Contacts of the strand formed by residues 467 - 474 (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 SER 467 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410H PHE* 3.6 4.0 - - - -
411H PHE* 2.8 35.3 + - - +
447H PHE* 4.1 2.9 - - - -
453H SER* 5.2 0.5 + - - -
455H SER* 3.6 25.3 - - - -
456H PHE* 4.0 14.7 - - - -
465H ILE 3.5 0.6 + - - -
466H ALA* 1.3 76.1 - - - +
468H GLY* 1.3 58.4 + - - +
250P PRO* 3.0 23.2 + - - +
251P VAL 3.4 14.9 + - - -
252P GLN* 3.7 4.8 + - - +
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Residues in contact with GLY 468 (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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429D LYS* 5.6 2.3 + - - -
409H LEU 3.9 5.2 - - - -
410H PHE* 3.3 6.9 - - - -
432H LEU* 5.2 0.2 - - - -
447H PHE* 4.0 16.4 - - - -
467H SER* 1.3 77.8 + - - +
469H CYS* 1.3 64.0 + - - -
470H PRO* 3.5 6.6 - - - +
249P ACE 4.8 0.5 - - - +
250P PRO* 3.6 7.2 - - - +
251P VAL* 2.7 36.5 + - - +
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Residues in contact with CYS 469 (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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429D LYS* 5.5 4.9 - - - -
409H LEU 2.9 35.0 + - - +
410H PHE* 4.2 2.4 - - - -
432H LEU* 4.1 20.4 - - - -
445H ASP* 3.5 32.1 - - - +
446H ALA 5.3 1.3 - - - -
447H PHE* 4.3 13.5 - - - -
468H GLY* 1.3 76.8 - - - -
470H PRO* 1.3 67.3 - - - +
471H LEU 3.2 1.8 - - - +
472H PHE* 3.3 25.6 + - + +
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Residues in contact with PRO 470 (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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399H ASP* 4.0 12.1 - - - +
400H GLY* 5.7 0.2 - - - -
401H THR* 3.3 25.1 - - - +
402H GLY* 3.7 11.3 - - - -
406H HIS* 3.8 3.3 - - - +
408H SER* 2.5 30.5 + - - +
410H PHE* 4.1 14.8 - - + -
468H GLY 3.5 10.1 - - - +
469H CYS* 1.3 84.2 - - - +
471H LEU* 1.3 60.7 + - + +
472H PHE 3.4 1.7 + - - -
251P VAL* 3.8 32.8 - - + -
252P GLN 5.1 0.9 - - - +
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Residues in contact with LEU 471 (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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401H THR* 3.7 21.8 - - - +
402H GLY* 3.6 22.0 - - - +
406H HIS* 3.6 42.9 + - + +
445H ASP* 5.4 1.8 - - - +
469H CYS* 3.2 2.4 - - - -
470H PRO* 1.3 80.5 - - + +
472H PHE* 1.3 63.2 + - - +
473H CYS 3.4 2.8 + - - -
474H PRO* 5.5 0.5 - - - +
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Residues in contact with PHE 472 (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* 3.4 19.5 + - + +
409H LEU* 4.0 29.2 - - + +
432H LEU* 3.5 42.2 - - + -
433H MET* 3.8 11.9 - - - -
434H LEU* 3.9 24.9 - - + -
443H VAL* 3.7 21.9 - - + +
445H ASP* 4.0 22.9 - - + +
469H CYS* 3.3 34.2 + - + +
470H PRO 3.4 1.6 - - - -
471H LEU* 1.3 78.6 - - - +
473H CYS* 1.3 67.0 + - + +
474H PRO* 4.7 1.1 - - - +
492H ILE* 5.1 3.4 - - + -
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Residues in contact with CYS 473 (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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406H HIS* 3.2 4.5 - - - -
407H LEU* 2.7 42.4 + - + +
434H LEU* 3.6 27.8 - - + -
443H VAL* 4.2 16.8 - - + -
471H LEU 3.4 1.4 - - - -
472H PHE* 1.3 94.9 - - + +
474H PRO* 1.3 84.1 - - - +
477H LYS* 4.5 5.4 - - - -
478H MET* 4.0 14.4 - - - -
484H TYR* 6.0 0.2 - - - -
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Residues in contact with PRO 474 (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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405H THR 3.7 3.4 - - - +
406H HIS* 3.4 28.9 - - + +
471H LEU 5.5 0.4 - - - +
472H PHE 4.7 0.9 - - - +
473H CYS* 1.3 90.1 - - - +
475H VAL* 1.3 66.7 + - - +
476H SER* 3.1 13.7 - - - +
477H LYS* 3.0 37.0 + - + +
478H MET* 3.8 3.5 + - - +
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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