Contacts of the strand formed by residues 358 - 364 (chain B) in PDB entry 4DY0
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 PHE 358 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B PHE* 4.3 3.8 - + - -
234B MET* 6.3 0.4 - - - -
236B ILE* 4.0 17.7 - - + -
237B ALA 3.7 10.5 - - - +
238B LEU* 3.9 7.2 - - + -
246B LEU* 3.6 8.6 - - - +
274B LEU* 6.1 0.4 - - + -
275B PRO* 4.0 19.1 - - + -
277B PHE* 3.9 21.3 - + - -
354B VAL* 3.2 33.2 - - + -
356B ARG 3.5 9.6 - - - +
357B PRO* 1.3 73.9 - - - +
359B LEU* 1.3 71.7 + - - +
360B PHE* 4.1 14.6 - + + -
374B GLY 3.9 0.2 - - - +
375B GLN* 3.3 3.3 - - - -
376B ILE* 2.8 77.3 + - + -
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Residues in contact with LEU 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B PHE* 4.2 11.9 - - + -
236B ILE* 3.4 7.4 - - - +
237B ALA* 2.8 44.2 + - + +
246B LEU* 4.1 6.4 - - + +
249B ILE* 5.1 5.2 - - + -
250B ILE* 3.7 39.3 - - + -
253B ILE* 3.5 32.5 - - + -
358B PHE* 1.3 74.1 - - - +
360B PHE* 1.3 61.9 + - - +
361B PHE* 4.0 21.3 - - + -
373B MET* 4.6 5.4 - - + -
374B GLY 3.3 12.6 - - - +
375B GLN* 4.1 9.2 - - + -
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Residues in contact with PHE 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B VAL* 4.0 20.0 - - + -
234B MET* 4.5 19.7 - - + -
235B LEU 3.1 9.6 - - - +
236B ILE* 4.2 13.0 - - + -
277B PHE* 4.3 8.1 - + - -
326B ILE* 4.0 30.3 - - + -
358B PHE* 4.1 10.8 - + + -
359B LEU* 1.3 76.0 - - - +
361B PHE* 1.3 72.7 + - - +
372B PHE* 4.4 13.2 - - + -
373B MET* 3.4 3.5 - - - +
374B GLY* 2.9 59.8 + - - -
376B ILE* 3.7 36.6 - - + -
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Residues in contact with PHE 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ILE* 5.0 1.1 - - + -
234B MET* 3.3 9.0 - - - +
235B LEU* 2.8 52.1 + - + +
236B ILE* 5.6 0.2 - - - -
237B ALA* 5.1 1.3 - - + -
253B ILE* 3.8 18.6 - - + -
258B ILE* 4.0 19.7 - - + -
261B TRP* 3.7 29.8 - + - -
359B LEU* 4.0 24.9 - - + -
360B PHE* 1.3 77.4 - - - +
362B ILE* 1.3 66.7 + - - +
363B ARG* 4.1 1.3 - - + -
370B VAL* 4.0 18.2 - - + -
372B PHE 3.2 7.2 - - - +
373B MET* 3.4 48.7 - - + -
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Residues in contact with ILE 362 (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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170B PHE* 4.0 11.9 - - + -
227B TYR* 3.5 29.8 - - + +
232B ILE* 3.6 21.8 - - + -
233B SER 3.5 0.7 - - - -
234B MET* 3.8 22.0 - - + -
326B ILE* 3.8 17.3 - - + -
360B PHE* 4.9 0.7 - - + -
361B PHE* 1.3 81.1 - - - +
363B ARG* 1.3 61.8 + - - +
370B VAL* 3.7 3.3 - - - +
371B LEU* 2.8 40.1 + - + +
372B PHE* 3.0 41.6 + - + +
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Residues in contact with ARG 363 (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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232B ILE* 3.2 9.8 - - - +
233B SER* 2.9 37.2 + - - +
235B LEU* 4.1 14.4 - - + -
258B ILE* 3.7 25.7 - - - +
259B ASP* 3.7 21.2 + - - -
262B MET* 3.2 29.2 - - - +
361B PHE* 5.5 2.0 - - + -
362B ILE* 1.3 75.8 - - - +
364B HIS* 1.3 64.9 + - - +
365B ASN* 2.8 50.7 + - - +
368B GLY* 3.9 28.2 + - - +
369B ALA 3.6 9.4 - - - +
370B VAL* 4.8 6.2 - - + +
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Residues in contact with HIS 364 (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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79B ALA* 3.5 24.4 + - + -
80B ILE* 4.0 12.6 - - + +
85B ASN* 2.9 31.1 + - - -
231B SER 3.8 1.3 - - - -
232B ILE* 3.8 17.0 - - + -
363B ARG* 1.3 70.1 - - - +
365B ASN* 1.3 53.6 + - - +
366B PRO* 3.9 24.3 - - + +
367B THR* 2.8 41.7 + - + +
368B GLY* 2.7 36.2 + - - -
369B ALA* 2.9 14.3 + - + +
371B LEU* 4.1 20.5 - - + +
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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