Contacts of the helix formed by residues 474 - 484 (chain D) in PDB entry 1S77
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 PRO 474 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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473D VAL* 1.3 105.3 - - + +
475D PHE* 1.3 67.3 + - - +
476D PRO* 3.3 13.0 - - + -
477D GLU* 3.1 17.5 + - + +
478D ARG* 3.4 7.3 + - - +
565D GLU* 3.6 38.6 - - - +
566D THR* 5.0 4.3 - - - +
567D VAL* 4.0 9.8 - - + +
880D PHE* 3.6 14.8 - - + -
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Residues in contact with PHE 475 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458D TYR* 3.5 24.9 - - - +
459D TRP* 3.7 28.9 - + - -
462D ILE* 3.8 15.7 - - + +
474D PRO* 1.3 72.0 - - - +
476D PRO* 1.3 73.0 - - + +
478D ARG* 2.9 53.7 + - - +
479D ILE* 3.0 17.2 + - - +
825D PHE* 4.3 2.5 - + - -
879D ASP* 3.4 54.7 + - + +
880D PHE* 4.1 4.5 - + - -
882D PHE* 3.8 16.2 - + - -
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Residues in contact with PRO 476 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458D TYR* 5.8 0.7 - - - +
474D PRO* 3.5 12.3 - - + -
475D PHE* 1.3 94.7 - - + +
477D GLU* 1.3 59.5 + - - +
479D ILE* 3.5 9.1 + - + +
480D LYS* 3.1 27.6 + - - +
565D GLU* 6.0 1.1 - - - +
879D ASP* 6.0 0.4 - - - +
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Residues in contact with GLU 477 (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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470D VAL* 4.4 7.4 - - - +
473D VAL* 2.6 49.3 - - + +
474D PRO* 3.1 10.1 + - + +
476D PRO* 1.3 80.4 - - - +
478D ARG* 1.3 58.9 + - - +
480D LYS* 3.7 7.7 - - + +
481D PHE* 3.1 24.4 + - - +
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Residues in contact with ARG 478 (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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461D LYS 5.2 0.2 - - - -
462D ILE* 3.7 12.8 - - + +
465D ALA* 3.4 24.4 - - + +
466D ASN* 2.7 37.1 + - - +
470D VAL* 3.4 22.4 - - - +
471D ASP* 3.0 26.8 + - - +
473D VAL* 2.7 26.3 + - + +
474D PRO 3.4 10.3 - - - +
475D PHE* 2.9 40.5 + - - +
477D GLU* 1.3 75.8 - - - +
479D ILE* 1.3 66.7 + - - +
481D PHE* 3.1 8.4 + - - +
482D ILE* 3.1 18.9 + - - +
567D VAL* 5.0 2.4 - - - +
880D PHE* 3.8 16.4 - - - +
882D PHE* 3.9 11.9 - - - -
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Residues in contact with ILE 479 (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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458D TYR* 3.7 44.4 - - + +
461D LYS* 3.6 20.4 - - + -
462D ILE* 3.5 22.2 - - + -
475D PHE 3.0 14.0 + - - +
476D PRO* 3.8 8.7 - - + +
478D ARG* 1.3 75.3 - - - +
480D LYS* 1.3 60.7 + - - +
482D ILE* 3.1 7.5 + - - +
483D GLU* 2.8 58.4 + - - +
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Residues in contact with LYS 480 (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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476D PRO 3.1 16.9 + - - +
477D GLU* 3.7 11.2 - - + +
479D ILE* 1.3 78.5 - - - +
481D PHE* 1.3 60.9 + - - +
483D GLU* 3.2 33.1 + - - +
484D GLU* 2.8 66.6 + - - +
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Residues in contact with PHE 481 (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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465D ALA* 4.2 5.4 - - - -
468D ALA* 3.5 28.9 - - + -
470D VAL* 3.5 37.7 - - + -
477D GLU* 3.1 12.2 + - - +
478D ARG 3.1 10.2 + - - +
480D LYS* 1.3 82.2 - - - +
482D ILE* 1.3 80.7 + - + +
484D GLU* 3.7 1.6 + - - -
485D ASN* 2.7 54.4 + - - +
501D TRP* 4.2 20.2 - + - -
505D GLN* 4.8 3.4 - - - -
511D PHE* 4.8 0.4 - + - -
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Residues in contact with ILE 482 (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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461D LYS* 3.4 37.5 - - + +
464D GLY 3.8 2.7 - - - +
465D ALA* 3.7 17.3 - - - +
478D ARG 3.1 8.0 + - - +
479D ILE 3.1 7.6 + - - +
481D PHE* 1.3 93.6 - - + +
483D GLU* 1.3 59.8 + - - +
485D ASN* 3.0 17.4 + - - -
486D HIS* 3.0 10.6 + - - -
489D ILE* 3.4 15.0 - - + +
511D PHE* 4.4 2.0 - - + -
514D PHE* 3.5 29.4 - - + -
518D TYR* 3.5 30.5 + - + -
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Residues in contact with GLU 483 (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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461D LYS* 3.6 20.9 + - + -
479D ILE* 2.8 38.2 + - + +
480D LYS* 3.2 35.5 + - - +
482D ILE* 1.3 68.6 - - - +
484D GLU* 1.3 58.7 + - + +
485D ASN 3.0 9.3 + - - -
486D HIS* 3.1 20.2 + - - +
518D TYR* 4.7 8.5 - - - +
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Residues in contact with GLU 484 (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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480D LYS* 2.8 52.0 + - + +
481D PHE* 3.8 2.7 - - - +
483D GLU* 1.3 77.1 - - + +
485D ASN* 1.3 65.4 + - - +
486D HIS 3.5 0.4 - - - -
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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