Contacts of the helix formed by residues 196 - 201 (chain D) in PDB entry 5J0Z
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 196 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193D GLN 4.2 6.2 + - - -
195D PHE* 1.3 81.9 - - - +
197D TYR* 1.3 84.6 + - - +
199D PRO* 3.2 11.0 - - - +
200D ASN* 3.1 32.4 + - - +
248E LYS* 3.5 27.8 - - - +
249E THR 3.2 25.3 + - - -
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Residues in contact with TYR 197 (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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32D ASP* 5.6 0.5 + - - -
119D TYR* 3.1 38.1 + + - -
120D PRO* 3.6 37.9 - - + -
192D ARG* 3.9 18.4 + - - -
193D GLN 4.2 6.3 - - - -
194D TYR* 3.0 19.6 + - - +
195D PHE 2.9 0.4 + - - -
196D SER* 1.3 96.6 + - - +
198D ILE* 1.3 60.5 + - + +
200D ASN* 4.6 2.0 - - - -
201D ILE* 3.1 34.2 + - + +
202D ILE* 3.0 35.2 + - + +
242D VAL* 6.0 0.2 - - + -
248E LYS* 3.2 35.5 + - + +
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Residues in contact with ILE 198 (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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121D PHE* 4.5 8.5 - - + -
194D TYR* 3.7 34.5 - - + +
195D PHE* 3.0 16.6 + - + +
197D TYR* 1.3 78.7 - - - +
199D PRO* 1.4 68.6 - - + +
200D ASN 3.3 0.4 - - - -
202D ILE* 3.2 22.7 + - + -
203D LEU* 2.9 52.7 + - + +
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Residues in contact with PRO 199 (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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195D PHE* 3.2 20.0 - - + +
196D SER* 3.2 5.8 - - - +
198D ILE* 1.4 102.4 - - + +
200D ASN* 1.3 73.1 + - - +
204D PRO* 3.6 11.0 - - - +
239E ASN* 5.4 1.7 + - - -
252E MET* 3.8 28.5 - - + -
260E PHE* 3.6 46.8 - - + +
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Residues in contact with ASN 200 (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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196D SER* 3.1 28.7 + - - +
197D TYR* 4.6 1.6 - - - -
198D ILE 3.3 0.4 - - - -
199D PRO* 1.3 95.9 + - - +
201D ILE* 1.3 68.9 + - + +
204D PRO* 3.9 5.5 - - - +
238D PHE* 3.9 14.4 - - - -
239E ASN* 4.5 7.7 + - - +
243E GLU* 3.8 42.2 - - - +
248E LYS* 6.0 2.1 - - - +
252E MET* 5.4 5.9 - - - +
256E GLY* 5.7 5.9 + - - -
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Residues in contact with ILE 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197D TYR* 3.1 39.6 + - + +
200D ASN* 1.3 88.6 - - + +
202D ILE* 1.3 70.0 + - + +
203D LEU 3.7 0.7 - - - -
204D PRO* 3.8 2.5 - - - +
205D MET* 2.9 47.8 + - + +
238D PHE* 4.4 7.8 - - + +
241D LEU* 4.8 13.5 - - + -
242D VAL* 3.7 34.1 - - + -
245D ASN* 4.5 8.3 - - - +
255D THR* 5.4 7.4 - - + -
243E GLU* 4.7 10.1 - - - +
248E LYS* 5.5 2.9 - - - -
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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