Contacts of the strand formed by residues 217 - 220 (chain B) in PDB entry 2JI8
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216B PRO* 1.3 76.2 - - - +
218B ILE* 1.3 67.6 + - - +
219B MET* 4.9 0.4 - - + +
242B ILE* 3.9 0.4 - - - -
243B PRO* 3.4 21.1 - - + +
245B LEU* 3.7 30.3 - - + -
262B ALA* 5.3 0.2 - - + -
269B ALA* 4.6 11.9 - - + +
270B LEU* 4.7 8.5 - - + -
273B CYS* 4.2 17.3 - - + -
275B VAL 2.9 7.7 + - - +
276B CYS* 3.5 31.5 - - + -
277B VAL* 2.8 29.1 + - - +
347B TRP* 5.1 2.0 - - + -
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Residues in contact with ILE 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B ILE* 6.4 0.4 - - + -
217B VAL* 1.3 79.1 - - - +
219B MET* 1.3 56.2 + - - +
220B LEU* 3.7 29.4 - - + -
236B LEU* 4.7 16.2 - - + -
237B VAL* 4.1 22.7 - - + -
240B THR* 4.3 6.7 - - - +
242B ILE* 3.8 32.3 - - + +
243B PRO 3.0 10.5 + - - +
244B PHE* 3.2 7.2 - - + -
245B LEU* 2.8 33.3 + - - +
277B VAL* 3.5 20.2 - - + +
279B ILE* 3.9 13.5 - - + -
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Residues in contact with MET 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B VAL* 4.1 2.3 - - + +
218B ILE* 1.3 71.3 - - - +
220B LEU* 1.3 61.3 + - - +
221B GLY 3.9 0.3 + - - -
245B LEU* 3.2 53.6 - - + +
246B PRO 4.2 1.1 - - - -
247B MET* 3.3 26.5 - - + +
266B ARG* 3.6 31.4 - - - +
270B LEU* 4.3 10.1 - - + -
276B CYS* 4.5 8.7 - - - -
277B VAL 2.7 10.7 + - - +
278B LEU* 3.7 16.1 - - + -
279B ILE* 3.0 28.9 + - - +
281B ALA* 4.3 2.3 - - + +
287B MET* 3.5 30.3 - - + -
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Residues in contact with LEU 220 (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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218B ILE* 3.7 25.1 - - + -
219B MET* 1.3 71.9 - - - +
221B GLY* 1.3 60.1 + - - +
224B ALA* 4.7 3.1 - - + -
233B ILE* 3.7 32.8 - - + -
237B VAL* 5.0 2.2 - - + -
244B PHE* 3.8 30.7 - - + -
245B LEU 2.8 14.3 + - - +
246B PRO* 4.4 4.0 - - + -
247B MET* 2.8 30.7 + - - +
250B ALA* 3.0 12.2 - - + +
253B LEU* 4.5 19.5 - - + -
254B LEU* 4.5 7.6 - - + +
279B ILE* 3.9 20.0 - - + -
281B ALA* 4.5 0.2 - - - -
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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