Contacts of the helix formed by residues 395 - 406 (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 ILE 395 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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379I GLY* 5.5 2.7 - - - +
383I LYS* 5.3 12.1 - - + +
391I TYR* 3.4 46.4 + - + +
392I ARG* 3.8 20.6 + - + +
394I TRP* 1.3 76.7 - - - +
396I LYS* 1.3 69.7 + - + +
397I GLU 3.2 0.6 + - - -
398I GLU* 3.6 12.1 + - - +
399I LEU* 3.2 21.2 + - + +
454I HIS* 4.2 23.3 - - + +
458I ARG* 5.0 22.0 - - - +
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Residues in contact with LYS 396 (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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393I HIS 5.7 0.9 - - - +
394I TRP 2.8 1.6 + - - -
395I ILE* 1.3 88.3 - - + +
397I GLU* 1.3 57.9 + - - +
399I LEU* 3.2 33.4 - - + +
400I ASP* 2.7 49.6 + - - +
458I ARG* 5.0 19.4 - - - +
633I ASP* 2.9 34.1 + - - +
634I MET* 4.6 3.1 + - + -
658I ASP* 5.4 1.2 + - - -
660I VAL* 3.0 51.2 - - + +
663I GLN* 6.3 0.9 - - - +
664I GLU* 6.1 0.2 - - + -
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Residues in contact with GLU 397 (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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394I TRP* 3.0 15.7 + - - +
396I LYS* 1.3 78.0 - - - +
398I GLU* 1.4 64.0 + - + +
400I ASP* 3.2 4.4 + - - +
401I LYS* 3.0 63.8 + - + +
693I ARG* 3.5 37.5 + - - -
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Residues in contact with GLU 398 (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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344I ARG* 5.4 4.9 + - - -
348I GLN* 5.1 1.4 + - - -
378I TYR* 4.4 14.0 - - - -
391I TYR* 3.9 20.7 + - - -
394I TRP 4.3 0.9 + - - +
395I ILE* 3.6 12.5 + - - +
396I LYS 3.5 0.2 - - - -
397I GLU* 1.4 81.6 - - + +
399I LEU* 1.3 64.3 + - - +
400I ASP 3.4 0.3 + - - -
401I LYS* 3.7 10.5 + - + +
402I ILE* 3.6 22.3 + - - +
450I GLN* 4.8 5.0 + - - -
451I CYS* 4.0 33.7 - - + +
454I HIS* 4.5 18.1 + - + -
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Residues in contact with LEU 399 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395I ILE* 3.2 9.9 + - + +
396I LYS* 3.0 55.5 + - + +
398I GLU* 1.3 79.0 - - - +
400I ASP* 1.3 59.0 + - - +
402I ILE* 3.0 26.2 - - + +
403I VAL* 3.6 6.8 - - - +
451I CYS 5.6 1.1 - - - -
454I HIS* 6.0 5.6 - - + -
455I LEU* 3.4 42.0 - - + -
458I ARG* 5.9 2.0 - - - +
634I MET 5.0 2.0 - - - +
637I LEU* 3.9 31.2 - - + -
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Residues in contact with ASP 400 (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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396I LYS* 2.7 39.3 + - - +
397I GLU* 4.1 3.8 - - - +
398I GLU 3.2 0.2 - - - -
399I LEU* 1.3 77.5 - - - +
401I LYS* 1.4 68.0 + - + +
402I ILE 3.3 0.7 - - - -
403I VAL* 3.2 21.5 + - + +
404I ALA* 3.4 6.8 + - - +
634I MET* 3.5 32.2 - - + +
637I LEU* 4.0 10.2 - - - +
664I GLU* 3.3 26.3 - - - +
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Residues in contact with LYS 401 (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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397I GLU* 3.0 55.2 + - + +
398I GLU* 4.3 8.3 - - + +
399I LEU 3.4 0.2 - - - -
400I ASP* 1.4 83.2 - - + +
402I ILE* 1.3 62.2 + - + +
404I ALA* 3.3 13.4 + - - +
405I TYR* 3.3 27.0 - - + -
447I SER* 6.5 0.9 - - - -
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Residues in contact with ILE 402 (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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398I GLU 3.6 11.6 + - - +
399I LEU* 3.0 27.8 - - + +
401I LYS* 1.3 76.2 - - + +
403I VAL* 1.4 62.0 + - + +
405I TYR* 3.3 9.7 + - - +
406I GLU* 3.0 48.4 + - + +
447I SER* 3.9 25.8 - - - +
448I MET* 4.7 6.7 - - + +
451I CYS* 3.6 30.3 - - + +
452I LYS* 3.9 20.6 - - + +
455I LEU* 4.0 13.9 - - + -
637I LEU* 5.4 2.7 - - + -
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Residues in contact with VAL 403 (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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399I LEU 3.6 17.5 - - - +
400I ASP* 3.2 15.7 + - + +
401I LYS 3.1 0.8 - - - -
402I ILE* 1.4 76.9 - - + +
404I ALA* 1.3 67.4 + - - +
406I GLU* 2.8 19.9 + - + +
407I LEU* 2.9 37.9 + - + +
634I MET* 5.9 2.7 - - + -
637I LEU* 3.7 52.0 - - + +
638I ARG* 5.8 1.3 - - - -
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Residues in contact with ALA 404 (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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400I ASP 3.4 5.5 + - - +
401I LYS* 3.3 16.2 + - - +
403I VAL* 1.3 81.7 - - - +
405I TYR* 1.3 63.9 + - + +
407I LEU* 3.8 14.0 + - - +
408I LYS* 3.3 25.0 + - - +
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Residues in contact with TYR 405 (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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401I LYS* 3.3 28.7 - - + -
402I ILE* 3.3 6.3 + - - +
403I VAL 3.2 0.4 - - - -
404I ALA* 1.3 82.2 - - + +
406I GLU* 1.3 51.9 - - - +
407I LEU 3.3 3.6 - - - -
408I LYS* 3.8 21.5 - - + +
413I LEU* 5.2 13.2 - - + -
414I LEU* 1.7 41.6 - - - +
446I TYR* 3.2 28.8 + + - -
447I SER* 4.2 17.9 - - - -
448I MET* 3.9 24.0 - - + -
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Residues in contact with GLU 406 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402I ILE* 3.0 34.0 + - - +
403I VAL* 2.8 11.3 + - + +
405I TYR* 1.3 74.3 - - - +
407I LEU* 1.3 60.6 + - - +
408I LYS 3.2 8.0 + - - -
409I THR* 5.0 0.9 + - - -
414I LEU* 3.3 15.8 - - + +
448I MET* 4.0 22.1 - - + +
452I LYS* 2.6 47.5 + - - +
522I TRP 4.7 0.7 - - - +
552I TYR* 6.2 0.7 - - - -
637I LEU* 6.1 0.3 - - - +
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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