Contacts of the helix formed by residues 466 - 478 (chain I) in PDB entry 5FUR
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 466 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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376I TYR* 3.6 20.2 - - - +
380I LEU* 6.0 7.4 - - + -
383I LYS* 6.2 1.8 - - - +
461I GLU* 3.8 24.2 - - + +
462I ASN* 5.3 8.7 - - - +
465I SER* 1.3 83.5 + - - +
467I GLU* 1.3 65.3 + - - +
469I MET* 2.8 5.4 + - - +
470I LEU* 2.8 24.5 + - - +
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Residues in contact with GLU 467 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609G ILE* 5.7 6.4 - - - +
682G GLU* 3.7 27.3 - - - +
465I SER* 4.1 4.6 + - - +
466I MET* 1.3 81.0 - - - +
468I PHE* 1.4 69.0 + - + +
470I LEU* 3.4 15.2 - - + +
471I GLN* 3.3 23.5 + - + +
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Residues in contact with PHE 468 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609G ILE* 6.4 1.8 - - + -
611G GLN* 3.0 41.7 - - + -
682G GLU* 3.7 18.8 - - - -
684G PHE* 5.8 3.8 - - + -
464I ILE* 3.3 22.7 - - - +
465I SER* 4.2 11.2 + - - -
466I MET 3.2 2.4 - - - +
467I GLU* 1.4 80.2 - - + +
469I MET* 1.4 60.0 + - - +
471I GLN* 2.8 37.4 + - - +
472I VAL* 3.0 15.7 + - - +
510I VAL* 3.4 25.5 - - + +
511I SER* 4.1 13.0 - - - -
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Residues in contact with MET 469 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373I ILE* 4.8 7.0 - - + -
457I MET* 4.3 18.4 - - + -
460I ILE* 6.2 0.2 - - - -
461I GLU* 3.1 35.0 - - - +
464I ILE* 3.8 23.9 + - + +
465I SER 3.8 3.2 + - - +
466I MET 2.8 7.5 + - - +
468I PHE* 1.4 73.0 - - - +
470I LEU* 1.3 64.5 + - - +
472I VAL* 3.0 21.0 - - + +
473I PHE* 3.0 36.0 + - + -
503I PHE* 4.1 11.9 - - + -
507I ILE* 3.6 36.1 - - + -
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Residues in contact with LEU 470 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294I ILE 5.5 5.2 - - - +
296I THR* 5.4 7.4 - - - +
466I MET 2.8 12.2 + - - +
467I GLU* 3.4 19.3 - - + +
469I MET* 1.3 79.5 - - - +
471I GLN* 1.3 74.7 - - + +
473I PHE* 2.9 34.8 + - + -
474I ASN* 3.1 25.9 + - + +
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Residues in contact with GLN 471 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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680G GLY 4.6 3.2 - - - +
681G GLY* 4.2 4.7 - - - -
682G GLU* 1.7 90.2 + - + +
467I GLU* 3.3 15.6 + - + +
468I PHE* 2.8 21.5 + - - +
470I LEU* 1.3 85.7 - - + +
472I VAL* 1.3 65.3 + - + +
474I ASN* 4.3 3.7 - - - +
475I LYS* 3.3 21.8 + - - +
510I VAL* 5.4 5.0 - - + +
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Residues in contact with VAL 472 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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678G SER 6.1 0.2 - - - -
464I ILE* 5.7 0.4 - - + -
468I PHE 3.0 14.0 + - - +
469I MET* 3.0 26.7 - - + +
470I LEU 2.9 0.8 + - - -
471I GLN* 1.3 79.4 - - - +
473I PHE* 1.3 65.7 + - - +
475I LYS* 3.1 4.0 + - - +
476I LEU* 3.1 19.9 + - + +
503I PHE* 4.3 10.1 - - + -
506I SER* 4.5 15.3 + - - +
507I ILE* 3.3 37.0 - - + -
510I VAL* 3.8 28.5 - - + -
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Residues in contact with PHE 473 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294I ILE 4.3 13.0 - - - -
295I LEU* 3.4 43.3 - - + -
296I THR* 5.7 1.1 - - - -
355I PHE* 3.5 29.3 - + + -
377I ILE* 6.2 1.3 - - + -
469I MET* 3.0 37.0 + - + +
470I LEU* 2.9 37.6 + - + -
472I VAL* 1.3 74.9 - - - +
474I ASN* 1.3 67.5 + - + +
476I LEU* 3.7 8.9 - - - +
477I LEU* 3.2 37.7 + - + +
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Residues in contact with ASN 474 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295I LEU 3.9 1.8 - - - +
296I THR* 3.2 48.5 + - - +
297I CYS* 5.5 0.2 - - - +
470I LEU* 3.1 26.6 + - + +
471I GLN* 4.3 4.6 - - - +
473I PHE* 1.3 90.1 - - + +
475I LYS* 1.3 62.5 + - - +
477I LEU* 3.8 6.1 + - - +
478I SER* 3.1 22.2 + - - -
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Residues in contact with LYS 475 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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675G ARG 2.9 13.3 + - - -
678G SER* 1.3 146.2 + - - +
679G GLY* 0.5 150.2 - - - +
680G GLY* 2.6 21.5 + - - +
683G MET* 5.8 1.2 - - - +
471I GLN 3.3 15.8 + - - +
472I VAL* 3.1 5.8 + - - +
474I ASN* 1.3 73.9 - - - +
476I LEU* 1.4 68.4 + - - +
478I SER* 2.8 8.6 + - - +
479I LEU* 2.8 28.5 + - + +
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Residues in contact with LEU 476 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355I PHE* 3.4 19.1 - - + -
359I ILE* 3.3 38.5 - - + +
369I VAL* 5.9 0.2 - - + -
472I VAL* 3.1 13.9 + - + +
473I PHE* 3.7 9.9 - - - +
474I ASN 3.4 0.6 - - - -
475I LYS* 1.4 76.8 - - - +
477I LEU* 1.3 63.5 + - - +
478I SER 3.1 0.2 + - - -
479I LEU* 3.3 26.2 + - + +
494I SER* 4.7 0.9 + - - -
498I VAL* 5.3 15.6 - - + +
499I SER 5.4 4.7 - - - +
502I GLY 6.0 0.4 - - - -
503I PHE* 3.6 37.9 - - + +
506I SER* 6.2 2.7 - - - -
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Residues in contact with LEU 477 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295I LEU* 4.3 12.6 - - + +
297I CYS* 3.6 36.9 - - + -
354I PHE* 4.1 13.0 - - + -
355I PHE* 4.2 25.1 - - + +
358I PHE* 4.1 21.0 - - + +
359I ILE* 3.5 26.5 - - + +
473I PHE* 3.2 25.9 + - + +
474I ASN* 4.1 7.4 - - - +
475I LYS 3.2 0.2 - - - -
476I LEU* 1.3 77.2 - - - +
478I SER* 1.3 59.7 + - - +
494I SER* 3.9 15.8 + - - +
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Residues in contact with SER 478 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679G GLY 5.4 3.0 + - - +
474I ASN* 3.1 17.6 + - - -
475I LYS* 2.8 12.0 + - - +
477I LEU* 1.3 74.7 - - - +
479I LEU* 1.3 62.0 + - - +
480I ALA* 3.7 6.1 + - - +
494I SER* 4.9 0.9 - - - -
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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