Contacts of the strand formed by residues 406 - 414 (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 HIS 406 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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397D ASN 3.4 1.6 - - - -
398D GLY* 2.8 32.2 + - - -
402D GLY* 2.9 6.2 + - - +
405D THR* 1.3 114.1 + - - +
407D LEU* 1.3 63.2 + - - +
470D PRO 3.8 17.7 - - - +
471D LEU* 3.6 43.1 + - + +
473D CYS 3.2 8.8 - - - +
474D PRO* 3.5 32.7 - - + +
475D VAL* 3.7 7.2 - - - -
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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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361D PHE* 6.2 0.4 - - + -
394D ILE* 3.4 39.3 - - + -
395D TYR 3.8 6.3 - - - +
396D LEU* 4.6 13.9 - - + +
406D HIS* 1.3 72.0 - - - +
408D SER* 1.3 69.1 + - - +
409D LEU* 4.1 9.9 - - + +
434D LEU* 4.2 25.8 - - + -
472D PHE* 3.4 17.8 + - + +
473D CYS* 2.6 40.2 + - + +
474D PRO 5.6 0.4 - - - -
475D VAL* 4.2 3.6 - - + +
478D MET* 4.8 17.0 - - + -
490D ILE* 5.0 4.5 - - + -
492D ILE* 5.0 6.3 - - + -
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Residues in contact with SER 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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393D ARG 4.1 0.5 - - - +
394D ILE* 3.4 5.7 - - - +
395D TYR* 3.0 35.0 + - - -
398D GLY* 3.3 5.1 - - - -
399D ASP* 3.0 30.1 + - - -
402D GLY* 4.3 0.3 - - - -
406D HIS 3.5 0.5 + - - -
407D LEU* 1.3 73.7 - - - +
409D LEU* 1.3 59.4 + - - +
410D PHE* 3.6 23.3 - - - -
469D CYS 3.6 4.7 - - - -
470D PRO* 2.6 26.4 + - - +
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Residues in contact with LEU 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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356D TRP* 6.0 0.4 - - + -
392D LEU* 4.6 11.0 - - + -
393D ARG 3.8 5.4 - - - +
394D ILE* 4.6 7.6 - - + +
407D LEU* 4.2 6.1 - - + -
408D SER* 1.3 74.6 - - - +
410D PHE* 1.3 80.5 + - - +
432D LEU* 3.4 39.2 - - + +
433D MET 4.7 1.1 - - - +
468D GLY* 3.7 0.5 - - - -
469D CYS* 2.9 34.5 + - - +
472D PHE* 3.7 45.0 - - + +
492D ILE* 3.8 29.6 - - + -
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Residues in contact with PHE 410 (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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392D LEU* 3.4 5.7 - - - +
393D ARG* 2.9 40.7 + - + +
395D TYR* 3.5 34.1 - + - -
399D ASP* 3.5 19.7 - - + -
408D SER* 3.6 22.9 - - - -
409D LEU* 1.3 87.0 - - - +
411D PHE* 1.3 61.0 + - - +
432D LEU* 4.6 0.9 - - - -
466D ALA* 3.6 18.8 - - + -
467D SER* 3.6 8.1 - - - -
468D GLY* 3.2 22.0 - - - -
470D PRO* 4.1 20.6 - - + -
251L VAL 3.4 17.5 - - - -
252L GLN 4.0 2.2 - - - -
253L GLU* 3.5 17.7 - - + -
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Residues in contact with PHE 411 (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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381D PHE* 4.4 4.7 - + - -
390D MET* 3.3 46.7 - - + -
391D CYS 4.0 1.8 - - - -
392D LEU* 4.1 15.9 - - + -
410D PHE* 1.3 73.5 - - - +
412D VAL* 1.3 64.0 + - - +
413D VAL* 3.8 19.3 - - + -
426D PHE* 3.5 29.8 - + - -
430D VAL* 4.0 23.1 - - + -
432D LEU* 4.7 2.0 - - + +
447D PHE* 4.1 13.0 - + + -
456D PHE* 4.0 17.9 - + - -
465D ILE 4.8 0.3 - - - +
466D ALA* 3.4 5.7 - - - -
467D SER* 2.9 37.4 + - - +
468D GLY* 4.5 0.2 - - - -
494D ALA* 5.8 0.7 - - + -
496D VAL* 3.9 14.1 - - + -
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Residues in contact with VAL 412 (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* 4.5 5.4 - - + -
390D MET* 3.2 9.2 - - - +
391D CYS* 2.8 65.5 + - - +
392D LEU 4.1 1.8 - - - -
393D ARG* 4.1 19.3 - - + +
411D PHE* 1.3 84.1 - - - +
413D VAL* 1.3 73.0 + - - +
414D MET* 3.6 1.5 + - + -
463D MET* 4.0 23.1 - - + -
464D ASN 4.2 8.5 - - - +
465D ILE 5.6 0.2 - - - -
466D ALA* 3.6 20.9 - - + +
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Residues in contact with VAL 413 (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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388D TYR* 5.6 1.6 - - + -
389D LYS 4.1 5.2 - - - +
390D MET* 4.7 4.0 - - + +
411D PHE* 3.8 23.3 + - + -
412D VAL* 1.3 72.9 - - - +
414D MET* 1.3 62.5 + - - +
424D TRP* 3.8 24.2 - - + -
426D PHE* 4.3 13.2 - - + -
455D SER 3.5 16.9 + - - +
456D PHE* 4.0 13.9 - - + -
459D PRO* 3.7 11.9 - - + -
463D MET* 3.8 1.2 - - - -
464D ASN* 3.0 50.9 + - - +
465D ILE 5.6 1.2 + - - -
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Residues in contact with MET 414 (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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380D ALA* 3.1 15.5 - - + -
389D LYS* 2.9 56.5 + - + +
390D MET 2.9 34.3 - - - +
391D CYS* 3.6 25.1 - - + -
412D VAL* 4.1 2.7 - - + +
413D VAL* 1.3 79.0 - - - +
415D LYS* 1.3 65.9 + - - +
416D GLY* 3.0 4.9 + - - -
419D ASP* 4.0 2.8 - - - +
424D TRP* 5.1 0.9 - - - -
459D PRO* 3.6 10.8 - - - +
462D ASP* 3.4 10.1 - - - +
463D MET* 3.9 27.8 - - + -
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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