Contacts of the helix formed by residues 185 - 190 (chain D) in PDB entry 4PEI
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 185 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184D GLN* 1.3 74.3 - - - +
186D ILE* 1.3 56.3 + - - +
187D VAL* 2.8 15.7 + - - -
188D MET* 2.9 24.2 + - - +
189D LYS* 4.1 3.8 + - - +
207D ALA* 3.5 19.6 + - - -
209D LEU 3.2 12.9 + - - -
215D LYS* 5.6 2.7 - - - -
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Residues in contact with ILE 186 (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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182D TRP* 4.0 10.5 - - + -
183D PRO* 3.1 26.5 + - + +
184D GLN 3.1 5.5 + - - -
185D GLY* 1.3 75.5 - - - +
187D VAL* 1.3 66.1 + - - +
188D MET 3.2 0.2 - - - -
189D LYS* 3.0 23.5 + - + +
218D LEU* 4.1 15.5 - - + -
235D TYR* 4.2 0.3 - - - -
237D ALA* 3.7 11.1 - - + +
239D GLU* 3.7 32.8 - - + +
244D PHE* 3.7 57.9 - - + -
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Residues in contact with VAL 187 (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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182D TRP* 3.9 14.3 - - + -
185D GLY* 2.8 8.6 + - - +
186D ILE* 1.3 84.5 - - - +
188D MET* 1.3 75.5 + - + +
189D LYS 3.1 0.5 + - - -
192D TYR* 3.6 8.4 - - + +
195D LEU* 3.5 32.3 - - + -
196D TYR* 4.2 12.1 - - + +
206D GLY 3.5 24.9 - - - +
207D ALA* 4.4 1.1 - - - -
209D LEU* 4.0 19.7 + - + +
235D TYR* 2.5 32.0 + - - +
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Residues in contact with MET 188 (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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185D GLY* 2.9 15.7 + - - +
187D VAL* 1.3 87.4 - - - +
189D LYS* 1.3 66.7 + - + +
190D GLY 3.3 3.5 + - - +
192D TYR* 3.5 58.9 - - + +
196D TYR* 4.1 11.2 - - + +
206D GLY* 4.5 0.7 - - - -
207D ALA* 3.5 37.7 - - + -
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Residues in contact with LYS 189 (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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185D GLY 4.6 2.9 - - - +
186D ILE* 3.0 23.4 + - + +
188D MET* 1.3 83.1 - - + +
190D GLY* 1.3 55.7 + - - +
237D ALA* 3.5 8.9 - - + -
238D GLU* 3.2 41.6 + - - +
239D GLU* 2.5 47.7 + - + +
240D GLY 4.9 0.8 - - - +
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Residues in contact with GLY 190 (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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188D MET 3.6 2.1 - - - +
189D LYS* 1.3 78.3 - - - +
191D ASN* 1.3 58.7 + - - -
192D TYR* 2.9 22.9 + - - -
235D TYR* 3.0 18.1 + - - -
236D HIS 3.6 17.3 - - - -
237D ALA* 3.6 3.3 - - - +
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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