Contacts of the strand formed by residues 389 - 395 (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 LYS 389 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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380H ALA* 3.4 24.2 - - + -
381H PHE 3.5 4.0 - - - +
382H TYR* 3.4 37.0 + - + +
387H GLY 3.8 1.2 + - - -
388H TYR* 1.3 71.1 - - - +
390H MET* 1.3 65.9 + - - +
413H VAL* 4.1 3.1 - - - +
414H MET* 3.0 49.7 + - + +
415H LYS 3.9 17.6 + - - +
416H GLY* 3.9 22.2 - - - +
417H PRO* 4.9 3.1 - - + -
419H ASP* 5.3 0.4 + - - -
462H ASP* 5.2 7.7 + - - -
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Residues in contact with MET 390 (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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352H GLY* 5.0 0.4 - - - -
381H PHE* 2.8 64.6 + - + +
382H TYR* 3.5 29.4 - - - -
383H THR* 3.5 23.3 - - + +
388H TYR* 3.7 9.4 - - + +
389H LYS* 1.3 79.2 - - - +
391H CYS* 1.3 58.7 + - - +
411H PHE* 3.4 36.8 - - + -
412H VAL 3.3 12.3 - - - +
413H VAL* 4.9 3.1 - - + -
414H MET* 3.0 13.9 - - - +
426H PHE* 4.2 9.2 - - + -
496H VAL* 3.9 9.2 - - + -
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Residues in contact with CYS 391 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377H PHE* 4.1 7.2 - - - -
378H SER* 3.8 13.9 - - - +
379H PRO 3.7 15.9 - - - +
380H ALA* 4.2 1.1 - - - -
381H PHE* 4.0 5.2 - - - -
390H MET* 1.3 76.7 - - - +
392H LEU* 1.3 77.2 + - - +
411H PHE* 4.3 1.2 - - - -
412H VAL* 2.8 49.6 + - - +
414H MET* 3.6 24.0 - - + -
463H MET* 4.1 13.9 - - - -
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Residues in contact with LEU 392 (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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354H PHE* 4.5 10.8 - - + -
356H TRP* 4.2 14.6 - - + -
377H PHE* 3.3 6.1 - - - -
378H SER* 2.9 36.2 + - - +
381H PHE* 4.4 9.4 - - + -
391H CYS* 1.3 84.4 - - - +
393H ARG* 1.3 63.1 + - - +
409H LEU* 4.1 9.4 - - + -
410H PHE 3.3 11.4 - - - +
411H PHE* 3.9 21.8 - - + -
412H VAL* 4.5 2.0 - - - -
432H LEU* 4.1 17.0 - - + -
492H ILE* 4.0 26.7 - - + -
493H LYS 5.2 0.2 - - - -
494H ALA* 3.9 24.0 - - + +
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Residues in contact with ARG 393 (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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375H ALA* 3.8 26.4 + - + +
376H ILE 3.2 14.6 - - - +
377H PHE* 3.3 49.7 - - + -
392H LEU* 1.3 76.2 - - - +
394H ILE* 1.3 60.4 + - - +
395H TYR* 4.0 8.9 + - + -
409H LEU* 3.7 2.1 - - - -
410H PHE* 2.8 43.8 + - + +
412H VAL* 4.2 9.4 - - + -
466H ALA* 4.6 5.8 - - + -
253P GLU* 3.0 38.0 + - - -
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Residues in contact with ILE 394 (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* 3.5 26.2 - - + -
358H ILE* 4.2 11.7 - - + -
375H ALA* 3.1 2.8 - - - -
376H ILE* 2.9 41.7 + - + +
393H ARG* 1.3 76.9 - - - +
395H TYR* 1.3 64.8 + - - +
396H LEU* 3.8 27.4 + - + -
407H LEU* 3.2 39.0 - - + -
408H SER 3.3 5.8 - - - +
409H LEU* 4.4 8.5 - - + -
490H ILE* 4.8 0.9 - - + -
492H ILE* 4.0 24.5 - - + -
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Residues in contact with TYR 395 (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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374H PRO* 3.1 32.1 - - + +
375H ALA* 3.6 18.6 - - + -
393H ARG* 4.0 11.1 + - - -
394H ILE* 1.3 76.4 - - - +
396H LEU* 1.3 62.7 + - - +
397H ASN 3.0 4.2 + - - -
398H GLY* 3.1 29.7 + - - +
399H ASP* 3.6 27.4 - - + -
407H LEU* 3.7 2.6 - - - +
408H SER* 2.8 26.5 + - - +
410H PHE* 3.5 35.9 - + - -
253P GLU* 2.5 31.1 + - + -
254P THR 3.6 11.6 + - - -
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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