Contacts of the helix formed by residues 216 - 226 (chain B) in PDB entry 4OE5
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 GLY 216 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165B GLU* 5.6 6.0 - - - +
208B SER* 5.7 1.8 - - - -
214B ALA* 3.2 11.2 - - - +
215B ILE* 1.3 79.4 - - - +
217B GLY* 1.3 58.9 + - - +
218B ASN* 3.1 3.6 - - - -
219B LEU* 2.9 44.5 + - - +
220B ALA 4.1 1.0 + - - -
232B TRP* 4.6 4.2 + - - -
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Residues in contact with GLY 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B GLU* 5.6 2.0 + - - +
166B LEU* 4.8 15.3 - - - +
170B PHE* 4.8 8.9 - - - -
215B ILE* 3.2 17.9 - - - +
216B GLY* 1.3 75.9 - - - +
218B ASN* 1.3 56.4 + - - +
219B LEU 3.3 0.5 + - - -
220B ALA* 3.3 4.7 + - - +
221B GLY* 2.8 25.6 + - - -
232B TRP* 4.5 9.8 - - - -
245B VAL* 5.2 4.9 - - - -
249B LEU* 6.0 1.4 - - - +
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Residues in contact with ASN 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B GLU* 4.1 19.3 + - - +
166B LEU* 5.8 0.2 - - - +
169B PHE* 3.5 36.5 - - + +
170B PHE* 5.4 4.6 - - - -
173B ASN* 2.7 29.3 + - - +
216B GLY* 3.1 1.6 + - - -
217B GLY* 1.3 72.3 - - - +
219B LEU* 1.3 61.9 + - + +
220B ALA 3.2 0.2 - - - -
221B GLY* 3.7 3.7 - - - +
222B ALA* 2.9 39.2 + - - +
223B PRO* 3.7 0.3 - - - +
283B ASN* 4.0 2.6 + - - +
530B ASP* 4.8 3.6 + - - -
536B HIS* 5.3 9.9 + - - +
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Residues in contact with LEU 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206B ALA* 3.5 20.4 - - + +
207B ILE 3.4 31.4 - - - +
208B SER* 4.2 12.1 - - - -
215B ILE 5.6 0.2 - - - +
216B GLY* 2.9 25.3 + - - +
218B ASN* 1.3 79.1 - - + +
220B ALA* 1.3 56.4 + - - +
223B PRO* 3.1 11.1 - - - +
232B TRP* 5.2 4.7 - - - +
283B ASN* 2.9 51.5 + - - +
284B PHE 4.3 1.8 - - - +
285B THR* 3.7 26.5 - - - +
314B GLU* 5.5 1.1 - - - +
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Residues in contact with ALA 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206B ALA* 4.0 4.3 - - + -
216B GLY 4.1 0.6 + - - -
217B GLY 3.3 5.5 + - - +
219B LEU* 1.3 77.8 - - - +
221B GLY* 1.3 67.1 + - - +
222B ALA 3.5 0.4 - - - -
223B PRO* 3.5 4.5 - - - +
224B ALA* 3.1 25.8 + - - +
230B VAL* 3.8 21.6 - - + +
232B TRP* 4.0 30.7 - - + -
259B ILE* 3.9 17.7 - - + -
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Residues in contact with GLY 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B PHE* 3.7 24.3 - - - -
170B PHE* 4.5 8.5 - - - -
173B ASN* 4.8 2.5 - - - -
217B GLY 2.8 17.6 + - - -
218B ASN* 4.0 2.7 - - - -
220B ALA* 1.3 78.1 - - - +
222B ALA* 1.3 61.6 + - - +
224B ALA* 4.5 0.7 - - - -
225B LEU* 3.0 26.4 + - - +
249B LEU* 5.6 2.0 - - - +
259B ILE* 4.7 3.1 - - - +
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Residues in contact with ALA 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173B ASN* 3.6 23.8 - - - +
218B ASN* 2.9 31.7 + - - +
221B GLY* 1.3 73.9 - - - +
223B PRO* 1.3 70.5 - - + +
225B LEU* 3.3 6.8 + - - +
226B MET* 3.2 22.7 - - - +
283B ASN* 5.1 1.1 - - - +
536B HIS 5.8 2.2 - - - +
538B ILE* 4.0 14.3 - - + +
541B TRP* 4.4 11.7 - - + +
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Residues in contact with PRO 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B VAL* 4.2 17.9 - - + -
219B LEU 3.1 27.1 - - - +
220B ALA 3.5 8.1 - - - +
222B ALA* 1.3 93.8 - - + +
224B ALA* 1.3 60.9 + - - +
226B MET 3.0 7.6 + - - -
228B ASN* 2.9 42.0 + - + +
230B VAL* 4.1 14.8 - - + -
283B ASN* 3.7 11.9 - - - +
541B TRP* 4.0 19.0 - - + -
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Residues in contact with ALA 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B TRP* 2.8 29.7 + - + -
128B PHE* 3.9 13.9 - - + -
220B ALA 3.1 20.7 + - - +
221B GLY 3.8 3.8 - - - +
222B ALA 3.3 0.2 - - - -
223B PRO* 1.3 74.5 - - - +
225B LEU* 1.3 64.1 + - - +
227B GLY 3.0 4.3 + - - -
228B ASN 3.6 13.5 - - - +
230B VAL* 4.1 3.9 - - + +
254B LEU* 5.2 0.7 - - + -
258B ILE* 4.4 8.7 - - + -
259B ILE* 4.0 21.8 - - + -
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Residues in contact with LEU 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B TRP* 4.9 1.1 - - - -
121B ILE* 3.5 11.6 - - + +
124B ARG* 2.8 24.1 + - - +
125B ALA* 3.9 26.9 - - + +
128B PHE* 3.7 34.7 - - + -
170B PHE 5.3 0.4 - - - +
173B ASN* 3.4 49.4 - - + +
174B ALA* 3.6 7.6 - - + +
177B ALA* 4.0 11.0 - - + -
221B GLY 3.0 18.1 + - - +
222B ALA 3.6 3.8 - - - +
224B ALA* 1.3 76.2 - - - +
226B MET* 1.3 56.3 + - - +
227B GLY 3.2 0.2 - - - -
538B ILE* 4.1 9.0 - - + -
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Residues in contact with MET 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B ILE* 5.1 2.0 - - + -
124B ARG* 3.5 12.2 + - - +
177B ALA* 4.0 24.7 - - + -
180B LEU* 4.2 17.9 - - + -
197B TYR* 4.9 4.4 - - + +
198B ARG 4.4 1.7 - - - +
199B GLY* 3.4 22.3 + - - -
222B ALA 3.2 15.0 - - - +
223B PRO 3.0 8.5 + - - +
225B LEU* 1.3 77.4 - - - +
227B GLY* 1.3 57.3 + - - +
228B ASN* 3.4 2.7 - - - +
538B ILE* 3.7 40.8 - - + +
541B TRP* 3.6 24.0 - - + +
542B THR* 4.0 27.2 - - + -
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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