Contacts of the strand formed by residues 422 - 427 (chain D) 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 VAL 422 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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371D ILE* 3.4 13.2 - - + +
373D LEU* 3.5 30.5 - - + -
410D ALA* 3.5 23.8 - - + +
413D VAL* 3.7 13.7 - - + +
414D GLN* 2.9 52.3 + - + +
417D GLU 4.9 0.2 - - - +
420D ARG 3.8 4.3 - - - +
421D GLN* 1.3 88.4 + - - +
423D ILE* 1.3 64.5 + - - +
448D THR* 4.2 3.8 - - + +
449D ILE 3.0 16.1 + - - -
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Residues in contact with ILE 423 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362D LEU* 4.3 19.1 - - + -
366D ALA* 3.9 28.3 - - + -
367D PRO* 5.1 0.2 - - + -
370D ALA* 4.6 3.8 - - + -
371D ILE 2.7 9.2 + - - +
372D TYR* 3.3 28.8 - - + +
373D LEU 3.1 19.5 + - - +
421D GLN* 4.0 20.9 - - + +
422D VAL* 1.3 80.3 - - - +
424D ALA* 1.3 60.9 + - - +
425D VAL* 3.8 8.1 + - + +
449D ILE* 3.4 14.6 - - + +
451D VAL* 4.0 25.6 - - + -
507D LEU* 6.4 0.2 - - + -
511D LEU* 5.0 7.2 - - + -
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Residues in contact with ALA 424 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373D LEU* 3.7 13.5 - - + +
406D ALA 4.5 0.4 - - - +
410D ALA* 3.7 28.7 - - + -
422D VAL* 4.1 1.0 - - - +
423D ILE* 1.3 71.7 - - - +
425D VAL* 1.3 57.3 + - - +
426D ILE* 3.7 23.4 + - + +
449D ILE 2.8 14.0 + - - +
450D PHE* 3.5 6.4 - - + -
451D VAL* 2.6 34.5 + - - +
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Residues in contact with VAL 425 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358D VAL* 5.5 0.4 - - + -
359D PHE* 4.2 15.7 - - + -
362D LEU* 4.1 24.2 - - + -
372D TYR* 5.0 1.1 - - + -
373D LEU 2.9 10.6 + - - +
374D ASN* 3.8 0.3 - - - -
375D GLU 2.9 24.1 + - - -
376D SER* 3.5 11.8 + - - -
383D MET* 3.9 25.6 - - + -
423D ILE* 4.4 11.0 - - + +
424D ALA* 1.3 72.4 - - - +
426D ILE* 1.3 60.4 + - - +
451D VAL* 3.4 9.4 - - + +
453D MET* 3.6 34.1 - - + -
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Residues in contact with ILE 426 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375D GLU* 3.8 6.3 - - + +
376D SER* 4.5 0.2 - - - -
406D ALA* 4.0 17.7 - - + -
407D LEU* 3.7 38.6 - - + +
424D ALA* 3.7 28.0 + - + +
425D VAL* 1.3 77.7 - - - +
427D GLY* 1.3 70.8 + - - +
430D SER* 3.9 10.5 - - - -
431D ALA* 3.4 26.7 - - + +
450D PHE* 4.6 4.7 - - + -
451D VAL 2.8 10.2 + - - +
452D ILE* 3.1 17.2 - - + +
453D MET* 2.7 32.6 + - - -
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Residues in contact with GLY 427 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375D GLU 3.1 15.5 + - - -
376D SER* 3.9 5.0 - - - +
426D ILE* 1.3 76.9 - - - +
428D ASP* 1.3 67.3 + - - -
429D GLY 3.0 3.4 - - - -
430D SER 3.3 0.5 + - - -
431D ALA* 3.1 21.7 + - - +
452D ILE* 4.4 0.7 - - - -
453D MET* 3.6 13.5 - - - -
602D TPP 3.2 20.9 - - - -
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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