Contacts of the helix formed by residues 493 - 504 (chain F) in PDB entry 4P0S
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 493 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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487F GLN* 3.7 4.7 - - - +
491F ARG 4.1 0.4 + - - -
492F VAL* 1.3 74.9 - - - +
494F LEU* 1.3 59.8 + - - +
495F GLU* 3.8 9.7 + - - +
496F MET* 3.5 29.7 + - - +
497F ALA* 2.9 30.8 + - - +
51T C 3.1 32.5 + - - -
52T A 3.1 12.0 + - - -
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Residues in contact with LEU 494 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483F ARG* 3.2 38.4 - - - +
487F GLN* 3.4 18.0 - - - +
493F SER* 1.3 72.4 - - - +
495F GLU* 1.3 69.4 + - + +
497F ALA* 3.7 2.4 - - - +
498F SER* 2.8 41.1 + - - +
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Residues in contact with GLU 495 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493F SER* 3.3 8.7 + - - +
494F LEU* 1.3 84.8 - - + +
496F MET* 1.3 66.0 + - - +
498F SER* 3.8 4.5 + - - -
499F ALA* 3.5 21.1 + - - +
532F VAL* 3.8 22.6 - - + +
533F ARG* 3.5 45.8 + - + +
534F ARG* 4.7 6.5 + - - -
51T C 4.2 19.8 + - - +
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Residues in contact with MET 496 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486F ILE* 5.4 0.2 - - - -
491F ARG 4.6 6.5 - - - +
492F VAL* 4.9 4.0 - - + -
493F SER* 3.5 18.0 + - - +
494F LEU 3.4 0.2 - - - -
495F GLU* 1.3 78.3 - - - +
497F ALA* 1.3 62.2 + - - +
499F ALA* 3.4 11.8 + - - +
500F VAL* 3.4 18.7 + - - +
532F VAL* 4.3 8.7 - - + -
541F THR* 4.1 9.9 - - + -
544F ARG 4.4 12.6 - - - +
545F ILE* 3.9 27.5 - - + +
549F LEU* 4.1 21.8 - - + -
50T G 4.0 2.0 - - - +
51T C 3.2 55.2 - - - +
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Residues in contact with ALA 497 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483F ARG* 3.9 18.8 - - + +
486F ILE* 3.9 20.2 - - + +
487F GLN* 3.7 22.7 - - + -
492F VAL* 4.0 1.7 - - + +
493F SER 2.9 20.8 + - - +
494F LEU* 3.8 4.3 - - - +
496F MET* 1.3 77.4 - - - +
498F SER* 1.3 61.7 + - - +
500F VAL* 3.7 2.3 + - - +
501F VAL* 3.4 26.9 + - - +
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Residues in contact with SER 498 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483F ARG* 3.7 23.2 - - - +
494F LEU* 2.8 33.7 + - - +
495F GLU* 4.1 5.4 - - - -
496F MET 3.4 0.2 - - - -
497F ALA* 1.3 72.0 - - - +
499F ALA* 1.3 52.5 + - - +
501F VAL* 3.3 5.3 + - - +
502F ASN* 2.9 46.2 + - - +
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Residues in contact with ALA 499 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495F GLU 3.5 11.7 + - - +
496F MET* 3.4 11.4 + - - +
498F SER* 1.3 76.3 - - - +
500F VAL* 1.3 66.5 + - - +
502F ASN* 3.7 9.6 + - - +
503F ALA* 3.7 14.6 + - - +
530F ILE* 3.7 30.9 - - + +
531F GLN 3.8 16.4 - - - +
532F VAL* 4.7 6.5 - - + -
545F ILE* 4.7 2.2 - - + -
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Residues in contact with VAL 500 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482F TRP* 6.0 2.9 - - + -
486F ILE* 4.5 26.5 - - + -
496F MET 3.4 14.1 + - - +
497F ALA 4.1 5.8 - - - +
498F SER 3.4 0.2 - - - -
499F ALA* 1.3 77.8 - - - +
501F VAL* 1.3 61.9 + - - +
503F ALA* 3.5 5.5 + - - +
504F TYR* 3.4 22.2 + - + +
510F LEU* 5.6 6.7 - - + -
527F LEU* 3.7 29.2 - - + -
530F ILE* 4.3 7.0 - - + -
545F ILE* 4.2 18.2 - - + -
549F LEU* 6.1 0.4 - - + -
553F ILE* 4.0 23.8 - - + -
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Residues in contact with VAL 501 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479F ALA 5.0 4.0 - - - +
482F TRP* 3.8 25.6 - - + +
483F ARG* 3.6 36.3 - - + +
486F ILE* 3.7 16.8 - - + -
497F ALA 3.4 13.7 - - - +
498F SER* 3.3 10.3 + - - +
500F VAL* 1.3 73.5 - - + +
502F ASN* 1.3 68.2 + - - +
503F ALA 3.2 2.5 - - - -
504F TYR 3.1 25.1 - - - -
505F PRO* 3.2 8.3 - - + +
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Residues in contact with ASN 502 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498F SER* 2.9 33.7 + - - +
499F ALA* 4.1 9.4 - - - +
500F VAL 3.5 0.2 - - - -
501F VAL* 1.3 75.1 - - - +
503F ALA* 1.3 59.8 + - - +
504F TYR 3.7 0.2 + - - -
505F PRO* 4.1 9.4 - - - +
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Residues in contact with ALA 503 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499F ALA 3.7 8.2 + - - +
500F VAL 3.5 10.3 + - - +
502F ASN* 1.3 80.7 - - - +
504F TYR* 1.3 84.9 + - + +
505F PRO* 3.7 4.9 - - - +
509F LEU* 5.8 0.3 - - - +
530F ILE* 4.3 13.5 - - + -
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Residues in contact with TYR 504 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482F TRP* 2.8 22.7 + - + -
500F VAL* 3.4 12.3 + - + +
501F VAL* 3.1 6.8 + - - +
503F ALA* 1.3 99.0 - - + +
505F PRO* 1.4 51.5 - - - -
506F SER 2.7 20.3 + - - +
509F LEU* 3.8 24.5 - - + -
510F LEU* 3.9 26.7 - - + +
513F ALA* 3.6 21.2 - - + +
526F LEU* 3.2 30.6 + - + +
527F LEU* 3.7 25.6 - - + -
530F ILE* 5.1 0.7 - - + -
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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