Contacts of the helix formed by residues 178 - 182 (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 THR 178 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174D VAL 3.4 3.5 + - - -
175D LEU 3.2 17.8 + - - +
176D LEU 3.3 0.6 - - - -
177D SER* 1.3 79.0 - - - +
179D PRO* 1.3 68.6 - - - +
180D ALA 4.0 0.2 - - - +
181D LEU* 2.9 42.3 + - + +
182D GLU* 3.5 7.6 + - - -
384D TRP* 5.3 0.2 - - + -
388D VAL* 4.1 8.5 - - + -
391D ASP* 2.7 30.5 + - - +
503D EDO 2.7 36.0 + - - +
504D DMS 4.5 0.3 - - - -
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Residues in contact with PRO 179 (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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177D SER 3.9 3.6 - - - +
178D THR* 1.3 84.3 - - - +
180D ALA* 1.3 60.9 + - - +
181D LEU 3.0 1.7 + - - -
182D GLU* 3.1 18.1 + - - +
297D VAL* 3.6 7.6 - - - +
391D ASP* 3.2 17.9 - - - +
504D DMS 3.8 34.5 - - + -
514D EDO 3.6 34.5 - - - +
515D PEG 4.0 13.5 - - - +
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Residues in contact with ALA 180 (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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179D PRO* 1.3 72.1 - - - +
181D LEU* 1.3 61.1 + - + +
182D GLU 3.5 0.2 - - - -
290D LYS* 6.1 0.4 - - - +
296D GLY 4.7 8.5 - - - +
297D VAL* 3.3 6.7 - - - +
298D LEU* 3.0 31.2 + - + +
387D LEU 4.8 2.5 - - - +
388D VAL* 3.7 34.8 - - + +
389D HIS 5.2 2.5 - - - +
391D ASP* 2.7 23.0 + - - +
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Residues in contact with LEU 181 (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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175D LEU 3.9 4.7 - - - +
176D LEU* 4.3 13.0 - - - +
178D THR* 2.9 30.1 + - + +
180D ALA* 1.3 82.6 - - - +
182D GLU* 1.3 66.6 + - - +
183D ALA 3.3 1.0 + - - -
184D VAL* 3.0 25.8 + - + +
185D PHE* 4.2 21.2 + - + -
298D LEU* 3.8 30.7 - - + -
309D VAL* 4.8 3.1 - - + -
313D MET* 3.5 32.1 - - + -
384D TRP* 4.1 14.8 - - + -
387D LEU* 5.7 0.2 - - + -
388D VAL* 4.5 6.7 - - + -
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Residues in contact with GLU 182 (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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176D LEU 5.7 0.9 - - - -
177D SER 6.2 0.4 - - - -
178D THR 3.5 4.2 + - - +
179D PRO 3.1 16.4 + - - +
180D ALA 3.5 0.6 - - - -
181D LEU* 1.3 77.0 - - - +
183D ALA* 1.3 70.7 + - + +
184D VAL 3.0 5.4 + - - -
297D VAL* 3.4 25.9 - - + +
504D DMS 3.2 35.2 + - + +
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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