Contacts of the helix formed by residues 505 - 512 (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 GLU 505 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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400B ANP 3.0 24.5 + - - +
504B GLY* 1.3 74.8 - - - -
506B LEU* 1.3 70.0 + - - +
507B PHE* 4.4 3.6 - - + +
508B GLU* 3.0 39.9 + - + +
509B ARG* 3.3 10.2 + - - +
547B PRO 4.6 4.3 - - - +
548B GLU* 2.8 35.2 - - - +
550B LEU 3.5 8.1 - - - +
551B LEU* 4.2 13.2 - - + -
552B PHE* 4.6 0.9 - - - -
712B HIS* 4.8 12.0 + - - -
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Residues in contact with LEU 506 (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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504B GLY 4.0 0.4 + - - -
505B GLU* 1.3 74.6 - - - +
507B PHE* 1.3 70.9 + - + +
509B ARG* 3.3 4.7 + - - +
510B ILE* 3.3 42.3 + - + +
524B ILE* 4.0 22.0 - - + -
528B LEU* 5.1 0.7 - - + -
547B PRO 4.2 5.9 + - - +
550B LEU* 2.9 50.1 + - + +
552B PHE* 3.9 14.1 - - + -
561B ILE* 3.8 19.3 - - + -
611B ILE* 4.1 17.5 - - + -
615B MET* 4.3 16.2 - - + -
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Residues in contact with PHE 507 (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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505B GLU* 3.2 2.7 - - + +
506B LEU* 1.3 86.7 - - + +
508B GLU* 1.3 62.7 + - + +
509B ARG 3.3 0.2 - - - -
510B ILE* 3.7 12.3 - - + +
511B LYS* 2.9 30.3 + - - +
547B PRO* 3.6 39.9 + - + -
611B ILE* 4.1 11.9 - - + -
614B THR* 3.8 34.1 - - + -
615B MET* 3.8 35.2 - - + -
704B LEU* 3.6 29.6 - - + +
711B VAL* 6.1 3.6 - - + -
715B VAL* 5.9 2.5 - - + -
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Residues in contact with GLU 508 (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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504B GLY* 4.9 4.5 - - - -
505B GLU* 3.0 42.2 + - + +
507B PHE* 1.3 77.5 - - + +
509B ARG* 1.3 65.4 + - - +
511B LYS* 3.3 32.4 + - - +
512B LYS* 3.1 41.9 + - - +
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Residues in contact with ARG 509 (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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503B GLY 3.4 26.6 + - - +
504B GLY* 5.2 0.4 - - - -
505B GLU 3.3 4.3 + - - +
506B LEU 3.7 8.7 - - - +
508B GLU* 1.3 78.1 - - - +
510B ILE* 1.3 65.3 + - + +
512B LYS* 3.1 24.4 + - - +
513B LYS* 3.5 23.7 + - - +
552B PHE* 3.4 33.9 - - + +
554B ASP* 3.4 24.2 + - - -
559B LEU* 3.3 44.2 - - - +
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Residues in contact with ILE 510 (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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506B LEU* 3.3 37.2 + - + +
507B PHE* 3.8 25.1 - - + +
508B GLU 3.3 0.4 - - - -
509B ARG* 1.3 74.9 - - + +
511B LYS* 1.3 67.2 + - - +
512B LYS 2.9 2.2 + - - -
513B LYS* 3.3 20.4 + - - +
516B PHE* 4.0 44.0 - - + -
524B ILE* 5.3 1.3 - - + -
552B PHE* 6.0 0.7 - - + -
615B MET* 4.1 9.9 - - + -
700B THR* 3.5 24.2 - - - +
701B PRO* 3.3 17.1 - - + +
704B LEU* 3.9 4.9 - - + -
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Residues in contact with LYS 511 (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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507B PHE 2.9 16.9 + - - +
508B GLU* 3.3 33.8 + - - +
510B ILE* 1.3 77.3 - - - +
512B LYS* 1.3 70.2 + - + +
513B LYS 3.3 5.9 + - - +
701B PRO* 3.8 20.0 - - - +
704B LEU* 3.6 32.7 + - + +
705B GLY* 3.9 16.7 - - - +
708B GLY* 5.5 6.8 - - - -
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Residues in contact with LYS 512 (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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508B GLU* 3.1 41.2 + - - +
509B ARG* 3.1 10.8 + - - +
510B ILE 2.9 1.6 - - - -
511B LYS* 1.3 89.3 - - + +
513B LYS* 1.3 59.2 + - - +
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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