Contacts of the helix formed by residues 492 - 505 (chain T) in PDB entry 3FKS
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 492 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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488T LYS* 5.3 10.9 - - - +
490T GLU 4.1 1.6 + - - -
491T LEU* 1.3 73.0 - - - +
493T LYS* 1.3 55.6 + - - +
494T GLU* 3.9 10.4 + - - +
495T LEU* 3.1 24.0 + - - +
496T LEU* 2.8 38.0 + - - +
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Residues in contact with LYS 493 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492T SER* 1.3 73.2 - - - +
494T GLU* 1.3 62.7 + - - +
496T LEU* 3.5 25.6 + - + +
497T ALA* 3.6 15.1 + - - +
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Residues in contact with GLU 494 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492T SER* 3.1 10.5 - - - +
493T LYS* 1.3 80.2 - - - +
495T LEU* 1.3 59.1 + - + +
497T ALA* 4.8 1.9 - - - +
498T SER* 3.9 17.3 + - - -
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Residues in contact with LEU 495 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481T LEU* 3.5 30.3 - - + -
484T GLU* 3.3 32.8 - - + +
485T ILE* 4.0 29.4 - - + +
488T LYS* 6.0 4.5 - - + -
490T GLU 4.7 7.9 - - - +
491T LEU* 4.1 18.9 - - + +
492T SER* 3.1 20.1 + - - +
494T GLU* 1.3 78.1 - - + +
496T LEU* 1.3 64.1 + - - +
497T ALA 3.4 0.2 - - - -
498T SER* 3.9 5.8 - - - -
499T LEU* 3.3 20.8 + - - +
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Residues in contact with LEU 496 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387T GLN* 5.2 9.6 - - + +
388T VAL* 6.2 0.2 - - + -
448T TYR* 4.8 16.6 + - + +
491T LEU* 4.9 20.4 - - + +
492T SER 2.8 18.1 + - - +
493T LYS* 4.0 22.2 - - + +
494T GLU 3.4 0.2 - - - -
495T LEU* 1.3 76.6 - - - +
497T ALA* 1.3 64.8 + - - +
499T LEU* 3.2 32.9 - - + +
500T LYS* 3.9 9.3 + - + +
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Residues in contact with ALA 497 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493T LYS 3.6 11.3 + - - +
494T GLU 4.8 2.7 - - - +
495T LEU 3.4 0.2 - - - -
496T LEU* 1.3 74.2 - - - +
498T SER* 1.3 62.9 + - - +
499T LEU 3.0 6.6 + - - -
500T LYS* 3.3 25.1 + - + +
501T SER* 4.0 4.3 + - - -
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Residues in contact with SER 498 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478T HIS* 5.9 1.0 + - - -
481T LEU* 4.3 17.2 - - - +
494T GLU 3.9 15.7 + - - -
495T LEU* 3.6 15.3 + - - -
496T LEU 3.3 0.6 - - - -
497T ALA* 1.3 77.4 - - - +
499T LEU* 1.3 58.3 + - - +
501T SER* 2.9 25.9 + - - -
502T ALA* 3.9 6.6 + - - +
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Residues in contact with LEU 499 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388T VAL* 5.0 7.2 - - + -
444T VAL 5.2 1.8 - - - +
445T PRO* 4.8 20.0 - - + -
448T TYR* 3.5 46.0 - - + -
470T PHE* 6.5 0.7 - - + -
481T LEU* 5.4 9.6 - - + -
491T LEU* 5.6 7.9 - - + -
495T LEU 3.3 10.8 + - - +
496T LEU* 3.2 21.5 + - + +
497T ALA 3.0 0.8 - - - -
498T SER* 1.3 77.9 - - - +
500T LYS* 1.3 65.9 + - - +
501T SER 3.1 1.1 + - - -
502T ALA* 3.2 16.8 + - + +
503T THR* 3.3 25.1 + - + +
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Residues in contact with LYS 500 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448T TYR* 3.8 28.7 - - + +
454T HIS* 5.1 9.4 + - - +
496T LEU 4.1 8.5 - - - +
497T ALA* 3.3 16.5 + - + +
499T LEU* 1.3 76.2 - - - +
501T SER* 1.3 60.2 + - - +
503T THR* 2.6 24.4 + - - +
504T GLU* 3.2 29.3 + - - +
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Residues in contact with SER 501 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478T HIS* 5.9 0.5 + - - -
497T ALA 4.0 3.6 + - - -
498T SER* 2.9 28.6 + - - -
499T LEU 3.1 0.2 - - - -
500T LYS* 1.3 79.9 - - - +
502T ALA* 1.3 61.8 + - - +
503T THR 3.1 1.1 + - - -
504T GLU* 3.5 5.8 + - - +
505T SER* 3.4 21.5 + - - -
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Residues in contact with ALA 502 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470T PHE* 3.5 31.1 - - + -
473T TYR* 5.5 2.0 - - + -
478T HIS* 4.5 19.3 - - + +
481T LEU* 4.3 19.3 - - + -
498T SER 4.3 7.2 - - - +
499T LEU* 3.2 11.2 + - + +
501T SER* 1.3 80.7 + - - +
503T THR* 1.3 58.8 + - + +
505T SER* 3.2 18.1 + - - -
506T PHE* 3.7 2.4 - - - -
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Residues in contact with THR 503 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445T PRO* 5.6 8.7 - - + +
448T TYR* 4.8 10.6 - - + -
449T ALA* 5.8 6.1 - - + -
454T HIS* 4.4 18.9 + - + +
455T LEU* 6.1 0.9 - - - +
466T PHE* 5.7 2.9 - - - -
470T PHE* 5.3 6.5 - - + -
499T LEU* 3.3 30.7 - - + +
500T LYS* 2.6 24.4 + - - -
502T ALA* 1.3 81.5 - - + +
504T GLU* 1.3 71.3 + - - +
505T SER 3.3 0.7 - - - -
506T PHE* 3.5 20.9 + - - +
507T VAL* 4.7 0.7 - - - +
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Residues in contact with GLU 504 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E LYS* 4.7 5.4 - - - +
454T HIS* 3.7 26.0 + - - -
500T LYS* 3.2 26.9 + - - +
501T SER* 3.5 5.4 + - - +
503T THR* 1.3 80.6 + - - +
505T SER* 1.3 65.7 + - - +
506T PHE 2.8 4.6 + - - -
507T VAL* 3.1 29.6 - - - +
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Residues in contact with SER 505 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E LYS* 4.8 11.7 - - - +
41E THR 5.2 3.5 - - - +
473T TYR* 5.0 6.9 + - - -
501T SER 3.4 10.8 + - - -
502T ALA* 3.2 11.3 + - - -
504T GLU* 1.3 78.6 - - - +
506T PHE* 1.3 81.5 + - - +
507T VAL 3.6 3.5 + - - -
509T THR* 3.7 15.6 + - - +
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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