Contacts of the strand formed by residues 371 - 375 (chain A) in PDB entry 4K9P
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 ILE 371 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A ALA* 5.8 0.7 - - + -
370A ALA* 1.3 71.9 - - - +
372A TYR* 1.3 65.8 + - - +
373A LEU* 4.2 3.8 - - + -
393A GLY 3.3 27.6 - - - +
394A SER 3.6 4.5 - - - -
396A TYR* 3.8 24.0 - - + -
413A VAL* 4.0 24.0 - - + -
417A GLU* 4.1 13.0 - - + +
420A ARG* 3.5 47.6 - - + +
421A GLN 2.9 10.4 + - - +
422A VAL* 3.4 10.7 - - + +
423A ILE* 2.8 29.3 + - - +
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Residues in contact with TYR 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362A LEU* 3.7 25.4 + - + -
363A ASN* 4.5 4.4 + - - -
366A ALA* 3.2 24.3 - - - +
367A PRO 5.0 0.9 + - - -
370A ALA* 4.2 20.1 - - + +
371A ILE* 1.3 76.3 - - - +
373A LEU* 1.3 64.5 + - - +
383A MET* 3.8 17.5 - - + -
387A LEU* 3.8 36.1 - - + +
388A ASN 5.1 4.5 - - - -
389A MET* 4.1 18.8 - - + -
394A SER 2.7 18.6 + - - +
395A TYR* 3.2 10.9 + - + -
396A TYR 3.0 22.0 + - - -
423A ILE* 3.3 35.0 - - + -
425A VAL* 5.0 1.1 - - + -
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Residues in contact with LEU 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371A ILE* 4.2 11.4 - - + -
372A TYR* 1.3 80.5 - - - +
374A ASN* 1.3 61.1 + - - +
383A MET* 4.5 1.6 - - - -
396A TYR* 3.3 28.9 - - + +
405A PHE* 4.3 2.5 - - + -
406A ALA* 3.7 17.4 - - + +
409A ALA* 3.8 15.5 - - + +
410A ALA* 3.6 29.6 - - + +
413A VAL* 4.5 6.7 - - + -
422A VAL* 3.5 31.0 - - + -
423A ILE 3.2 7.5 + - - +
424A ALA* 3.5 12.0 - - + +
425A VAL* 2.8 30.3 + - - +
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Residues in contact with ASN 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373A LEU* 1.3 74.5 - - - +
375A GLU* 1.3 61.9 + - - +
376A SER* 2.9 29.9 + - - +
380A THR* 3.0 30.9 + - - +
383A MET* 3.6 26.5 - - - +
395A TYR* 2.9 32.6 + - + +
396A TYR 2.8 9.8 + - - +
397A PHE* 3.4 31.4 - - + -
398A CYS 4.4 2.1 + - - -
406A ALA* 4.3 4.2 - - - +
425A VAL 3.7 2.0 - - - +
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Residues in contact with GLU 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373A LEU 4.1 0.2 + - - -
374A ASN* 1.3 74.5 - - - +
376A SER* 1.3 59.0 + - - +
377A THR* 3.7 3.6 - - + -
397A PHE* 5.2 4.3 - - - -
398A CYS* 4.2 9.5 - - - +
402A GLY 4.1 1.0 - - - +
403A LEU* 3.5 18.2 - - + -
404A GLY* 2.6 29.5 + - - -
405A PHE* 3.0 15.6 + - - +
406A ALA* 3.0 37.9 + - + +
407A LEU 5.3 1.0 + - - -
425A VAL 2.9 10.9 + - - -
426A ILE* 4.2 8.9 - - + +
427A GLY 3.0 17.1 + - - -
430A SER* 3.3 38.2 + - - +
602A TPP 3.8 1.4 + - - -
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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