Contacts of the strand formed by residues 406 - 413 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397H ASN 3.4 2.9 - - - -
398H GLY* 2.8 28.2 + - - -
402H GLY* 2.7 15.7 + - - +
405H THR* 1.3 107.6 + - - +
407H LEU* 1.3 64.3 + - - +
408H SER 3.8 0.4 - - - -
470H PRO 3.8 15.9 - - - +
471H LEU* 3.6 40.4 + - + +
473H CYS 3.2 6.7 - - - +
474H PRO* 3.4 39.0 - - + +
475H VAL* 3.7 8.1 - - - +
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Residues in contact with LEU 407 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361H PHE* 5.2 2.2 - - + -
394H ILE* 3.2 42.6 - - + -
395H TYR 3.7 9.4 - - - +
396H LEU* 4.5 18.6 - - + +
406H HIS* 1.3 74.3 - - - +
408H SER* 1.3 61.3 + - - +
409H LEU* 4.6 0.9 - - + +
434H LEU* 5.0 9.2 - - + -
472H PHE* 3.4 25.3 + - + +
473H CYS* 2.7 37.0 + - + +
475H VAL* 4.2 4.2 - - + +
478H MET* 4.5 30.5 - - + -
490H ILE* 4.8 7.0 - - + -
492H ILE* 5.3 1.1 - - + -
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Residues in contact with SER 408 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393H ARG 4.0 0.7 - - - +
394H ILE* 3.3 5.2 - - - +
395H TYR* 2.8 40.0 + - - -
398H GLY* 3.4 3.5 - - - -
399H ASP* 3.0 29.9 + - - -
406H HIS 3.7 0.4 + - - -
407H LEU* 1.3 72.3 - - - +
409H LEU* 1.3 58.9 + - - +
410H PHE* 3.7 21.1 - - - -
469H CYS 3.6 4.5 - - - -
470H PRO* 2.5 28.5 + - - +
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Residues in contact with LEU 409 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356H TRP* 5.2 0.2 - - + -
392H LEU* 4.1 18.8 - - + -
393H ARG 3.7 8.5 - - - +
394H ILE* 4.4 15.3 - - + -
407H LEU* 4.6 0.4 - - + -
408H SER* 1.3 72.6 - - - +
410H PHE* 1.3 87.3 + - - +
432H LEU* 3.9 34.7 - - + +
468H GLY* 3.9 0.5 - - - -
469H CYS* 2.9 36.3 + - - +
472H PHE* 4.0 34.2 - - + +
492H ILE* 3.6 29.8 - - + -
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Residues in contact with PHE 410 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392H LEU* 3.3 6.4 - - - +
393H ARG* 2.8 47.3 + - + +
395H TYR* 3.5 35.2 - + - -
399H ASP* 3.4 23.1 - - + -
408H SER* 3.7 19.3 - - - -
409H LEU* 1.3 81.9 - - - +
411H PHE* 1.3 59.9 + - - +
412H VAL* 4.8 0.2 - - - -
432H LEU* 5.0 1.8 - - - -
466H ALA* 3.5 19.3 - - + -
467H SER* 3.6 6.3 - - - +
468H GLY* 3.3 22.4 - - - -
469H CYS 4.4 2.2 - - - -
470H PRO* 4.1 20.6 - - + -
251P VAL 3.6 11.2 - - - -
252P GLN 4.0 0.9 - - - -
253P GLU* 3.5 25.6 - - + -
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Residues in contact with PHE 411 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381H PHE* 4.3 5.6 - + - -
390H MET* 3.4 48.2 - - + -
391H CYS 4.0 1.6 - - - -
392H LEU* 3.9 18.6 - - + -
410H PHE* 1.3 73.0 - - - +
412H VAL* 1.3 62.2 + - - +
413H VAL* 3.7 26.7 - - + -
426H PHE* 3.8 23.3 - + - -
430H VAL* 4.0 22.7 - - + -
432H LEU* 5.0 2.6 - - + +
447H PHE* 3.9 14.1 - + + -
455H SER* 6.0 0.2 - - - -
456H PHE* 4.3 13.0 - + - -
465H ILE 4.8 0.3 - - - +
466H ALA* 3.5 2.6 - - - -
467H SER* 2.8 36.6 + - - +
468H GLY* 4.5 0.6 - - - -
496H VAL* 4.0 13.7 - - + -
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Residues in contact with VAL 412 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377H PHE* 4.5 5.2 - - + -
390H MET* 3.3 9.0 - - - +
391H CYS* 2.8 59.4 + - - +
393H ARG* 4.2 17.9 - - + +
411H PHE* 1.3 84.0 - - - +
413H VAL* 1.3 75.1 + - - +
414H MET* 3.6 0.6 + - + -
463H MET* 3.8 26.2 - - + -
464H ASN 3.9 9.4 - - - +
465H ILE 5.6 0.4 - - - -
466H ALA* 3.5 22.9 - - + +
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Residues in contact with VAL 413 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388H TYR* 5.4 2.0 - - + -
389H LYS 4.1 6.3 - - - +
390H MET* 4.8 1.8 - - + +
411H PHE* 3.7 24.9 + - + -
412H VAL* 1.3 73.9 - - - +
414H MET* 1.3 62.8 + - - +
424H TRP* 3.9 29.6 - - + -
426H PHE* 4.2 14.6 - - + -
455H SER 3.5 17.1 + - - +
456H PHE* 4.1 13.7 - - + +
457H GLN 4.8 0.2 - - - +
459H PRO* 3.9 6.3 - - + -
464H ASN* 3.0 49.0 + - - +
465H ILE 5.7 0.4 + - - -
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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