Contacts of the strand formed by residues 467 - 474 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410D PHE* 3.6 5.6 - - - -
411D PHE* 2.9 32.5 + - - +
447D PHE* 3.9 2.8 - - - -
453D SER* 5.5 0.4 - - - -
455D SER* 3.5 12.4 - - - -
456D PHE* 3.0 36.0 - - - -
465D ILE 3.8 0.4 + - - -
466D ALA* 1.3 75.8 - - - +
468D GLY* 1.3 59.3 + - - +
250L PRO* 4.0 8.3 - - - -
251L VAL 3.2 16.6 - - - -
252L GLN* 3.7 11.0 - - - -
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Residues in contact with GLY 468 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409D LEU 3.7 8.3 - - - -
410D PHE* 3.2 5.0 - - - -
411D PHE 4.5 0.2 - - - -
432D LEU* 4.9 0.7 - - - -
447D PHE* 3.8 18.6 - - - -
467D SER* 1.3 75.8 - - - +
469D CYS* 1.3 64.9 + - - -
470D PRO* 3.7 4.3 - - - +
448H ARG* 5.8 1.6 + - - -
249L ACE 4.7 1.2 - - - +
250L PRO* 3.7 5.3 - - - +
251L VAL* 2.8 34.0 + - - +
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Residues in contact with CYS 469 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409D LEU 2.9 27.6 + - - +
410D PHE* 4.2 2.2 - - - -
432D LEU* 4.2 20.6 - - - -
445D ASP* 3.6 36.3 - - - +
447D PHE* 4.6 11.0 - - - -
468D GLY* 1.3 78.4 - - - -
470D PRO* 1.3 68.5 - - - +
471D LEU 3.1 2.2 - - - +
472D PHE* 3.2 28.7 + - + +
448H ARG* 5.0 8.5 - - - +
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Residues in contact with PRO 470 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399D ASP* 3.8 14.8 - - - +
400D GLY* 5.3 0.4 - - - -
401D THR* 3.4 24.5 - - + +
402D GLY* 3.6 11.4 - - - -
406D HIS* 3.8 2.9 - - - +
408D SER* 2.6 30.9 + - - +
410D PHE* 4.1 13.2 - - + -
468D GLY 3.7 9.9 - - - +
469D CYS* 1.3 83.0 - - - +
471D LEU* 1.3 61.9 + - + +
472D PHE 3.4 1.3 + - - -
251L VAL* 3.8 33.2 - - + -
252L GLN 5.9 0.2 - - - +
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Residues in contact with LEU 471 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401D THR* 3.4 42.6 - - - +
402D GLY* 3.5 13.9 - - - -
406D HIS* 3.6 36.4 + - + +
469D CYS* 3.1 3.0 - - - +
470D PRO* 1.3 80.4 - - + +
472D PHE* 1.3 63.9 + - - +
473D CYS 3.4 2.9 + - - -
474D PRO* 5.5 0.3 - - - +
429H LYS* 5.8 1.0 + - - -
448H ARG* 5.1 16.5 + - - +
499H THR* 4.8 22.0 - - + +
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Residues in contact with PHE 472 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407D LEU* 3.4 21.6 + - + +
409D LEU* 3.7 31.4 - - + +
432D LEU* 3.5 33.7 - - + -
433D MET* 3.7 14.6 - - - -
434D LEU* 3.8 24.5 - - + -
443D VAL* 3.8 22.8 - - + +
444D ILE 4.3 2.5 - - - -
445D ASP* 4.1 22.9 - - + -
469D CYS* 3.2 34.1 + - + +
470D PRO 3.4 1.2 - - - -
471D LEU* 1.3 77.8 - - - +
473D CYS* 1.3 67.9 + - + +
474D PRO* 4.7 0.9 - - - +
492D ILE* 5.3 0.7 - - + -
429H LYS* 4.9 9.7 + - - +
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Residues in contact with CYS 473 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406D HIS* 3.2 5.4 - - - -
407D LEU* 2.6 44.9 + - + +
434D LEU* 3.9 12.1 - - + -
443D VAL* 4.3 16.2 - - + -
471D LEU 3.4 1.2 + - - -
472D PHE* 1.3 95.5 - - + +
474D PRO* 1.3 79.1 - - - +
477D LYS* 4.4 5.2 - - - -
478D MET* 3.4 34.5 - - - -
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Residues in contact with PRO 474 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405D THR 3.7 8.1 - - - +
406D HIS* 3.7 22.2 - - + +
471D LEU 5.5 0.4 - - - +
472D PHE 4.7 1.1 - - - +
473D CYS* 1.3 99.7 - - - +
475D VAL* 1.3 66.1 + - - +
476D SER* 3.1 16.6 + - - +
477D LYS* 3.2 28.6 + - + +
478D MET* 3.7 2.9 + - - +
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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