Contacts of the strand formed by residues 368 - 375 (chain B) in PDB entry 4UQJ
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 PRO 368 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227B PHE* 4.2 11.9 - - + -
228B THR* 4.1 21.1 - - + -
232B LEU* 5.2 5.2 - - + -
236B GLN* 5.2 2.2 - - - +
361B MET* 3.9 17.9 - - + -
362B GLU 3.5 8.5 - - - +
363B LEU* 3.6 15.5 - - + -
366B ASN* 5.2 0.9 - - - +
367B GLY* 1.3 87.7 - - - +
369B ARG* 1.3 60.9 + - - +
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Residues in contact with ARG 369 (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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361B MET* 3.7 7.8 - - - +
362B GLU* 2.9 31.9 + - + +
364B LYS* 5.3 5.4 - - + -
366B ASN* 5.3 6.5 - - - +
367B GLY 4.2 4.3 - - - +
368B PRO* 1.3 76.9 - - - +
370B LYS* 1.3 66.3 + - - +
371B ILE* 3.4 8.5 + - + +
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Residues in contact with LYS 370 (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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251B ASP* 6.0 2.2 - - - +
359B ASN* 4.5 15.9 - - - +
360B ILE 3.6 7.9 - - - +
361B MET* 3.6 20.4 - - + +
369B ARG* 1.3 71.9 - - - +
371B ILE* 1.3 60.9 + - - +
372B GLY 3.4 6.5 - - - +
383B THR* 4.9 6.2 - - - +
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Residues in contact with ILE 371 (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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127B TYR* 4.1 23.6 - - + +
128B TYR* 4.0 3.4 - - - +
360B ILE* 3.0 36.3 + - + +
362B GLU* 3.3 48.5 - - + +
369B ARG* 3.5 15.9 - - + +
370B LYS* 1.3 74.0 - - - +
372B GLY* 1.3 57.8 + - - +
380B MET* 5.9 0.4 - - - -
382B LEU* 3.4 19.3 - - + +
383B THR* 3.1 25.9 + - - +
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Residues in contact with GLY 372 (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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359B ASN* 3.5 7.6 - - - +
360B ILE* 2.8 32.2 + - - +
370B LYS* 3.4 6.0 - - - +
371B ILE* 1.3 85.1 - - - +
373B TYR* 1.3 57.1 + - - +
380B MET* 6.0 0.9 - - - -
381B VAL 3.3 13.7 - - - -
382B LEU* 3.9 2.0 - - - -
383B THR* 3.8 13.4 - - - -
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Residues in contact with TYR 373 (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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357B THR* 3.7 31.2 - - + -
358B ILE 3.4 8.1 - - - +
359B ASN* 4.0 8.3 - - - +
360B ILE* 3.5 6.6 - - - +
372B GLY* 1.3 76.1 - - - +
374B TRP* 1.3 67.6 + - - +
375B SER* 4.0 21.5 - - - -
378B ASP* 4.3 9.7 + - - -
380B MET* 3.5 4.2 - - - +
381B VAL* 2.9 73.7 + - + +
383B THR* 4.5 11.4 - - - -
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Residues in contact with TRP 374 (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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116B ASP 4.7 2.2 - - - -
119B GLY* 3.6 25.1 + - - -
120B ALA* 3.7 28.7 - - + -
123B SER* 2.8 34.7 + - - -
356B TYR* 3.7 33.9 - + - +
357B THR* 3.7 5.0 - - - -
358B ILE* 2.8 35.7 + - + +
360B ILE* 3.6 10.8 - - + -
373B TYR* 1.3 78.1 - - - +
375B SER* 1.3 67.2 + - - +
376B GLU* 3.6 28.3 - - + -
379B LYS* 3.2 28.1 - - - +
380B MET* 3.6 6.5 - - + -
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Residues in contact with SER 375 (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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355B ASN* 5.3 4.5 + - - -
356B TYR 4.0 10.4 + - - -
357B THR* 5.2 2.0 - - - -
373B TYR* 4.0 15.8 - - - -
374B TRP* 1.3 81.1 - - - +
376B GLU* 1.3 62.0 + - - +
377B VAL* 2.9 22.7 + - - +
378B ASP* 3.7 23.6 + - - -
379B LYS* 2.8 33.7 + - - -
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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