Contacts of the strand formed by residues 218 - 222 (chain F) in PDB entry 3JCA
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 MET 218 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216F LYS 4.0 7.8 + - - +
217F PRO* 1.3 79.4 - - - +
219F VAL* 1.3 67.8 + - - +
232F PRO* 3.2 46.4 - - + +
233F ASP* 3.2 7.9 - - - +
234F VAL* 4.0 27.6 - - + -
235F LEU 4.3 0.2 - - - +
263F PRO* 3.8 0.7 - - - +
264F PHE* 2.7 39.2 + - + +
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Residues in contact with VAL 219 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217F PRO* 5.2 2.0 - - + -
218F MET* 1.3 81.5 - - - +
220F MET* 1.3 67.2 + - - +
221F TRP 3.4 1.4 + - - +
232F PRO* 3.2 6.0 - - - +
233F ASP* 2.9 37.0 + - - +
235F LEU* 4.1 25.6 - - + -
245F VAL* 3.8 24.0 - - + -
261F ILE* 3.6 35.9 - - + -
262F ARG 3.3 5.6 - - - +
263F PRO* 4.0 13.9 - - + -
264F PHE 3.9 0.4 - - - +
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Residues in contact with MET 220 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219F VAL* 1.3 76.5 - - - +
221F TRP* 1.3 59.1 + - - +
229F TRP* 3.5 35.7 - - + +
230F LYS* 3.6 23.1 - - - +
231F GLY 3.9 7.9 - - - +
232F PRO* 3.5 30.1 - - + -
261F ILE* 3.5 9.4 - - - +
262F ARG* 2.8 45.2 + - + +
264F PHE* 4.0 16.8 - - + -
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Residues in contact with TRP 221 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219F VAL 4.5 2.7 - - - +
220F MET* 1.3 73.2 - - - +
222F LYS* 1.3 73.9 + - - +
223F ASP* 2.7 38.6 + - + +
224F LEU 4.9 0.6 - - - +
225F LEU* 6.3 0.9 - - + -
229F TRP* 3.8 1.3 - - - -
230F LYS* 2.7 64.4 + - + +
233F ASP* 3.5 23.3 - - + +
245F VAL* 4.5 15.7 - - + -
247F PRO* 3.7 20.6 - - + -
254F ILE* 3.6 31.6 - - + +
256F VAL* 3.7 29.8 - - + +
260F PHE 4.3 0.9 - - - -
261F ILE* 4.5 4.0 - - + -
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Residues in contact with LYS 222 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221F TRP* 1.3 79.4 + - - +
223F ASP* 1.3 59.8 + - - +
224F LEU* 2.7 33.1 + - + +
227F GLY* 3.8 22.9 - - - -
228F SER 3.3 18.6 - - - +
229F TRP* 3.4 30.9 - - + +
256F VAL* 4.6 4.3 - - - +
260F PHE* 3.1 57.9 + - + +
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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