Contacts of the strand formed by residues 438 - 445 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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434B GLU* 3.6 12.1 + - - +
435B GLY* 3.4 23.6 + - - +
436B SER 3.0 9.9 + - - -
437B PHE* 1.3 81.2 - - - +
439B ILE* 1.3 66.4 + - - +
455B LYS* 4.3 16.7 - - - +
456B ILE 3.1 11.9 - - - -
457B ILE* 3.9 17.7 - - - -
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Residues in contact with ILE 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431B PRO* 3.6 28.3 - - + -
433B GLY 3.4 13.7 - - - +
434B GLU* 4.0 16.2 - - + +
438B SER* 1.3 78.1 + - - +
440B CYS* 1.3 64.8 + - - +
441B ARG* 3.7 26.7 - - + +
454B VAL 3.6 0.9 - - - +
455B LYS* 3.4 4.6 - - - -
456B ILE* 2.8 61.2 + - + +
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Residues in contact with CYS 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400B ANP 4.1 26.0 - - + +
431B PRO* 3.4 7.6 - - - +
432B LEU* 2.7 49.1 + - + -
433B GLY* 2.9 23.5 + - - +
439B ILE* 1.3 74.8 - - - +
441B ARG* 1.3 60.7 + - - +
453B ALA* 4.1 6.1 - - - -
454B VAL 3.2 15.9 - - - -
455B LYS* 4.5 11.2 - - + -
498B MET* 5.8 2.7 - - - -
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Residues in contact with ARG 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425B LEU* 4.1 30.4 - - + +
426B ASP 5.1 4.5 - - - +
427B LEU* 3.9 31.3 + - - +
429B ASP 3.8 19.6 + - - +
430B LYS 5.9 0.2 - - - -
431B PRO* 4.1 17.5 - - + +
432B LEU* 3.7 10.1 - - - +
439B ILE* 3.7 34.4 - - + +
440B CYS* 1.3 79.0 - - - +
442B LYS* 1.3 67.3 + - - +
453B ALA* 3.2 2.8 - - - -
454B VAL* 2.7 43.4 + - + +
456B ILE* 4.6 9.0 - - + +
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Residues in contact with LYS 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425B LEU* 4.1 1.4 - - - +
426B ASP* 3.8 28.9 + - + +
429B ASP* 5.4 13.0 - - + +
430B LYS 5.9 0.4 + - - -
432B LEU* 3.9 19.1 - - + +
441B ARG* 1.3 79.9 - - - +
443B CYS* 1.3 63.0 + - - +
444B VAL* 4.2 17.2 - - + +
451B ALA* 3.8 24.7 - - - +
452B PHE 3.5 7.4 - - - +
453B ALA* 4.4 1.3 - - - +
500B LEU* 4.1 20.0 - - + +
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Residues in contact with CYS 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419B PHE* 4.2 8.5 - - + -
423B TYR* 3.8 22.2 - - + -
424B ASP 3.2 15.5 - - - +
425B LEU* 4.0 14.1 - - + -
426B ASP* 5.1 0.4 - - - +
442B LYS* 1.3 76.1 - - - +
444B VAL* 1.3 71.7 + - - +
451B ALA* 3.4 4.3 - - - +
452B PHE* 2.9 46.8 + - - +
453B ALA 4.5 0.2 - - - -
454B VAL* 4.0 24.5 - - + -
497B VAL* 4.6 1.3 - - - -
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Residues in contact with VAL 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423B TYR* 3.2 6.5 - - - -
424B ASP* 2.8 48.2 + - + +
426B ASP* 6.1 5.4 - - + -
442B LYS* 4.2 19.5 - - + +
443B CYS* 1.3 81.4 - - - +
445B HIS* 1.3 66.0 + - - +
446B LYS* 3.3 1.9 + - - -
449B ASN* 3.7 42.8 - - - +
450B GLN 3.4 5.8 - - - +
451B ALA* 4.9 2.2 - - + -
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Residues in contact with HIS 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422B HIS* 3.6 24.9 + - + +
423B TYR* 3.5 39.6 - + + -
444B VAL* 1.3 70.5 - - - +
446B LYS* 1.3 57.3 + - - +
447B LYS* 3.3 25.4 + - + +
448B SER* 2.6 35.5 + - - +
449B ASN* 2.6 34.8 + - - -
450B GLN 2.9 9.4 + - - +
452B PHE* 3.8 12.1 - + + -
485B HIS* 5.7 3.1 - + - -
486B GLU* 4.9 4.5 + - - -
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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