Contacts of the strand formed by residues 217 - 221 (chain H) in PDB entry 2W3S
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 VAL 217 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190H VAL* 3.6 13.7 - - + -
192H ILE* 4.6 1.1 - - + -
203H GLN* 2.8 64.1 + - + +
206H VAL* 3.9 18.8 - - + -
207H ALA* 3.8 28.0 - - + +
212H LEU* 4.0 16.6 - - + -
213H ALA 4.3 4.0 - - - +
214H PHE 2.9 6.0 + - - +
215H HIS 3.5 1.2 - - - -
216H ASP* 1.3 85.7 - - - +
218H ARG* 1.3 62.9 + - - +
219H VAL* 4.4 7.4 - - + -
518H THR* 4.1 0.2 + - - -
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Residues in contact with ARG 218 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218F ARG* 3.9 21.6 - - - +
220F GLU* 5.5 4.9 + - - -
514F THR* 5.9 2.2 - - - +
517F ASP* 5.2 4.4 + - - -
520F LYS* 4.2 15.7 - - - +
190H VAL 3.1 12.3 + - - +
191H VAL* 3.3 20.6 - - + +
192H ILE* 2.8 26.5 + - - +
217H VAL* 1.3 72.7 - - - +
219H VAL* 1.3 69.0 + - - +
220H GLU* 3.8 19.3 + - + -
517H ASP* 2.5 32.3 + - - +
518H THR* 3.8 5.4 - - - +
519H SER* 3.0 31.3 + - - +
520H LYS* 4.8 2.0 - - - +
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Residues in contact with VAL 219 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192H ILE* 3.3 26.5 - - + +
194H CYS* 4.2 10.3 - - - -
199H PRO* 3.7 39.2 - - + +
202H ILE* 3.7 24.0 - - + -
203H GLN* 3.9 15.5 - - + +
217H VAL* 4.4 1.3 - - + -
218H ARG* 1.3 79.0 - - - +
220H GLU* 1.3 69.0 + - - +
221H MET* 5.1 0.4 - - + -
516H THR 3.9 0.9 - - - +
517H ASP* 3.4 5.4 - - - -
518H THR* 3.2 35.4 + - + +
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Residues in contact with GLU 220 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218F ARG* 5.4 5.7 + - - -
191H VAL* 4.1 11.1 - - + +
192H ILE 2.8 15.6 + - - +
193H HIS* 3.3 47.5 - - + +
194H CYS 3.5 2.9 + - - -
218H ARG* 3.8 22.7 + - + +
219H VAL* 1.3 76.5 - - - +
221H MET* 1.3 66.9 + - - +
515H ALA* 4.9 11.4 - - + +
516H THR 3.4 4.0 - - - +
517H ASP* 3.4 25.1 - - + +
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Residues in contact with MET 221 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194H CYS* 3.3 28.9 - - - +
196H SER 3.6 16.6 - - - +
199H PRO* 4.5 12.1 - - + -
219H VAL* 5.1 0.2 - - + -
220H GLU* 1.3 77.5 - - - +
222H ARG* 1.3 59.8 + - - +
223H ARG* 3.4 38.4 - - - +
224H MET* 3.2 35.9 - - + -
486H THR* 3.8 20.6 - - + -
487H GLU 3.5 9.6 + - - +
515H ALA* 4.2 1.5 - - - +
516H THR* 3.0 35.1 + - - +
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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
------------------------------------------------------------
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