Contacts of the strand formed by residues 406 - 409 (chain D) in PDB entry 5WYF
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 406 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223D GLY 4.3 5.4 - - - +
224D GLY* 3.7 24.5 - - - +
226D ILE* 5.6 1.6 - - + -
361D ARG* 3.2 24.7 - - - +
368D GLY* 3.8 17.9 - - - -
369D ILE 3.8 6.1 - - - +
370D GLU* 3.6 31.0 - - + +
401D THR* 3.1 6.2 - - - -
402D LEU* 2.7 46.6 + - + +
403D ALA* 4.4 7.0 - - + -
404D GLY 3.6 1.2 + - - -
405D ASN* 1.3 87.4 - - - +
407D LEU* 1.3 72.3 + - - +
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Residues in contact with LEU 407 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347D PHE* 6.2 1.1 - - + -
367D GLY 3.6 0.5 - - - +
368D GLY* 3.2 8.5 - - - -
369D ILE* 3.0 51.4 + - + +
371D LEU* 4.0 11.4 - - + -
385D ALA* 3.9 17.5 - - + +
388D VAL* 3.7 24.7 - - + -
389D ILE* 3.4 32.3 - - + -
399D ILE* 4.4 15.0 - - + -
400D ILE 3.9 1.3 - - - +
401D THR* 4.0 7.2 - - + -
406D ILE* 1.3 70.6 - - - +
408D ARG* 1.3 61.6 + - - +
409D PHE 3.8 0.6 + - - -
427D LEU* 5.4 5.2 - - + -
431D PHE* 3.8 22.0 - - + -
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Residues in contact with ARG 408 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C TYR* 3.5 20.6 + - - -
50D LEU 3.7 8.0 - - - +
51D LEU* 3.9 24.4 - - + +
54D ALA* 3.4 12.7 - - - +
221D GLY 6.0 1.5 - - - -
222D ASP* 4.6 0.4 - - - -
225D ILE* 5.1 1.7 - - + +
253D ASN* 3.3 10.3 - - - +
367D GLY 3.8 4.3 - - - +
399D ILE* 3.3 21.7 - - - +
400D ILE* 2.8 29.3 + - + +
402D LEU* 3.8 42.5 - - + +
406D ILE 3.6 0.4 + - - -
407D LEU* 1.3 70.8 - - - +
409D PHE* 1.3 60.3 + - - +
410D GLN* 2.8 36.5 + - + +
1001D ILP 2.8 43.0 + - - -
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Residues in contact with PHE 409 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D LEU* 3.8 37.9 - - + -
343D ALA* 3.9 17.9 - - + -
347D PHE* 4.1 25.4 - + + -
362D MET* 3.7 23.3 - - + -
365D LEU* 3.5 26.5 - - + -
366D ASN* 3.5 2.9 - - - -
367D GLY* 2.8 40.3 + - - +
369D ILE* 5.1 4.9 - - + -
399D ILE* 4.7 3.4 - - + -
407D LEU 3.8 2.2 + - - +
408D ARG* 1.3 71.9 - - - +
410D GLN* 1.3 62.0 - - - +
411D PRO* 4.0 7.2 - - + -
420D LEU* 3.6 28.3 - - + -
423D ALA* 5.8 0.7 - - + -
424D LEU* 4.6 3.8 - - + -
427D LEU* 4.9 1.8 - - + -
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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