Contacts of the strand formed by residues 406 - 414 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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397B ASN* 3.4 2.3 - - - -
398B GLY* 2.7 38.7 + - - -
402B GLY 2.8 8.1 + - - +
405B THR* 1.3 111.5 + - - +
407B LEU* 1.3 56.7 + - - +
470B PRO 3.6 18.4 - - - +
471B LEU* 3.2 46.6 + - + +
473B CYS 3.2 6.2 - - - +
474B PRO* 3.5 36.3 - - + +
475B VAL* 3.4 6.9 - - - +
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Residues in contact with LEU 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361B PHE* 5.4 3.1 - - + -
394B ILE* 3.4 40.4 - - + -
395B TYR 3.8 7.0 - - - +
396B LEU* 4.5 14.8 - - + +
406B HIS* 1.3 70.9 - - - +
408B SER* 1.3 60.4 + - - +
409B LEU* 4.4 2.2 - - + +
434B LEU* 4.4 24.5 - - + -
472B PHE* 3.2 30.1 + - + +
473B CYS* 2.6 40.4 + - + +
474B PRO 5.7 0.4 - - - -
475B VAL* 4.4 3.7 - - + +
478B MET* 4.6 13.7 - - + -
490B ILE* 4.8 11.0 - - + -
492B ILE* 5.4 1.3 - - + -
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Residues in contact with SER 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393B ARG 3.9 0.9 - - - +
394B ILE* 3.4 4.5 - - - +
395B TYR* 2.8 41.2 + - - +
398B GLY* 3.3 3.8 - - - -
399B ASP* 2.9 29.8 + - - -
406B HIS 3.5 0.4 + - - -
407B LEU* 1.3 72.1 - - - +
409B LEU* 1.3 60.5 + - - +
410B PHE* 3.6 22.1 - - - -
469B CYS 3.6 4.7 - - - -
470B PRO* 2.6 26.8 + - - +
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Residues in contact with LEU 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356B TRP* 5.5 0.7 - - + -
392B LEU* 4.3 16.4 - - + -
393B ARG 3.8 7.2 - - - +
394B ILE* 4.7 12.1 - - + -
407B LEU* 3.9 3.7 + - + -
408B SER* 1.3 73.0 - - - +
410B PHE* 1.3 88.2 + - - +
432B LEU* 4.0 27.7 - - + +
468B GLY* 3.9 0.5 - - - -
469B CYS* 2.8 36.7 + - - +
472B PHE* 3.6 43.1 - - + -
492B ILE* 3.7 29.2 - - + -
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Residues in contact with PHE 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392B LEU* 3.4 5.6 - - - +
393B ARG* 2.9 42.5 + - + +
395B TYR* 3.6 26.9 - + - -
399B ASP* 3.6 23.1 - - + -
408B SER* 3.6 28.0 - - - -
409B LEU* 1.3 83.0 - - - +
411B PHE* 1.3 61.0 + - - +
432B LEU* 4.9 2.0 - - - -
466B ALA* 3.6 18.4 - - + -
467B SER* 3.7 5.4 - - - +
468B GLY* 3.4 21.3 - - - -
470B PRO* 4.3 21.8 - - + -
251J VAL 3.6 10.8 - - - -
252J GLN 3.9 2.0 - - - -
253J GLU* 3.4 27.6 - - + -
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Residues in contact with PHE 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381B PHE* 4.6 4.7 - + - -
390B MET* 3.4 47.8 - - + -
391B CYS 4.1 1.1 - - - -
392B LEU* 4.0 15.3 - - + -
410B PHE* 1.3 72.5 - - - +
412B VAL* 1.3 64.4 + - - +
413B VAL* 3.6 24.0 - - + -
426B PHE* 3.7 24.0 - + - -
430B VAL* 4.0 23.1 - - + -
432B LEU* 4.9 2.2 - - + +
447B PHE* 3.9 13.0 - - + -
456B PHE* 4.0 17.3 - + - -
465B ILE 4.7 0.7 - - - +
466B ALA* 3.4 3.8 - - - -
467B SER* 2.8 37.9 + - - +
468B GLY* 4.5 0.6 - - - -
494B ALA* 6.0 0.7 - - + -
496B VAL* 4.0 14.8 - - + -
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Residues in contact with VAL 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377B PHE* 4.4 5.2 - - + -
390B MET* 3.2 9.2 - - - +
391B CYS* 2.9 57.8 + - - +
393B ARG* 4.1 22.0 - - + +
411B PHE* 1.3 81.8 - - - +
413B VAL* 1.3 66.5 + - - +
414B MET* 3.6 3.3 + - + -
463B MET* 3.9 30.7 - - + -
464B ASN 4.1 7.6 - - - +
465B ILE 5.5 0.7 - - - -
466B ALA* 3.7 22.4 - - + +
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Residues in contact with VAL 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388B TYR* 5.4 1.8 - - + -
389B LYS 4.1 6.5 - - - +
390B MET* 4.8 2.0 - - + +
411B PHE* 3.6 26.4 + - + -
412B VAL* 1.3 72.0 - - - +
414B MET* 1.3 63.2 + - - +
424B TRP* 3.8 29.4 - - + -
426B PHE* 4.3 13.7 - - + -
455B SER 3.5 16.9 + - - +
456B PHE* 4.1 13.0 - - + -
459B PRO* 3.9 5.8 - - + -
463B MET* 3.8 0.5 - - - -
464B ASN* 3.0 48.1 + - - +
465B ILE 5.6 0.8 + - - -
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Residues in contact with MET 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380B ALA* 3.1 25.8 - - + -
389B LYS* 3.0 37.7 + - + +
390B MET 3.0 41.3 - - - +
391B CYS* 3.6 17.3 - - + -
412B VAL* 3.6 10.1 + - + +
413B VAL* 1.3 78.4 - - - +
415B LYS* 1.3 65.8 + - - +
416B GLY 3.2 3.8 + - - -
419B ASP* 4.1 1.9 - - - +
424B TRP* 5.0 1.2 - - - -
459B PRO* 3.5 11.3 - - - +
462B ASP* 3.2 12.8 - - - +
463B MET* 3.8 28.3 - - + -
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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