Contacts of the strand formed by residues 450 - 458 (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 GLN 450 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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444B VAL* 3.4 2.7 - - - -
445B HIS 2.9 24.9 + - - -
448B SER* 3.1 23.7 + - - +
449B ASN* 1.3 79.5 - - - +
451B ALA* 1.3 66.0 + - - +
452B PHE* 3.4 36.9 - - + -
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Residues in contact with ALA 451 (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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442B LYS* 3.8 33.7 - - - +
443B CYS 3.4 5.4 - - - +
444B VAL* 4.5 2.9 - - + +
449B ASN 4.1 1.6 + - - -
450B GLN* 1.3 82.6 + - - +
452B PHE* 1.3 66.1 + - - +
500B LEU* 3.8 25.0 + - + +
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Residues in contact with PHE 452 (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* 3.7 17.9 - + - -
442B LYS* 3.5 5.2 - - - +
443B CYS* 2.9 34.3 + - - +
445B HIS* 3.8 17.7 - + + -
448B SER* 4.7 0.9 - - - -
450B GLN* 3.4 53.2 - - + -
451B ALA* 1.3 74.8 - - - +
453B ALA* 1.3 60.0 + - - +
485B HIS* 3.8 34.3 - + + -
497B VAL* 3.6 22.0 - - + -
498B MET 3.3 20.0 - - - +
499B GLU* 4.4 7.4 - - + -
500B LEU* 3.8 12.6 - - - +
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Residues in contact with ALA 453 (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 3.8 29.4 - - + +
432B LEU* 3.5 28.0 - - + -
440B CYS* 4.1 6.3 - - - -
441B ARG 3.2 4.7 - - - -
442B LYS* 4.4 0.4 - - - +
443B CYS* 4.3 1.6 - - - -
452B PHE* 1.3 76.3 - - - +
454B VAL* 1.3 61.1 + - - +
497B VAL* 3.5 3.1 - - - -
498B MET* 2.7 36.9 + - + +
500B LEU* 4.0 4.7 - - + +
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Residues in contact with VAL 454 (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* 4.0 18.2 - - + -
425B LEU* 3.9 26.2 - - + -
439B ILE 3.6 1.4 - - - +
440B CYS* 3.2 6.0 - - - -
441B ARG* 2.7 44.9 + - + +
443B CYS* 4.0 13.2 - - - -
453B ALA* 1.3 76.1 - - - +
455B LYS* 1.3 66.7 + - - +
456B ILE* 3.9 13.8 + - + +
495B PHE* 3.8 28.0 - - + -
496B LEU 3.3 12.3 - - - +
497B VAL* 4.3 2.2 - - - +
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Residues in contact with LYS 455 (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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438B SER* 4.3 18.2 - - - -
439B ILE 3.4 11.9 - - - +
440B CYS* 4.3 12.6 - - + +
454B VAL* 1.3 71.2 - - - +
456B ILE* 1.3 61.0 + - - +
457B ILE* 3.8 23.2 + - + +
468B GLU* 2.7 34.9 + - - +
494B THR 3.3 4.7 - - - +
495B PHE* 3.5 0.9 - - - -
496B LEU* 2.9 46.3 + - + +
498B MET* 5.0 8.2 - - + +
565B ASP* 3.5 26.5 + - - +
567B GLY* 4.6 3.0 - - - +
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Residues in contact with ILE 456 (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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420B TYR* 5.4 0.9 - - - +
425B LEU* 4.3 22.9 - - + -
437B PHE 4.0 0.2 - - - +
438B SER* 3.1 4.2 - - - -
439B ILE* 2.8 56.6 + - + +
441B ARG* 4.6 9.6 - - + +
454B VAL* 4.1 22.2 - - + +
455B LYS* 1.3 73.7 - - - +
457B ILE* 1.3 65.6 + - - +
493B HIS* 3.6 41.1 - - + +
494B THR 3.4 3.1 - - - -
495B PHE* 3.8 24.7 - - + -
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Residues in contact with ILE 457 (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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437B PHE 3.4 10.8 - - - +
438B SER* 3.9 14.8 - - - -
455B LYS* 3.8 31.2 - - + +
456B ILE* 1.3 81.8 - - - +
458B SER* 1.3 71.7 + - - +
461B MET* 3.8 13.7 - - + -
462B GLU* 5.3 0.2 - - - +
465B THR* 3.6 31.0 - - + -
468B GLU* 4.3 8.5 - - - +
493B HIS* 3.3 5.3 - - - -
494B THR* 2.8 39.3 + - - +
496B LEU* 3.9 29.8 - - + -
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Residues in contact with SER 458 (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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437B PHE* 2.9 35.1 + - - -
457B ILE* 1.3 75.4 - - - +
459B LYS* 1.3 58.7 + - - +
460B ARG* 2.8 36.4 + - - +
461B MET* 2.9 19.6 + - - +
462B GLU* 4.1 2.8 + - - +
492B LEU 3.8 1.2 + - - -
493B HIS* 3.7 19.8 + - - -
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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