Contacts of the strand formed by residues 288 - 294 (chain B) in PDB entry 4I6J
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 ASN 288 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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515A LEU* 3.4 33.1 - - + +
253B GLU 3.4 22.3 + - - +
254B HIS* 3.6 3.3 - - + -
255B LEU* 3.0 26.7 + - - +
286B LYS 4.2 7.8 + - - +
287B VAL* 1.3 80.8 - - - +
289B LEU* 1.3 60.3 + - - +
290B VAL* 3.8 0.8 + - + -
311B THR* 3.5 13.2 + - + +
312B HIS* 3.5 17.4 + - + -
335B VAL* 5.7 1.0 - - - +
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Residues in contact with LEU 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B LEU* 3.6 36.1 - - + +
257B ILE* 4.4 4.7 - - + -
277B TRP* 3.6 14.1 - - + -
280B PHE* 4.7 7.2 - - + -
287B VAL* 4.0 3.1 + - + -
288B ASN* 1.3 73.4 - - - +
290B VAL* 1.3 57.1 - - - +
291B MET* 3.3 39.7 + - + +
309B PRO* 3.6 33.2 - - + +
310B ALA* 3.5 20.7 - - - +
311B THR* 3.0 31.6 + - - +
312B HIS 3.2 5.9 + - - +
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Residues in contact with VAL 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A LYS* 5.8 0.9 - - - +
515A LEU* 4.3 17.5 - - + +
254B HIS* 3.9 23.1 - - + +
255B LEU 3.1 8.6 + - - +
256B ARG* 3.3 18.6 - - - +
257B ILE* 2.9 26.7 + - - +
289B LEU* 1.3 74.0 - - - +
291B MET* 1.3 64.7 + - - +
292B TYR* 3.5 32.8 - - + +
311B THR* 4.8 0.2 - - + -
312B HIS* 3.5 35.9 - - + -
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Residues in contact with MET 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B LEU* 6.5 0.4 - - - -
257B ILE* 3.5 16.6 - - + +
259B VAL* 5.6 2.2 - - + -
277B TRP* 4.1 16.8 - - + -
289B LEU* 3.3 46.7 - - + +
290B VAL* 1.3 77.9 - - - +
292B TYR* 1.3 63.7 + - - +
293B PHE* 3.7 25.9 - - + -
303B PHE* 6.1 1.8 - - - -
304B PHE* 5.5 0.7 - - - -
308B ILE* 4.3 13.5 - - + -
310B ALA* 4.1 11.2 - - + -
312B HIS 2.8 8.7 + - - -
313B LEU* 3.4 24.0 - - + +
314B TYR 3.1 22.7 + - - +
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Residues in contact with TYR 292 (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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499A ILE* 4.2 19.7 - - + -
503A LYS* 2.9 24.0 + - - -
515A LEU 4.6 5.4 + - - -
517A LEU* 3.5 26.0 - - + +
256B ARG* 3.0 41.5 - - - +
257B ILE 3.0 7.7 + - - +
258B ASP* 3.7 4.9 - - - +
259B VAL* 2.9 28.1 + - - +
290B VAL* 3.5 23.2 - - + +
291B MET* 1.3 78.6 - - - +
293B PHE* 1.3 61.9 + - - +
294B PHE* 3.8 17.1 - + + -
312B HIS* 5.4 1.3 - - + -
313B LEU 4.7 2.5 - - - -
314B TYR* 3.2 40.2 - + + +
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Residues in contact with PHE 293 (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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259B VAL* 3.6 24.9 - - + -
291B MET* 3.7 37.5 - - + -
292B TYR* 1.3 75.7 - - - +
294B PHE* 1.3 62.3 + - - +
295B LEU* 3.7 4.0 + - + +
300B PHE* 3.6 32.5 - + + -
303B PHE* 3.6 41.7 - + + -
304B PHE* 3.8 28.3 - + - -
313B LEU* 4.3 3.6 - - + -
314B TYR 2.8 14.5 + - - +
315B PHE* 3.6 16.6 - + + -
316B GLY 2.8 28.2 + - - -
317B ARG 3.9 1.4 + - - -
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Residues in contact with PHE 294 (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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492A ALA* 3.6 24.6 - - + +
495A SER* 3.6 26.7 - - - -
496A ARG* 3.2 53.6 - - + -
499A ILE* 4.6 4.3 - - + -
258B ASP* 4.6 2.5 - - - -
259B VAL 2.7 20.2 + - - +
260B VAL* 4.3 7.2 - - + -
261B SER* 3.4 13.3 + - - -
292B TYR* 3.8 34.1 - + + -
293B PHE* 1.3 73.3 - - - +
295B LEU* 1.3 65.6 + - - +
296B TYR* 4.8 0.2 - - - -
314B TYR* 4.4 14.8 - + - -
316B GLY* 4.0 21.3 - - - -
317B ARG* 3.8 11.3 - - + +
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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