Contacts of the strand formed by residues 406 - 414 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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397G ASN* 3.4 3.5 - - - -
398G GLY* 2.8 29.3 + - - -
401G THR 4.9 0.4 - - - -
402G GLY* 2.9 6.7 + - - +
405G THR* 1.3 108.1 + - - +
407G LEU* 1.3 62.9 + - - +
408G SER 3.7 0.2 - - - -
470G PRO 3.7 17.9 - - - +
471G LEU* 3.4 42.6 + - + +
473G CYS 3.2 7.4 - - - +
474G PRO* 3.4 39.5 - - + +
475G VAL* 3.9 6.0 - - - +
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Residues in contact with LEU 407 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361G PHE* 5.2 2.2 - - + -
394G ILE* 3.4 42.2 - - + -
395G TYR 3.7 7.4 - - - +
396G LEU* 4.6 18.6 - - + +
398G GLY 4.6 0.2 - - - +
406G HIS* 1.3 71.9 - - - +
408G SER* 1.3 61.4 + - - +
409G LEU* 4.4 1.8 - - + -
434G LEU* 4.8 12.6 - - + -
472G PHE* 3.2 42.9 + - + +
473G CYS* 2.6 24.3 + - + +
475G VAL* 4.3 4.6 - - + +
478G MET* 4.3 23.6 - - - -
490G ILE* 4.7 9.9 - - + -
492G ILE* 5.5 1.1 - - + -
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Residues in contact with SER 408 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394G ILE* 3.3 5.0 - - - +
395G TYR* 2.8 40.0 + - - +
398G GLY* 3.4 3.1 - - - -
399G ASP* 2.9 31.2 + - - -
406G HIS 3.6 1.0 + - - -
407G LEU* 1.3 74.1 - - - +
409G LEU* 1.3 58.3 + - - +
410G PHE* 3.6 22.2 - - - -
469G CYS 3.6 5.4 - - - -
470G PRO* 2.6 27.0 + - - +
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Residues in contact with LEU 409 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356G TRP* 5.7 0.7 - - + -
392G LEU* 4.4 13.7 - - + -
393G ARG 3.7 6.5 - - - +
394G ILE* 4.6 11.0 - - + -
407G LEU* 3.9 4.4 + - + -
408G SER* 1.3 72.2 - - - +
410G PHE* 1.3 79.2 + - - +
432G LEU* 3.7 31.6 - - + +
433G MET 4.8 0.2 - - - +
469G CYS* 2.9 36.5 + - - +
472G PHE* 3.8 45.5 - - + +
492G ILE* 3.7 31.0 - - + -
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Residues in contact with PHE 410 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392G LEU* 3.4 5.2 - - - +
393G ARG 2.8 42.7 + - - +
395G TYR* 3.4 36.3 - + - -
399G ASP* 3.4 24.2 - - + -
408G SER* 3.6 20.0 - - - -
409G LEU* 1.3 85.6 - - - +
411G PHE* 1.3 60.6 + - - +
412G VAL* 4.7 0.2 - - - -
432G LEU* 4.8 1.3 - - - -
466G ALA* 3.6 19.7 - - + -
467G SER 3.7 5.6 - - - +
468G GLY* 3.4 22.2 - - - -
470G PRO* 4.1 22.4 - - + -
251O VAL 3.6 14.8 - - - -
252O GLN 4.1 2.2 - - - -
253O GLU* 3.6 21.1 - - + -
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Residues in contact with PHE 411 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381G PHE* 4.4 4.5 - + - -
390G MET* 3.3 48.7 - - + -
391G CYS 4.0 2.2 - - - -
392G LEU* 4.1 16.4 - - + -
410G PHE* 1.3 70.5 - - - +
412G VAL* 1.3 67.6 + - - +
413G VAL* 3.7 18.8 - - + -
426G PHE* 3.7 28.5 - + - -
430G VAL* 3.9 25.1 - - + -
432G LEU* 4.9 2.6 - - + +
447G PHE* 4.0 14.4 - + + -
455G SER* 6.0 0.2 - - - -
456G PHE* 4.2 15.3 - + - -
465G ILE 4.8 0.3 - - - +
466G ALA* 3.3 4.3 - - - -
467G SER* 2.7 36.4 + - - +
468G GLY* 4.6 0.4 - - - -
494G ALA* 5.9 0.4 - - + -
496G VAL* 3.8 14.8 - - + -
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Residues in contact with VAL 412 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377G PHE* 4.7 4.0 - - + -
390G MET* 3.2 9.9 - - - +
391G CYS* 2.9 57.3 + - - +
393G ARG* 4.1 20.6 - - + +
411G PHE* 1.3 84.8 - - - +
413G VAL* 1.3 68.7 + - - +
414G MET* 3.6 0.8 + - + -
463G MET* 3.8 32.3 - - + -
464G ASN 3.9 9.9 - - - +
466G ALA* 3.4 22.7 - - + +
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Residues in contact with VAL 413 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388G TYR* 5.4 1.8 - - + -
389G LYS 4.0 5.8 - - - +
390G MET* 4.7 2.5 - - + +
411G PHE* 3.7 24.0 - - + -
412G VAL* 1.3 73.7 - - - +
414G MET* 1.3 64.7 + - - +
424G TRP* 3.7 25.1 - - + -
426G PHE* 4.2 22.7 - - + -
455G SER 3.6 24.7 + - - +
456G PHE* 4.3 5.4 - - + -
459G PRO* 3.6 19.7 - - + +
463G MET* 3.7 1.0 - - - -
464G ASN* 3.0 32.9 + - - +
465G ILE 5.6 0.6 + - - -
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Residues in contact with MET 414 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380G ALA* 3.1 16.6 - - + -
389G LYS* 2.9 56.2 + - + +
390G MET 2.9 32.8 - - - +
391G CYS* 3.6 26.0 - - - -
412G VAL* 4.2 3.4 - - + +
413G VAL* 1.3 80.4 - - - +
415G LYS* 1.3 66.5 + - - +
416G GLY* 3.0 4.5 + - - -
419G ASP* 3.9 2.1 - - - +
424G TRP* 5.0 0.9 - - - -
459G PRO* 3.7 9.2 - - - +
462G ASP* 3.4 11.0 - - - +
463G MET* 3.9 25.4 - - + +
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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