Contacts of the helix formed by residues 198 - 203 (chain D) in PDB entry 2WFY
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 198 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196D LYS* 5.1 1.0 - - - +
197D VAL* 1.3 79.9 - - - +
199D TYR* 1.3 61.9 + - - -
200D MET* 3.3 2.7 - - - -
201D LYS* 3.3 42.8 + - - +
202D LYS* 4.0 11.6 + - - +
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Residues in contact with TYR 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 PRO* 4.6 0.7 - - + -
196D LYS* 3.6 26.5 - - + +
197D VAL 3.1 5.7 + - - -
198D GLY* 1.3 76.5 - - - +
200D MET* 1.3 87.9 + - + +
201D LYS 3.2 1.0 + - - -
202D LYS* 3.3 19.4 + - - +
203D GLN* 3.5 12.2 + - - +
208D ASN* 5.7 0.9 - - - -
211D ARG* 3.4 16.8 - - - -
240D ASP* 2.6 39.5 + - + -
243D LEU* 3.4 45.7 - - + +
244D SER* 3.5 33.0 - - - +
344D ALA* 5.7 0.9 - - + -
348D LEU* 3.7 20.4 - - + -
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Residues in contact with MET 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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198D GLY 3.3 0.8 - - - -
199D TYR* 1.3 114.7 - - + +
201D LYS* 1.3 60.2 + - + +
202D LYS 3.4 0.2 - - - -
203D GLN* 3.2 26.7 + - - +
206D ILE* 3.9 21.0 - - + +
207D THR* 3.7 35.2 - - - +
208D ASN* 3.3 42.4 - - - +
211D ARG* 3.7 17.5 - - + -
243D LEU* 4.6 7.0 - - + -
253D LEU* 6.3 0.7 - - + -
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Residues in contact with LYS 201 (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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198D GLY* 3.4 28.3 - - - +
199D TYR 3.1 0.2 - - - -
200D MET* 1.3 78.9 - - + +
202D LYS* 1.3 59.5 + - + +
203D GLN 3.2 5.0 + - - +
204D PRO* 5.8 0.3 - - - +
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Residues in contact with LYS 202 (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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59A ASN* 5.6 4.0 + - - -
65A LYS* 5.9 6.3 - - - +
196D LYS* 5.6 12.3 - - - +
198D GLY 4.4 12.1 - - - +
199D TYR* 3.3 9.7 + - - +
201D LYS* 1.3 77.1 - - + +
203D GLN* 1.3 59.8 + - - +
204D PRO* 3.4 12.0 - - - +
247D SER* 4.7 4.2 + - - -
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Residues in contact with GLN 203 (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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199D TYR* 3.5 9.5 + - - +
200D MET* 3.2 25.9 - - - +
201D LYS 3.2 4.1 - - - +
202D LYS* 1.3 78.8 + - - +
204D PRO* 1.3 67.8 - - + +
205D ASP 3.4 0.2 - - - -
206D ILE* 3.0 47.2 - - + +
243D LEU* 2.9 36.5 + - - +
246D MET 3.1 12.6 + - - -
247D SER* 2.7 13.3 + - - -
248D VAL 2.5 32.3 + - - +
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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