Contacts of the strand formed by residues 389 - 395 (chain D) in PDB entry 1D00
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 LYS 389 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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380D ALA* 3.6 11.4 - - + -
381D PHE 3.9 0.4 - - - -
382D TYR* 3.5 41.9 + - + +
387D GLY 3.6 1.0 + - - -
388D TYR* 1.3 72.1 - - - +
390D MET* 1.3 66.0 + - - +
413D VAL* 4.0 1.9 - - - +
414D MET* 2.9 60.2 + - + +
415D LYS 3.7 18.7 + - - +
416D GLY* 3.8 20.8 - - - -
417D PRO* 4.7 3.5 - - + +
419D ASP* 5.1 0.6 + - - -
462D ASP* 5.4 5.7 + - - -
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Residues in contact with MET 390 (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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352D GLY* 5.0 0.2 - - - -
380D ALA* 3.2 0.7 - - - -
381D PHE* 2.9 70.4 + - + +
382D TYR 3.8 0.4 - - - -
383D THR* 3.5 38.6 - - + +
388D TYR* 3.8 9.4 - - + +
389D LYS* 1.3 79.9 - - - +
391D CYS* 1.3 59.8 + - - +
411D PHE* 3.3 38.1 - - + -
412D VAL 3.2 13.0 - - - +
413D VAL* 4.8 4.0 - - + -
414D MET* 2.9 18.0 - - - +
426D PHE* 4.1 10.1 - - + -
496D VAL* 3.8 9.0 - - + -
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Residues in contact with CYS 391 (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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377D PHE* 4.0 14.8 - - - -
378D SER* 3.6 25.1 - - - +
379D PRO 3.6 6.5 - - - +
381D PHE* 4.1 4.7 - - - -
390D MET* 1.3 76.5 - - - +
392D LEU* 1.3 77.7 + - - +
411D PHE* 4.3 1.6 - - - -
412D VAL* 2.8 49.3 + - - -
414D MET* 3.6 23.6 - - + -
463D MET* 4.1 6.3 - - - -
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Residues in contact with LEU 392 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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354D PHE* 4.1 15.5 - - + -
356D TRP* 4.1 13.7 - - + -
377D PHE* 3.4 3.6 - - - -
378D SER* 2.7 40.9 + - - +
381D PHE* 4.2 9.6 - - + -
391D CYS* 1.3 88.5 - - - +
393D ARG* 1.3 61.6 + - - +
409D LEU* 4.6 7.0 - - + -
410D PHE 3.4 13.9 - - - +
411D PHE* 4.1 13.0 - - + -
412D VAL* 4.1 2.5 - - - -
432D LEU* 4.1 12.3 - - + -
492D ILE* 4.1 25.4 - - + -
493D LYS 5.1 0.2 - - - -
494D ALA* 3.9 32.5 - - + +
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Residues in contact with ARG 393 (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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356D TRP* 4.8 0.7 - - - -
375D ALA* 3.6 29.8 + - + +
376D ILE 3.2 15.0 - - - +
377D PHE* 3.2 48.0 - - + -
392D LEU* 1.3 74.7 - - - +
394D ILE* 1.3 61.5 + - - +
395D TYR* 3.7 8.0 + - + -
409D LEU* 3.8 2.1 - - - +
410D PHE* 2.9 37.9 + - + -
412D VAL* 4.1 10.3 - - + +
466D ALA* 4.6 6.5 - - + -
253L GLU* 2.8 46.4 + - - -
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Residues in contact with ILE 394 (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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356D TRP* 3.5 28.7 - - + -
358D ILE* 4.1 19.1 - - + -
375D ALA* 3.1 3.5 - - - -
376D ILE* 3.0 38.4 + - + +
393D ARG* 1.3 76.0 - - - +
395D TYR* 1.3 65.7 + - - +
396D LEU* 3.6 28.6 + - + -
407D LEU* 3.4 30.3 - - + -
408D SER 3.4 11.7 - - - +
409D LEU* 4.7 7.2 - - + -
490D ILE* 4.9 1.3 - - + -
492D ILE* 4.4 14.4 - - + -
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Residues in contact with TYR 395 (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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374D PRO* 3.2 32.8 - - + +
375D ALA* 3.7 16.4 - - + -
393D ARG* 3.7 12.6 + - + -
394D ILE* 1.3 78.0 - - - +
396D LEU* 1.3 65.1 + - - +
397D ASN 3.0 3.2 + - - +
398D GLY* 3.1 31.0 + - - +
399D ASP* 3.4 26.5 - - + -
407D LEU* 3.8 1.4 - - - -
408D SER* 3.0 24.2 + - - +
410D PHE* 3.5 34.8 - + - -
253L GLU* 2.7 28.1 + - + +
254L THR 3.4 16.0 + - - -
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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