Contacts of the helix formed by residues 505 - 513 (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 GLU 505 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400A ANP 3.3 24.8 + - - +
504A GLY* 1.3 74.8 - - - +
506A LEU* 1.3 66.7 + - - +
507A PHE* 3.4 4.0 - - + +
508A GLU* 3.3 30.4 + - + +
509A ARG* 3.0 22.0 + - - +
547A PRO 4.7 2.1 - - - +
548A GLU* 3.7 30.9 + - - +
550A LEU 3.5 4.3 - - - +
551A LEU* 3.6 20.6 - - + -
552A PHE* 4.4 0.4 - - - -
712A HIS* 5.4 4.2 + - - -
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Residues in contact with LEU 506 (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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505A GLU* 1.3 74.4 - - - +
507A PHE* 1.3 83.5 + - + +
509A ARG* 3.2 4.7 + - - +
510A ILE* 3.0 41.7 + - + +
524A ILE* 4.3 15.7 - - + -
528A LEU* 5.3 0.2 - - + -
547A PRO* 4.4 6.8 + - + +
550A LEU* 2.9 45.0 + - + +
552A PHE* 3.7 30.3 - - + -
561A ILE* 3.9 12.6 - - + -
611A ILE* 4.4 9.0 - - + -
615A MET* 4.2 12.1 - - + -
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Residues in contact with PHE 507 (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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505A GLU* 4.5 2.8 - - + +
506A LEU* 1.3 92.4 - - + +
508A GLU* 1.3 62.0 + - + +
510A ILE* 3.7 11.6 - - + +
511A LYS* 2.9 33.8 + - - +
547A PRO* 3.5 38.2 + - + +
611A ILE* 4.1 8.1 - - + -
614A THR* 3.5 39.9 - - + -
615A MET* 3.7 32.5 - - + -
704A LEU* 4.1 21.1 - - + +
711A VAL* 4.9 12.3 - - + -
715A VAL* 5.2 2.7 - - + -
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Residues in contact with GLU 508 (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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504A GLY* 4.9 3.4 - - - -
505A GLU* 3.3 39.6 + - + +
507A PHE* 1.3 76.5 - - + +
509A ARG* 1.3 62.0 + - - +
511A LYS* 3.2 48.5 + - - +
512A LYS* 3.3 15.6 + - - +
514B LYS* 4.4 18.0 - - - +
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Residues in contact with ARG 509 (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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503A GLY* 2.6 38.0 + - - +
505A GLU 3.0 9.8 + - - +
506A LEU 3.2 11.0 - - - +
508A GLU* 1.3 75.1 - - - +
510A ILE* 1.3 66.2 + - + +
512A LYS* 3.0 29.3 + - + +
513A LYS* 3.4 28.6 + - - +
552A PHE* 3.7 31.3 - - + +
554A ASP* 4.9 2.8 - - - +
559A LEU* 3.0 43.2 - - - +
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Residues in contact with ILE 510 (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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506A LEU* 3.0 27.9 + - + +
507A PHE* 3.4 19.7 + - + +
509A ARG* 1.3 77.1 - - + +
511A LYS* 1.3 62.6 + - - +
512A LYS 3.2 0.7 + - - -
513A LYS* 3.2 17.6 - - + +
516A PHE* 3.6 50.5 - - + -
524A ILE* 5.2 0.7 - - + -
615A MET* 3.9 22.9 - - + -
700A THR* 3.6 22.0 - - - +
701A PRO* 3.2 27.6 - - + +
704A LEU* 4.5 3.4 - - + -
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Residues in contact with LYS 511 (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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507A PHE* 2.9 14.3 + - - +
508A GLU* 3.2 39.0 + - - +
510A ILE* 1.3 77.1 - - - +
512A LYS* 1.3 60.3 + - - +
513A LYS 3.6 1.0 + - - +
701A PRO* 4.0 13.8 - - - +
704A LEU* 3.3 34.5 + - + +
705A GLY* 3.6 20.4 - - - +
708A GLY* 3.7 26.3 + - - +
515B HIS* 4.5 23.1 - - + +
695B SER 5.1 0.2 - - - +
696B ASN* 3.6 9.2 - - - +
697B PRO* 3.4 18.5 - - + +
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Residues in contact with LYS 512 (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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508A GLU 3.3 15.2 + - - +
509A ARG* 3.0 19.8 + - + +
511A LYS* 1.3 78.6 - - - +
513A LYS* 1.3 61.1 + - - +
514A LYS 3.7 0.2 + - - -
514B LYS 6.0 0.2 + - - -
655B ASN* 5.3 1.6 - - - +
696B ASN* 3.5 15.7 + - - -
697B PRO* 3.9 43.3 + - + +
698B LEU 4.4 7.5 + - - -
699B MET* 5.3 7.2 - - - +
702B ASP* 4.7 10.7 + - - -
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Residues in contact with LYS 513 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509A ARG* 3.4 27.9 + - - +
510A ILE* 3.2 24.3 + - - +
512A LYS* 1.3 80.6 - - - +
514A LYS* 1.3 61.3 + - - +
515A HIS 3.8 17.3 - - - +
516A PHE* 3.5 40.1 - - + -
520A GLU* 4.5 11.5 + - - +
524A ILE* 5.2 6.5 - - - +
552A PHE* 5.9 3.6 - - - -
701A PRO* 3.1 28.6 - - - +
696B ASN* 3.8 3.9 - - - +
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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