Contacts of the strand formed by residues 406 - 414 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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397F ASN 3.4 2.6 - - - -
398F GLY* 2.9 29.3 + - - -
402F GLY* 2.9 9.3 + - - +
405F THR* 1.3 114.9 + - - +
407F LEU* 1.3 68.6 + - - +
470F PRO 3.9 10.3 - - - +
471F LEU* 3.6 43.8 + - + +
473F CYS 3.2 6.3 - - - +
474F PRO* 3.6 33.8 - - + +
475F VAL* 3.6 7.3 - - - +
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Residues in contact with LEU 407 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361F PHE* 5.2 1.8 - - + -
394F ILE* 3.2 39.0 - - + -
395F TYR 3.8 7.0 - - - +
396F LEU* 4.6 18.6 - - + +
398F GLY 4.4 0.2 - - - +
406F HIS* 1.3 76.2 - - - +
408F SER* 1.3 65.2 + - - +
409F LEU* 4.3 3.8 - - + +
434F LEU* 4.6 15.5 - - + -
472F PHE* 3.5 25.2 + - + +
473F CYS* 2.6 36.0 + - + +
475F VAL* 4.1 5.3 - - + +
478F MET* 4.5 26.2 - - + -
490F ILE* 4.7 6.5 - - + -
492F ILE* 5.3 1.6 - - + -
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Residues in contact with SER 408 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394F ILE* 3.3 4.9 - - - +
395F TYR* 2.9 39.9 + - - -
398F GLY* 3.2 5.6 - - - -
399F ASP* 2.8 31.8 + - - -
406F HIS 3.7 0.2 + - - -
407F LEU* 1.3 73.4 - - - +
409F LEU* 1.3 59.9 + - - +
410F PHE* 3.5 21.5 - - - -
469F CYS 3.6 4.7 - - - -
470F PRO* 2.7 24.5 + - - -
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Residues in contact with LEU 409 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356F TRP* 5.2 0.7 - - + -
392F LEU* 4.3 18.6 - - + -
393F ARG 3.8 9.2 - - - +
394F ILE* 4.5 14.8 - - + -
407F LEU* 4.4 1.8 - - + -
408F SER* 1.3 73.2 - - - +
410F PHE* 1.3 85.9 + - - +
432F LEU* 4.0 29.8 - - + +
433F MET 4.6 0.4 - - - +
468F GLY* 3.9 0.3 - - - -
469F CYS* 2.8 35.0 + - - +
472F PHE* 4.0 39.7 - - + +
492F ILE* 3.6 28.7 - - + -
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Residues in contact with PHE 410 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392F LEU* 3.5 7.0 - - - +
393F ARG* 2.8 40.0 + - + +
395F TYR* 3.6 26.5 - + - -
399F ASP* 3.5 18.8 - - - -
408F SER* 3.5 24.0 - - - -
409F LEU* 1.3 82.6 - - - +
411F PHE* 1.3 59.1 + - - +
432F LEU* 4.9 2.7 - - - -
466F ALA* 3.6 18.8 - - + -
467F SER* 3.6 9.9 - - - +
468F GLY* 3.2 21.8 - - - -
470F PRO* 4.0 29.4 - - + -
251N VAL 3.5 16.4 - - - -
252N GLN 4.0 2.2 - - - -
253N GLU* 3.5 18.6 - - + -
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Residues in contact with PHE 411 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381F PHE* 4.3 5.4 - + - -
390F MET* 3.4 48.7 - - + -
391F CYS 4.1 1.1 - - - -
392F LEU* 4.0 16.4 - - + -
410F PHE* 1.3 73.4 - - - +
412F VAL* 1.3 65.2 + - - +
413F VAL* 3.7 18.8 - - + -
426F PHE* 3.7 28.3 - + - -
430F VAL* 3.9 21.8 - - + -
432F LEU* 4.9 2.6 - - + +
447F PHE* 4.1 15.0 - + + -
455F SER* 5.9 0.3 - - - -
456F PHE* 4.2 17.0 - + - -
465F ILE 4.8 0.2 - - - +
466F ALA* 3.4 4.2 - - - -
467F SER* 2.9 35.0 + - - +
468F GLY* 4.5 0.6 - - - -
494F ALA* 5.9 0.4 - - + -
496F VAL* 4.0 13.0 - - + -
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Residues in contact with VAL 412 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377F PHE* 4.5 4.9 - - + -
390F MET* 3.2 10.2 - - - +
391F CYS* 2.8 63.9 + - - +
393F ARG* 4.0 22.7 - - + +
411F PHE* 1.3 82.3 - - - +
413F VAL* 1.3 75.2 + - - +
414F MET* 4.2 0.4 - - + -
463F MET* 4.0 16.2 - - + -
464F ASN 3.9 16.8 - - - +
465F ILE 5.7 0.2 - - - -
466F ALA* 3.5 22.2 - - + +
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Residues in contact with VAL 413 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388F TYR* 5.4 1.6 - - + -
389F LYS 4.0 5.4 - - - +
390F MET* 4.6 2.5 - - + +
411F PHE* 3.7 24.2 + - + -
412F VAL* 1.3 74.1 - - - +
414F MET* 1.3 62.7 - - - +
424F TRP* 3.8 24.2 - - + -
426F PHE* 4.3 15.0 - - + -
455F SER 3.6 23.6 + - - +
456F PHE* 4.2 13.2 - - + -
457F GLN 4.7 0.2 - - - +
459F PRO* 3.8 20.4 - - + -
464F ASN* 3.0 32.2 + - - +
465F ILE 5.7 0.8 + - - -
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Residues in contact with MET 414 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380F ALA* 3.1 24.5 - - + -
389F LYS* 2.9 46.5 + - + +
390F MET 3.0 31.0 - - - +
391F CYS* 3.5 29.8 - - + -
412F VAL* 4.2 1.8 - - + -
413F VAL* 1.3 80.3 - - - +
415F LYS* 1.3 67.5 + - - +
416F GLY 3.2 3.3 + - - -
419F ASP* 4.1 2.1 - - - +
424F TRP* 5.0 0.7 - - - -
459F PRO* 3.5 11.7 - - - +
462F ASP* 3.5 11.4 - - - +
463F MET* 3.9 23.1 - - + +
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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