Contacts of the strand formed by residues 430 - 434 (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 VAL 430 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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411H PHE* 4.0 27.1 - - + -
426H PHE* 4.2 16.2 - - + -
428H GLN 3.7 9.2 - - - +
429H LYS* 1.3 81.2 - - - +
431H THR* 1.3 64.8 + - - +
432H LEU* 3.9 23.7 + - + -
446H ALA* 3.2 4.7 - - - +
447H PHE* 3.0 68.2 + - + -
494H ALA* 5.6 0.9 - - + -
495H ILE 3.6 4.7 - - - +
496H VAL* 4.4 6.5 - - + -
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Residues in contact with THR 431 (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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444D ILE 5.1 0.4 + - - +
429H LYS* 3.9 14.6 + - - +
430H VAL* 1.3 76.5 - - - +
432H LEU* 1.3 65.6 + - - +
433H MET* 3.9 15.5 - - + -
444H ILE* 3.4 33.9 - - + -
445H ASP 3.6 6.7 - - - +
446H ALA* 3.7 11.1 - - + +
493H LYS 3.9 0.3 - - - +
494H ALA* 3.3 5.5 - - - +
495H ILE* 2.8 52.5 + - + +
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Residues in contact with LEU 432 (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* 4.1 17.5 - - + -
409H LEU* 3.9 42.0 - - + +
410H PHE 5.0 5.2 - - - -
411H PHE* 5.0 0.7 - - + +
430H VAL* 3.9 17.0 - - + +
431H THR* 1.3 82.1 - - - +
433H MET* 1.3 66.0 + - - +
444H ILE* 3.5 1.7 - - - -
445H ASP 2.9 35.5 + - - +
447H PHE* 4.2 15.5 - - + -
469H CYS* 4.1 18.2 - - - -
472H PHE* 3.5 17.2 - - + -
493H LYS 3.5 1.6 - - - +
494H ALA* 4.0 17.3 - - + -
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Residues in contact with MET 433 (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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441D GLU* 6.3 2.7 - - + -
409H LEU* 4.9 0.4 - - - +
431H THR* 3.9 13.0 - - + -
432H LEU* 1.3 81.4 - - - +
434H LEU* 1.3 61.2 + - - +
435H LEU* 3.9 20.0 - - + -
442H HIS* 5.5 8.5 - - + -
443H VAL 3.2 7.4 - - - +
444H ILE* 3.5 33.7 - - + -
472H PHE* 3.8 5.6 - - - -
492H ILE* 3.3 10.9 - - - +
493H LYS* 2.7 62.6 + - + +
495H ILE* 4.0 17.7 - - + -
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Residues in contact with LEU 434 (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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407H LEU* 5.0 5.4 - - + -
433H MET* 1.3 72.5 - - - +
435H LEU* 1.3 64.8 + - - +
436H ASP 3.7 0.3 + - - -
442H HIS* 3.8 0.9 - - - +
443H VAL* 2.9 40.3 + - + -
472H PHE* 3.9 12.7 - - + -
473H CYS* 3.6 32.5 - - + -
478H MET* 4.1 20.4 - - + -
484H TYR* 3.9 27.1 - - + -
490H ILE* 4.2 20.2 - - + -
491H PHE 3.7 7.9 - - - +
492H ILE* 3.8 20.4 - - + -
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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