Contacts of the helix formed by residues 526 - 532 (chain C) in PDB entry 4KPE
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 MET 526 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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479C MET 6.0 0.2 - - - -
480C ILE* 5.6 7.9 - - - -
483C ILE* 3.9 20.6 - - + -
486C GLY 4.5 3.4 - - - +
487C VAL* 5.2 2.9 - - + -
488C GLY 5.1 0.9 - - - -
491C PHE* 3.8 31.6 - - + -
521C PHE* 4.2 13.0 - - + -
522C PHE* 3.0 46.1 + - + +
525C TYR* 1.3 89.5 - - + +
527C ARG* 1.3 69.2 + - - +
528C PRO* 3.2 8.7 - - - -
529C LEU* 2.7 56.8 + - + +
530C VAL 3.7 0.7 + - - -
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Residues in contact with ARG 527 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488C GLY 5.7 0.2 + - - -
522C PHE 3.3 7.1 + - - -
523C TYR* 3.9 20.8 + - + +
524C ARG 5.3 0.2 - - - -
525C TYR 4.0 0.4 - - - -
526C MET* 1.3 74.4 - - - +
528C PRO* 1.4 63.9 - - + +
530C VAL* 2.7 28.6 + - - +
531C GLU* 2.8 18.0 + - + +
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Residues in contact with PRO 528 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488C GLY 5.4 4.5 - - - +
491C PHE* 3.3 36.3 - - + +
493C ILE* 4.1 17.5 - - + -
526C MET* 3.2 3.6 - - - -
527C ARG* 1.4 94.3 - - + +
529C LEU* 1.3 51.6 + - - +
531C GLU* 3.7 4.3 - - + +
532C ALA* 2.8 41.6 + - - +
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Residues in contact with LEU 529 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483C ILE* 4.5 6.5 - - + -
491C PHE* 3.9 14.1 - - + -
493C ILE* 5.9 5.2 - - + -
496C ALA* 5.7 8.1 - - + -
498C TYR 5.6 2.0 - - - +
501C ILE* 4.0 23.6 - - + -
522C PHE* 5.4 0.7 - - + +
526C MET* 2.7 46.5 + - + +
527C ARG 2.9 0.8 + - - -
528C PRO* 1.3 78.3 - - - +
530C VAL* 1.3 61.5 + - - +
532C ALA* 3.5 1.9 + - + -
533C GLY 3.3 2.6 + - - -
534C HIS* 3.1 68.3 + - + +
535C VAL* 3.8 15.6 + - + -
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Residues in contact with VAL 530 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A LEU* 5.7 4.9 - - + -
522C PHE* 4.5 17.9 + - + +
523C TYR* 5.1 9.6 - - + -
526C MET 3.7 0.8 + - - -
527C ARG* 2.7 15.8 + - - +
529C LEU* 1.3 75.8 - - - +
531C GLU* 1.3 55.1 + - - +
533C GLY* 3.3 8.3 + - - -
535C VAL* 4.1 14.3 - - + +
606C VAL* 3.2 35.7 - - + +
607C THR* 4.2 6.2 - - - -
608C ILE* 4.2 8.2 + - + +
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Residues in contact with GLU 531 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527C ARG* 2.8 17.4 + - + +
528C PRO* 3.7 4.3 - - + +
530C VAL* 1.3 75.7 - - - +
532C ALA* 1.3 60.2 + - - +
533C GLY 3.3 0.4 - - - -
608C ILE* 4.9 17.0 - - + +
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Residues in contact with ALA 532 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493C ILE* 6.1 3.8 - - + -
528C PRO 2.8 20.0 + - - +
529C LEU* 3.9 6.5 - - + +
530C VAL 3.2 0.2 - - - -
531C GLU* 1.3 77.3 - - - +
533C GLY* 1.3 62.3 + - - +
534C HIS* 3.4 24.0 + - + +
605C ARG* 5.1 1.2 + - - -
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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