Contacts of the strand formed by residues 365 - 370 (chain C) in PDB entry 1P4K
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 LEU 365 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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352C GLY* 3.6 24.2 - - - -
363C VAL* 3.7 17.5 - - + -
364C THR* 1.3 72.5 - - - +
366C ASP* 1.3 64.8 + - - +
379C VAL* 4.2 1.2 - - - +
380C ALA* 3.6 1.9 - - - -
381C CYS 3.0 6.2 + - - -
382C MET* 2.8 42.0 + - + +
385C ILE 3.3 26.5 - - - +
386C LYS 4.2 0.9 - - - +
388C PRO* 3.5 30.1 - - + -
423C LEU* 3.8 15.3 - - + -
470C THR 3.5 5.6 - - - +
471C SER* 3.4 33.0 - - - -
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Residues in contact with ASP 366 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2C GOL 4.4 4.3 + - - -
4C GOL 4.4 0.3 + - - -
364C THR 4.5 2.2 - - - +
365C LEU* 1.3 77.4 - - - +
367C ALA* 1.3 64.7 + - - +
379C VAL* 3.4 5.8 - - - +
380C ALA* 3.5 3.3 - - - +
381C CYS* 2.7 33.1 + - - +
388C PRO* 4.6 1.7 - - - +
469C THR* 3.4 1.4 + - - -
470C THR* 3.0 47.4 + - + +
472C GLY* 4.4 7.8 + - - -
476C LYS* 4.5 6.1 + - - -
480C ARG* 4.5 5.2 + - - +
481C VAL* 4.6 7.5 - - - +
482C GLY 4.3 12.0 + - - -
485C PRO* 3.7 28.0 - - + -
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Residues in contact with ALA 367 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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366C ASP* 1.3 79.0 - - - +
368C CYS* 1.3 62.9 + - - +
378C SER* 3.3 3.5 + - - -
379C VAL* 2.9 34.0 + - - +
388C PRO* 3.9 10.1 - - + +
389C ILE* 3.8 24.2 - - - +
392C ALA* 3.9 1.7 - - - +
468C CYS 3.0 15.0 - - - +
469C THR* 3.7 16.4 - - - +
484C SER 4.3 0.2 - - - -
485C PRO* 3.5 7.0 - - - +
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Residues in contact with CYS 368 (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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367C ALA* 1.3 76.0 - - - +
369C ILE* 1.3 61.1 + - - +
377C GLY 3.1 13.9 - - - +
378C SER* 3.7 3.1 - - - -
389C ILE* 3.1 7.8 - - - +
392C ALA* 4.2 1.1 - - - -
467C ALA* 3.5 0.5 - - - -
468C CYS* 3.0 30.0 + - - -
484C SER 3.2 21.9 + - - -
485C PRO 3.4 23.3 - - - +
486C ILE 4.2 4.3 - - - -
487C ILE* 3.8 23.1 - - + -
491C LEU* 3.9 19.7 - - - -
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Residues in contact with ILE 369 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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332C LEU* 3.5 30.3 - - + +
335C VAL* 4.8 0.4 - - + -
336C GLU* 4.4 16.2 - - + -
368C CYS* 1.3 75.8 - - - +
370C MET* 1.3 65.4 + - - +
376C ILE* 3.4 5.2 - - - +
377C GLY 2.9 35.5 + - - +
389C ILE* 3.8 22.9 - - + -
392C ALA 4.1 0.2 - - - -
393C ARG* 3.9 41.3 - - + +
396C MET* 4.1 10.3 - - - -
466C GLY 3.3 14.8 - - - +
467C ALA* 4.4 3.4 - - + -
487C ILE* 4.1 1.7 - - - +
491C LEU* 4.0 3.4 - - - -
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Residues in contact with MET 370 (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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211A ARG 5.4 2.0 - - - +
332C LEU* 4.5 3.7 - - - +
369C ILE* 1.3 76.5 - - - +
371C ASP* 1.3 65.6 + - - +
374C TYR* 5.0 7.9 - - - -
375C ASN 3.4 6.7 - - - +
376C ILE* 3.5 20.6 - - + -
396C MET* 4.9 0.2 - - - -
465C SER* 3.3 4.5 - - - -
466C GLY 3.0 32.8 + - - +
487C ILE* 3.2 33.4 - - + -
491C LEU* 3.3 12.3 - - + +
492C PHE* 3.2 35.4 - - - +
493C VAL* 3.4 36.9 - - + +
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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