3 69.6 - - - +
188e ALA* 1.3 50.4 + - - +
190e ARG* 3.4 20.1 + - - +
191e THR* 2.3 39.8 + - - +
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Residues in contact with ALA 188 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50e ALA 4.2 7.0 - - - +
51e LEU* 3.6 10.8 - - + +
184e LEU 3.0 5.9 + - - -
185e ARG* 3.2 6.3 + - - +
187e THR* 1.3 73.9 - - - +
189e GLU* 1.3 60.8 + - - +
191e THR* 3.1 11.6 + - - -
192e LEU* 3.0 29.5 + - - +
204e PHE* 3.6 27.4 - - + -
234e PHE* 3.7 23.8 - - + -
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Residues in contact with GLU 189 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1678 ASN* 5.6 2.8 + - - -
185e ARG* 2.9 42.8 + - - +
186e GLY* 3.8 14.0 - - - +
187e THR 3.3 0.2 - - - -
188e ALA* 1.3 77.5 - - - +
190e ARG* 1.3 61.4 + - - +
192e LEU* 3.3 22.1 + - + +
193e ALA* 4.0 4.7 + - - +
204e PHE* 3.6 23.0 - - + -
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Residues in contact with ARG 190 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176e ALA* 3.6 22.9 - - - +
177e GLU 2.5 36.6 + - - +
182e GLU* 3.2 31.4 + - - -
186e GLY 2.9 16.5 + - - +
187e THR* 3.7 8.2 + - - +
189e GLU* 1.3 75.2 - - - +
191e THR* 1.3 58.4 + - - +
192e LEU 3.4 0.2 + - - -
193e ALA* 4.0 1.4 + - - +
194e THR* 2.3 47.2 + - - +
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Residues in contact with THR 191 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50e ALA 4.9 3.8 + - - -
51e LEU* 4.5 14.8 - - + -
174e PRO* 4.4 12.8 - - + +
175e GLN 3.3 30.7 - - - +
176e ALA* 3.2 17.9 - - + +
187e THR* 2.3 28.7 + - - +
188e ALA* 3.1 14.6 + - - -
190e ARG* 1.3 76.6 - - - +
192e LEU* 1.3 64.8 + - - +
194e THR* 3.8 7.5 + - - -
195e LEU* 4.1 14.0 + - + +
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Residues in contact with LEU 192 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51e LEU* 3.8 27.1 - - + -
53e LEU* 4.6 5.2 - - + -
188e ALA 3.0 14.8 + - - +
189e GLU* 3.4 12.6 - - + +
190e ARG 3.2 1.0 - - - -
191e THR* 1.3 81.4 - - - +
193e ALA* 1.3 61.2 + - + +
194e THR 3.2 3.5 + - - -
195e LEU* 4.4 2.9 + - - +
196e SER* 4.5 5.4 + - - -
198e ASN* 4.5 2.1 - - - +
200e MET* 3.9 33.5 - - + +
202e ALA* 3.9 34.3 - - + +
204e PHE* 3.6 24.9 - - + -
236e ALA* 4.7 0.9 - - + -
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Residues in contact with ALA 193 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189e GLU 4.0 6.8 + - - +
190e ARG 4.0 1.2 + - - +
192e LEU* 1.3 77.3 - - + +
194e THR* 1.3 61.9 + - - +
197e GLU* 4.8 10.2 + - - +
198e ASN* 4.6 17.5 + - - +
200e MET* 5.8 3.6 - - + -
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Residues in contact with THR 194 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190e ARG* 2.3 44.3 + - - +
191e THR* 4.2 5.2 - - - -
192e LEU 3.2 2.0 - - - -
193e ALA* 1.3 79.7 - - - +
195e LEU* 1.3 71.2 + - + +
196e SER 3.5 0.7 - - - -
197e GLU* 3.4 21.8 - - - +
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Residues in contact with LEU 195 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159e LEU* 6.0 2.5 - - + -
161e VAL* 3.8 40.8 - - + -
163e GLU* 5.0 10.1 - - + +
174e PRO* 4.3 17.9 - - + -
175e GLN 5.2 8.5 - - - +
191e THR* 4.1 11.0 + - + +
194e THR* 1.3 81.7 - - + +
196e SER* 1.3 65.2 + - - +
197e GLU* 3.5 6.2 + - - +
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Residues in contact with SER 196 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159e LEU* 3.9 27.4 - - - +
192e LEU 4.5 5.5 + - - -
194e THR 3.5 0.2 - - - -
195e LEU* 1.3 79.3 - - - +
197e GLU* 1.3 67.9 - - - +
198e ASN* 3.6 27.1 - - - -
200e MET* 4.1 10.4 - - - +
243e PHE* 4.2 11.7 - - - -
248e ASN* 4.1 20.3 + - - +
252e HIS* 5.7 5.0 - - - +
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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