Contacts of the helix formed by residues 470 - 479 (chain A) in PDB entry 4K71
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 470 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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414A LYS 5.0 2.3 + - - -
415A VAL* 3.9 16.8 - - - +
417A GLN* 3.9 14.3 + - - +
464A HIS* 3.2 20.2 + - - -
468A PRO* 5.2 0.9 - - - +
469A VAL* 1.3 79.1 - - - +
471A ASP* 1.3 64.3 + - - +
472A ARG* 3.1 25.5 + - - +
473A VAL* 3.1 31.9 + - - +
474A THR* 3.2 2.6 + - - -
494A ASP* 5.0 0.7 + - - -
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Residues in contact with ASP 471 (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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469A VAL 4.3 0.7 - - - -
470A SER* 1.3 73.8 + - - +
472A ARG* 1.3 58.0 + - + +
474A THR* 3.4 10.7 + - - +
475A LYS* 3.0 29.1 + - - +
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Residues in contact with ARG 472 (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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414A LYS* 2.7 30.7 + - - +
470A SER* 3.1 10.0 + - - +
471A ASP* 1.3 77.4 - - + +
473A VAL* 1.3 60.4 + - + +
475A LYS* 3.3 8.7 + - - +
476A CYS* 2.9 33.2 + - - +
491A LEU* 4.0 36.7 - - + +
492A GLU* 2.7 35.8 + - - +
493A VAL 4.3 2.0 + - - -
494A ASP* 3.5 36.8 + - - +
496A THR* 6.0 0.4 - - - -
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Residues in contact with VAL 473 (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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415A VAL* 3.7 33.7 - - + -
418A MET* 5.0 3.4 - - + -
460A LEU* 4.4 7.4 - - + -
464A HIS* 3.6 30.7 - - + +
470A SER* 3.1 23.3 + - - +
472A ARG* 1.3 74.7 - - + +
474A THR* 1.3 53.0 + - - +
476A CYS* 3.2 6.5 + - - +
477A CYS* 2.6 57.4 + - - -
488A PHE* 4.2 17.0 - - + -
491A LEU* 5.4 2.9 - - + -
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Residues in contact with THR 474 (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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464A HIS* 3.2 22.8 + - - -
468A PRO* 4.5 7.4 - - - +
470A SER 3.2 5.2 + - - -
471A ASP* 3.4 15.5 + - - +
473A VAL* 1.3 72.9 - - - +
475A LYS* 1.3 56.5 + - - +
477A CYS* 3.3 5.7 + - - -
478A THR* 2.7 54.7 + - + +
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Residues in contact with LYS 475 (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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471A ASP 3.0 17.8 + - - +
472A ARG* 3.6 8.1 - - - +
474A THR* 1.3 75.9 - - - +
476A CYS* 1.3 64.0 + - - +
478A THR* 3.2 5.5 + - - -
479A GLU* 2.9 59.9 + - + +
487A CYS* 5.6 4.0 - - - -
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Residues in contact with CYS 476 (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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472A ARG 2.9 19.9 + - - +
473A VAL 3.7 2.2 - - - +
475A LYS* 1.3 76.6 - - - +
477A CYS* 1.3 60.9 + - - +
478A THR 3.6 0.2 + - - -
479A GLU* 4.4 3.7 + - - +
480A SER 4.4 3.3 + - - +
484A ARG* 3.5 21.5 - - - +
487A CYS* 2.1 61.9 - - + +
488A PHE* 3.6 24.2 - - + -
491A LEU* 4.1 18.8 - - - -
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Residues in contact with CYS 477 (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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206A PHE* 3.5 7.3 - - - -
461A CYS* 2.0 60.1 - - + +
464A HIS* 5.1 1.8 - - - +
473A VAL* 2.6 44.2 + - - +
474A THR* 3.7 7.9 - - - +
475A LYS 3.1 0.4 - - - -
476A CYS* 1.3 74.5 - - - +
478A THR* 1.3 61.8 + - + +
479A GLU 3.8 0.2 - - - -
480A SER 5.1 0.7 - - - +
484A ARG* 2.8 29.3 + - - +
488A PHE* 3.9 4.5 - - - -
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Residues in contact with THR 478 (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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206A PHE* 3.7 16.6 - - - -
465A GLU* 6.4 3.4 - - + -
474A THR* 2.7 38.4 + - + +
475A LYS* 3.5 5.5 + - - -
477A CYS* 1.3 82.9 - - + +
479A GLU* 1.3 65.4 + - - +
480A SER 3.5 1.7 + - - -
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Residues in contact with GLU 479 (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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206A PHE* 4.9 0.4 - - - -
351A LYS* 5.0 1.9 + - - -
475A LYS* 2.9 46.1 + - + +
476A CYS* 4.4 2.2 + - - +
477A CYS 3.8 0.4 - - - -
478A THR* 1.3 80.1 + - - +
480A SER* 1.3 64.4 + - - +
487A CYS* 4.5 13.3 - - - -
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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