Contacts of the helix formed by residues 216 - 219 (chain B) in PDB entry 4H3E
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 TRP 216 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B PHE* 3.9 13.7 - + - -
143B LYS* 3.6 59.6 + - + +
146B PHE* 3.6 36.3 - + - -
147B VAL* 3.7 15.2 - - + +
191B LEU* 4.2 9.2 - - + -
193B VAL* 5.7 0.7 - - + -
212B LEU 3.6 13.8 + - - -
213B LYS* 3.1 25.7 - - + +
214B GLU 3.1 0.4 + - - -
215B ILE* 1.3 80.6 - - + +
217B SER* 1.3 61.9 + - - +
218B VAL 3.3 0.9 + - - -
219B ILE* 3.4 23.2 + - + +
221B TRP* 3.7 43.9 + + - -
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Residues in contact with SER 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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49B PRO* 4.4 12.6 - - - +
50B VAL* 3.7 9.9 - - - +
120B ASN* 3.3 25.1 - - - +
121B GLY* 3.3 1.4 + - - -
214B GLU* 2.7 22.3 + - - +
216B TRP* 1.3 79.6 - - - +
218B VAL* 1.3 59.8 + - - +
219B ILE 3.6 0.2 - - - -
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Residues in contact with VAL 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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47B CYS* 3.8 11.7 - - - +
48B ALA 3.4 26.5 - - - +
49B PRO* 3.7 2.7 - - + -
50B VAL* 3.6 22.0 - - + -
51B PHE* 4.0 18.2 - - + -
117B ILE* 3.2 10.9 - - + -
118B THR 2.9 35.0 + - - +
120B ASN 4.0 0.2 - - - +
121B GLY* 3.6 6.7 - - - +
215B ILE* 2.9 29.9 + - + +
217B SER* 1.3 83.2 + - - +
219B ILE* 1.3 63.0 + - - +
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Residues in contact with ILE 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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116B CYS* 3.3 14.8 - - + +
117B ILE* 4.3 5.4 - - + -
121B GLY* 3.3 1.8 - - - -
122B LYS 3.1 22.0 + - - +
191B LEU* 3.9 19.1 - - + -
192B ALA 5.5 0.2 - - - +
193B VAL* 4.7 7.0 - - + -
215B ILE* 3.4 33.7 - - + +
216B TRP* 3.4 29.4 + - + +
217B SER 3.6 0.2 - - - -
218B VAL* 1.3 77.5 - - - +
220B ASP* 1.3 64.6 + - - +
221B TRP* 3.3 46.9 + - + +
224B VAL* 4.0 9.0 - - + -
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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