Contacts of the strand formed by residues 438 - 445 (chain A) in PDB entry 3KN5
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 SER 438 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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434A GLU* 3.8 5.2 - - - +
435A GLY* 3.0 40.4 + - - +
436A SER 3.8 5.7 + - - -
437A PHE* 1.3 81.8 - - - +
439A ILE* 1.3 64.3 + - - +
455A LYS* 4.0 25.3 - - - -
456A ILE 3.2 11.7 - - - -
457A ILE* 4.1 13.2 - - - -
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Residues in contact with ILE 439 (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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431A PRO* 3.5 23.1 - - + -
433A GLY 3.4 14.8 - - - +
434A GLU* 3.3 25.4 - - + +
438A SER* 1.3 76.7 - - - +
440A CYS* 1.3 67.2 + - - +
441A ARG* 3.5 33.2 - - + +
454A VAL 3.7 0.3 - - - +
455A LYS* 3.4 5.2 - - - +
456A ILE* 2.9 45.9 + - + +
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Residues in contact with CYS 440 (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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400A ANP 4.5 20.2 - - + +
431A PRO* 3.5 6.6 - - - +
432A LEU* 2.9 44.3 + - - -
433A GLY* 2.9 24.8 + - - +
439A ILE* 1.3 74.3 - - - +
441A ARG* 1.3 62.8 + - - +
453A ALA* 4.2 10.3 - - - -
454A VAL 3.1 18.6 - - - -
455A LYS* 4.6 11.0 - - + -
498A MET* 6.1 2.5 - - - -
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Residues in contact with ARG 441 (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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425A LEU* 3.8 27.8 - - + +
426A ASP 5.4 3.3 + - - +
427A LEU* 3.8 31.3 + - - +
429A ASP 4.1 13.7 + - - -
431A PRO* 4.1 19.5 - - + +
432A LEU* 3.9 11.4 - - - +
439A ILE* 3.5 33.6 + - + +
440A CYS* 1.3 79.2 - - - +
442A LYS* 1.3 68.5 + - - +
453A ALA* 3.4 2.4 - - - -
454A VAL* 2.7 42.8 + - + +
456A ILE* 4.6 7.8 - - + +
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Residues in contact with LYS 442 (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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425A LEU* 4.1 1.2 - - - +
426A ASP* 3.8 32.4 + - + +
429A ASP* 6.5 1.1 - - + -
430A LYS 6.0 0.4 + - - -
432A LEU* 4.0 15.6 - - + +
441A ARG* 1.3 82.5 - - - +
443A CYS* 1.3 69.8 + - - +
444A VAL* 3.9 17.0 - - - +
451A ALA* 3.3 31.8 - - - +
452A PHE 3.5 11.4 - - - +
500A LEU* 4.3 17.3 - - + -
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Residues in contact with CYS 443 (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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419A PHE* 4.3 7.6 - - + -
423A TYR* 3.7 27.1 - - + -
424A ASP 3.4 16.4 - - - +
425A LEU* 4.2 13.9 - - + -
426A ASP* 3.9 2.2 - - - -
442A LYS* 1.3 78.0 - - - +
444A VAL* 1.3 65.1 + - - +
451A ALA* 3.5 4.2 - - - -
452A PHE* 2.9 49.1 + - - +
453A ALA 4.5 0.4 - - - -
454A VAL* 4.1 20.9 - - + -
497A VAL* 4.8 1.3 - - - -
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Residues in contact with VAL 444 (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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423A TYR* 3.3 6.3 - - - -
424A ASP* 3.0 38.9 + - + +
426A ASP* 3.4 22.7 - - - +
442A LYS* 3.9 18.6 - - - +
443A CYS* 1.3 79.9 - - - +
445A HIS* 1.3 73.8 + - - +
446A LYS* 3.4 1.6 + - - -
449A ASN* 3.5 30.1 - - - +
450A GLN 3.2 11.0 - - - +
451A ALA* 4.8 1.3 - - + -
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Residues in contact with HIS 445 (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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422A HIS* 3.7 22.3 + - - +
423A TYR* 3.5 43.7 + + + -
444A VAL* 1.3 73.3 - - - +
446A LYS* 1.3 56.4 + - - +
447A LYS* 3.3 27.7 + - + +
448A SER* 2.8 34.1 + - - +
449A ASN* 2.7 34.3 + - - -
450A GLN* 2.6 16.9 + - + +
452A PHE* 3.9 11.8 - + + -
486A GLU* 4.9 3.8 + - - -
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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