Contacts of the helix formed by residues 217 - 223 (chain D) in PDB entry 4OGB
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 217 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243B GLU* 3.5 22.7 - - - -
212D LEU* 2.8 41.2 + - - +
215D THR* 3.2 10.3 - - - -
216D ASN* 1.3 80.8 - - - +
218D GLU* 1.3 58.9 + - - +
219D LEU* 3.7 5.3 + - - +
220D ALA* 3.1 14.2 + - - +
221D LEU* 3.0 24.0 + - - +
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Residues in contact with GLU 218 (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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239B LYS* 4.8 21.9 - - + +
243B GLU* 4.3 4.4 + - - +
216D ASN 3.7 1.4 + - - -
217D SER* 1.3 72.3 - - - +
219D LEU* 1.3 57.5 + - + +
221D LEU* 3.8 13.9 - - + +
222D MET* 3.0 42.5 + - + +
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Residues in contact with LEU 219 (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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205D PRO* 5.6 3.8 - - + -
212D LEU* 4.2 9.2 - - + -
217D SER* 3.1 8.6 - - - +
218D GLU* 1.3 78.2 - - - +
220D ALA* 1.3 64.8 + - - +
222D MET* 3.1 31.3 + - + +
223D TYR* 3.3 18.1 + - + -
228D VAL* 3.3 25.0 - - + +
229D LEU* 4.1 17.5 - - + -
232D HIS* 3.7 52.0 - - + +
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Residues in contact with ALA 220 (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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261C ARG* 3.9 0.2 + - - -
212D LEU* 3.1 35.9 - - + +
213D ILE* 3.7 7.9 - - + +
216D ASN* 4.9 1.3 - - - -
217D SER* 3.1 9.5 + - - +
219D LEU* 1.3 77.6 - - - +
221D LEU* 1.3 59.3 + - + +
223D TYR 3.7 0.2 - - - -
224D ASN* 3.1 9.0 + - - -
225D ASP* 2.9 42.9 + - - +
228D VAL* 3.6 13.9 - - - +
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Residues in contact with LEU 221 (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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242B GLN* 5.8 4.7 - - + +
261C ARG* 3.8 34.3 + - - +
216D ASN* 3.5 42.4 - - - +
217D SER 3.0 17.7 + - - +
218D GLU* 3.8 13.2 - - + +
220D ALA* 1.3 78.8 - - + +
222D MET* 1.3 63.5 + - - +
223D TYR 3.3 0.9 + - - -
224D ASN* 3.6 13.5 + - - +
225D ASP* 5.3 0.2 - - - +
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Residues in contact with MET 222 (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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222C MET* 2.2 42.2 - - + -
223C TYR* 3.5 24.1 + - + +
231C ASN* 5.1 0.2 - - - +
235C ALA* 6.5 0.7 - - - -
512C EDO 3.8 10.1 - - - +
218D GLU* 3.0 34.5 + - + +
219D LEU* 3.1 22.2 + - + +
221D LEU* 1.3 77.3 - - - +
223D TYR* 1.3 73.1 + - + +
224D ASN* 4.9 4.0 + - - +
232D HIS* 5.9 0.7 - - - -
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Residues in contact with TYR 223 (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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222C MET* 2.7 42.7 + - + +
223C TYR* 4.1 16.2 - + - -
231C ASN* 5.5 0.9 - - - -
219D LEU* 3.3 24.6 + - + +
221D LEU 3.2 0.2 - - - -
222D MET* 1.3 102.3 - - + +
224D ASN* 1.3 66.6 + - - +
225D ASP 3.2 2.5 - - - -
226D SER* 2.8 32.2 + - - +
228D VAL* 3.8 28.0 - - + -
231D ASN* 3.6 30.4 + - + +
232D HIS* 4.0 17.2 + - - -
235D ALA* 3.7 14.9 - - - +
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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