Contacts of the strand formed by residues 415 - 420 (chain B) in PDB entry 3K5N
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 415 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412B TYR* 4.7 4.5 - - + +
414B SER* 1.3 76.0 - - - +
416B LEU* 1.3 75.1 + - - +
542B ILE* 3.9 17.5 - - + -
550B PHE* 4.6 3.6 - - + -
551B VAL 2.8 24.9 - - - +
552B TRP* 4.1 5.6 - - + -
553B LEU* 4.0 1.1 - - - -
597B HIS* 3.4 1.0 - - - -
598B PHE* 2.6 42.1 + - + +
601B PHE* 2.6 59.2 - - + +
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Residues in contact with LEU 416 (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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415B VAL* 1.3 77.3 - - - +
417B VAL* 1.3 63.6 + - - +
418B LEU* 4.2 3.3 + - + -
549B THR 3.8 0.7 - - - +
550B PHE* 3.7 4.5 - - - -
551B VAL* 2.6 55.6 + - + +
553B LEU* 3.7 31.6 - - + -
562B ALA* 3.9 8.3 - - + +
566B GLY* 3.8 28.9 - - - -
569B LEU* 5.1 6.7 - - + -
594B TYR* 3.9 9.0 - - + -
596B THR 3.5 9.2 - - - +
597B HIS* 3.0 40.6 - - + -
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Residues in contact with VAL 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B LEU* 1.3 73.1 - - - +
418B LEU* 1.3 56.2 + - - +
419B ASP* 3.9 12.3 - - - +
548B SER* 4.5 4.3 - - - +
549B THR 4.1 3.6 - - - +
550B PHE* 3.1 43.1 - - + -
594B TYR* 4.2 1.9 - - - -
595B GLU* 2.7 56.2 + - + +
596B THR* 2.7 30.3 + - + +
598B PHE* 5.0 11.2 - - + -
601B PHE* 5.3 0.7 - - + -
617B TYR* 5.3 3.8 - - - +
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Residues in contact with LEU 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B LEU* 4.5 6.7 - - + +
417B VAL* 1.3 80.7 - - - +
419B ASP* 1.3 62.0 + - - +
530B THR* 6.3 0.9 - - + -
534B ILE* 4.8 17.7 - - + -
548B SER* 4.0 2.1 + - - -
549B THR* 2.9 54.1 + - + +
551B VAL* 4.9 10.3 - - + -
566B GLY* 5.7 0.9 - - - +
569B LEU* 4.9 18.8 - - + -
570B VAL* 5.0 3.4 - - + +
573B VAL* 6.3 0.4 - - + -
592B LEU* 4.2 23.2 - - + +
593B GLU 2.8 20.4 - - - +
594B TYR* 3.9 9.6 - - + -
595B GLU 3.8 0.4 - - - +
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Residues in contact with ASP 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417B VAL* 3.9 7.3 - - - +
418B LEU* 1.3 73.3 - - - +
420B TYR* 1.3 60.7 + - - +
547B ASP* 2.6 35.1 - - - +
548B SER* 3.4 18.1 + - - -
592B LEU* 4.2 2.2 - - - -
593B GLU* 2.4 51.3 + - + +
595B GLU* 3.5 31.8 - - - +
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Residues in contact with TYR 420 (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 ASP* 1.3 78.1 - - - +
421B LYS* 1.3 64.1 + - - +
422B SER 3.3 2.6 + - - -
423B LEU* 3.6 36.1 + - + +
526B ILE* 3.8 15.1 - - + +
527B MET* 4.5 10.5 - - + -
530B THR* 3.2 34.2 + - + +
547B ASP* 3.5 29.6 + - + +
573B VAL* 3.8 2.6 - - - +
574B ASN* 5.1 0.4 - - - -
577B TRP* 3.0 27.8 + + - -
590B LEU* 4.5 16.4 - - + -
591B GLU 4.0 5.2 - - - -
592B LEU* 2.9 43.1 - - + +
593B GLU* 4.2 1.1 - - - -
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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