Contacts of the strand formed by residues 371 - 375 (chain C) in PDB entry 4K9N
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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C ALA* 5.8 0.9 - - + -
369C ASN 4.2 0.4 - - - +
370C ALA* 1.3 72.1 - - - +
372C TYR* 1.3 64.6 + - - +
373C LEU* 4.4 4.0 - - + -
393C GLY 3.4 26.7 - - - +
394C SER 3.6 6.7 - - - -
396C TYR* 3.8 23.3 - - + -
413C VAL* 3.7 25.6 - - + -
417C GLU* 4.0 14.6 - - + -
420C ARG* 3.6 44.6 - - + +
421C GLN 2.9 6.5 + - - -
422C VAL* 3.3 12.8 - - + +
423C ILE* 2.8 28.4 + - - +
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Residues in contact with TYR 372 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362C LEU* 3.9 19.4 + - + -
363C ASN* 4.6 4.9 + - - -
366C ALA* 3.3 22.3 - - - +
367C PRO 4.9 0.9 + - - -
370C ALA* 4.0 20.7 - - + +
371C ILE* 1.3 75.0 - - - +
373C LEU* 1.3 65.9 + - - +
383C MET* 3.8 18.4 - - + -
387C LEU* 3.6 38.5 - - + +
388C ASN 5.2 5.2 + - - -
389C MET* 3.9 20.2 - - + -
394C SER 2.8 19.4 + - - +
395C TYR* 3.2 10.0 + - + -
396C TYR 3.0 21.5 + - - -
423C ILE* 3.2 39.0 - - + +
425C VAL* 5.0 0.7 - - + -
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Residues in contact with LEU 373 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371C ILE* 4.4 8.5 - - + -
372C TYR* 1.3 82.9 - - - +
374C ASN* 1.3 60.7 + - - +
375C GLU 4.1 0.2 - - - -
383C MET* 3.9 4.7 - - - +
395C TYR* 5.4 0.2 - - - -
396C TYR* 3.3 27.6 - - + +
405C PHE* 4.3 1.8 - - + -
406C ALA* 3.8 19.5 - - + +
409C ALA* 3.7 19.3 - - + +
410C ALA* 3.6 29.6 - - + +
413C VAL* 4.4 6.3 - - + -
422C VAL* 3.4 33.2 - - + -
423C ILE 3.0 7.8 + - - +
424C ALA* 4.2 7.2 - - + -
425C VAL* 2.8 30.0 + - - +
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Residues in contact with ASN 374 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373C LEU* 1.3 73.4 - - - +
375C GLU* 1.3 63.2 + - - +
376C SER* 2.8 34.2 + - - +
379C THR* 4.9 0.5 + - - -
380C THR* 2.8 34.3 + - - +
383C MET* 3.6 23.3 - - - +
395C TYR* 3.1 33.3 + - + +
396C TYR 2.8 8.8 + - - +
397C PHE* 3.4 32.6 - - + -
398C CYS 4.3 1.7 + - - -
406C ALA* 4.3 4.8 - - - +
425C VAL 3.7 2.0 - - - +
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Residues in contact with GLU 375 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373C LEU 4.1 0.4 - - - -
374C ASN* 1.3 74.3 - - - +
376C SER* 1.3 57.4 + - - +
377C THR* 3.7 6.5 - - + +
397C PHE* 5.2 0.9 - - - -
398C CYS* 4.2 9.1 - - - +
402C GLY 4.1 1.0 - - - +
403C LEU* 3.7 17.8 - - + -
404C GLY* 2.8 28.8 + - - -
405C PHE* 3.1 15.2 + - - +
406C ALA* 2.9 37.0 + - + +
407C LEU 5.2 1.0 + - - -
425C VAL 2.8 13.4 + - - +
426C ILE* 4.4 7.1 - - + +
427C GLY 3.0 15.8 + - - -
430C SER* 3.2 41.1 + - - +
602C TZD 3.8 0.9 + - - -
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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