Contacts of the helix formed by residues 485 - 499 (chain T) in PDB entry 6FF7
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 GLN 485 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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481T PHE* 5.2 9.6 - - + -
482T PRO* 3.3 13.1 + - + +
483T GLU 3.0 1.8 + - - -
484T SER* 1.3 77.0 - - - +
486T THR* 1.3 63.8 + - - +
487T LYS 3.3 2.0 - - - -
488T GLU* 3.0 13.4 + - + +
489T LEU* 2.9 22.7 + - + +
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Residues in contact with THR 486 (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 PHE* 6.5 0.4 - - - -
482T PRO 4.2 2.1 + - - -
483T GLU* 3.0 21.4 + - - -
484T SER 3.3 0.2 - - - -
485T GLN* 1.3 77.0 - - - +
487T LYS* 1.3 63.7 + - - +
489T LEU* 3.2 7.8 + - - +
490T CYS* 3.0 26.5 + - - +
520T GLU* 5.4 11.7 - - - -
521T TYR* 6.1 2.5 - - - -
524T SER* 4.7 10.0 - - - -
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Residues in contact with LYS 487 (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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484T SER 4.5 6.1 + - - +
485T GLN 3.3 0.4 - - - -
486T THR* 1.3 77.1 - - - +
488T GLU* 1.3 57.8 + - - +
490T CYS* 3.6 2.3 + - - +
491T ASN* 3.0 28.1 + - - +
524T SER* 4.3 18.2 - - - -
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Residues in contact with GLU 488 (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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484T SER 5.3 0.2 + - - -
485T GLN* 3.0 16.3 + - + +
487T LYS* 1.3 79.2 - - - +
489T LEU* 1.3 66.6 + - - +
491T ASN* 3.2 6.8 + - - +
492T MET* 2.9 23.8 + - - +
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Residues in contact with LEU 489 (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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459T ILE* 6.1 5.6 - - + -
481T PHE* 6.0 5.4 - - + -
485T GLN* 2.9 12.9 + - + +
486T THR* 3.2 10.7 + - - +
488T GLU* 1.3 74.9 - - - +
490T CYS* 1.3 55.7 + - - +
492T MET* 2.6 28.3 + - - +
493T ILE* 2.9 13.8 + - - +
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Residues in contact with CYS 490 (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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486T THR 3.0 15.8 + - - +
487T LYS 4.1 3.1 - - - +
489T LEU* 1.3 75.4 - - - +
491T ASN* 1.3 57.0 + - - +
493T ILE* 3.4 8.6 + - - +
494T LEU* 3.0 26.9 + - - +
521T TYR* 5.2 4.7 - - + +
524T SER* 4.9 5.8 - - - -
525T PHE* 4.5 28.0 - - + +
528T ILE* 5.5 5.5 - - + +
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Residues in contact with ASN 491 (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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487T LYS 3.0 19.9 + - - +
488T GLU* 3.5 8.5 - - - +
489T LEU 3.0 1.0 - - - -
490T CYS* 1.3 77.8 - - - +
492T MET* 1.3 58.4 + - - +
494T LEU* 3.3 8.9 - - - +
495T ASP* 3.0 24.9 + - - +
528T ILE* 5.4 9.4 - - + +
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Residues in contact with MET 492 (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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456T ARG* 5.2 20.4 - - + +
459T ILE* 5.3 15.9 - - + +
488T GLU 2.9 10.8 + - - +
489T LEU* 2.6 17.5 + - - +
491T ASN* 1.3 71.4 - - - +
493T ILE* 1.3 59.7 + - - +
495T ASP* 3.7 5.9 - - - +
496T CYS* 2.9 33.4 + - - +
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Residues in contact with ILE 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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459T ILE 6.1 0.7 - - - -
489T LEU 2.9 10.3 + - - +
490T CYS* 3.7 11.4 - - - +
492T MET* 1.3 77.0 - - - +
494T LEU* 1.3 63.8 + - - +
496T CYS* 4.4 4.2 - - - +
497T CYS* 3.4 20.3 + - - +
507T PHE* 5.3 2.4 - - - +
510T LEU* 6.6 0.7 - - + -
511T ALA* 5.6 13.2 - - + +
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Residues in contact with LEU 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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490T CYS 3.0 14.9 + - - +
491T ASN* 3.3 13.0 - - - +
492T MET 3.1 0.2 - - - -
493T ILE* 1.3 78.9 - - - +
495T ASP* 1.3 64.9 + - - +
497T CYS* 3.3 6.2 + - - +
498T ALA* 3.0 19.8 + - - +
528T ILE* 5.7 7.2 - - + -
547T VAL* 6.0 0.9 - - - +
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Residues in contact with ASP 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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491T ASN 3.0 14.6 + - - +
492T MET* 3.1 7.8 + - - +
494T LEU* 1.3 78.6 - - - +
496T CYS* 1.3 56.9 + - - +
498T ALA* 2.6 36.0 + - - +
499T GLN* 3.3 5.4 + - - +
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Residues in contact with CYS 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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459T ILE 5.5 2.9 - - - +
460T TYR* 5.4 15.3 - - + -
463T ILE* 6.4 2.2 - - + -
492T MET 2.9 20.3 + - - +
493T ILE* 4.4 4.3 - - - +
495T ASP* 1.3 73.1 - - - +
497T CYS* 1.3 64.6 + - - +
499T GLN* 3.2 22.7 + - - +
500T GLN* 4.9 1.7 - - - +
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Residues in contact with CYS 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 ILE 3.4 12.0 + - - +
494T LEU* 3.3 10.4 + - - +
495T ASP 3.1 0.4 - - - -
496T CYS* 1.3 79.4 - - - +
498T ALA* 1.3 64.4 + - - +
499T GLN 2.9 1.2 + - - -
500T GLN* 3.5 14.3 + - - +
503T TYR* 5.8 1.7 - - - -
507T PHE* 3.7 28.9 - - + -
546T ASN* 3.9 11.7 - - - +
550T MET* 5.5 11.2 - - + -
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Residues in contact with ALA 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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494T LEU 3.0 11.9 + - - +
495T ASP* 2.6 24.8 + - - +
497T CYS* 1.3 72.8 - - - +
499T GLN* 1.3 56.2 + - + +
500T GLN 3.8 1.4 + - - -
542T ASN 5.0 0.3 - - - -
543T LYS* 3.6 34.6 + - + +
546T ASN* 3.6 23.0 - - - +
547T VAL* 5.0 9.9 - - + +
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Residues in contact with GLN 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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495T ASP 3.3 3.7 + - - +
496T CYS* 3.2 17.5 + - - +
497T CYS 3.0 0.4 - - - -
498T ALA* 1.3 79.8 - - + +
500T GLN* 1.3 59.1 + - - +
501T ARG 4.1 1.1 - - - +
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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