Contacts of the helix formed by residues 477 - 488 (chain A) in PDB entry 1P9W
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 477 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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445A HIS 4.7 0.4 - - - -
446A GLU* 3.5 9.0 - - - -
472A ARG* 3.3 31.2 - - - +
476A PRO* 1.3 74.9 - - - +
478A ILE* 1.3 67.6 + - - +
479A ARG* 3.5 15.8 + - - +
480A ASP* 2.6 35.1 + - - +
481A ASP* 3.0 20.4 + - - +
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Residues in contact with ILE 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361A ASN 4.3 14.1 - - - +
362A THR* 5.0 7.2 - - + -
389A ALA* 4.2 18.2 - - + +
390A GLN* 4.8 2.5 - - - +
391A ARG* 3.2 42.6 - - + +
444A ILE* 3.9 27.5 - - + +
445A HIS* 3.7 29.6 - - - +
446A GLU* 3.2 21.8 + - + +
477A SER* 1.3 73.7 - - - +
479A ARG* 1.3 57.7 + - - +
481A ASP* 3.3 2.9 + - - +
482A GLY* 2.9 25.1 + - - -
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Residues in contact with ARG 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391A ARG* 4.8 3.4 - - - +
413A LEU* 4.3 16.0 + - - +
477A SER* 3.1 13.6 + - - +
478A ILE* 1.3 80.7 - - - +
480A ASP* 1.3 59.8 + - - +
482A GLY* 3.1 3.3 + - - -
483A LEU* 2.7 62.0 + - + +
496A VAL* 4.2 6.5 - - + +
497A MSE 4.3 25.3 - - - +
500A SER* 3.7 32.3 - - - +
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Residues in contact with ASP 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472A ARG* 5.3 2.3 + - - -
476A PRO* 4.0 16.8 - - + +
477A SER* 2.6 36.2 + - - +
479A ARG* 1.3 84.9 + - - +
481A ASP* 1.3 64.3 + - - +
483A LEU* 3.3 16.4 + - - +
484A ASP* 2.9 31.6 + - - +
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Residues in contact with ASP 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A GLY 5.2 0.3 - - - +
242A THR* 3.0 33.5 - - - +
245A ASN* 3.9 5.3 + - - -
443A GLY 4.5 0.7 - - - +
444A ILE* 3.2 13.6 - - + +
445A HIS* 2.8 47.8 + - - +
476A PRO* 5.1 3.9 - - + +
477A SER 3.0 8.5 + - - +
478A ILE 3.3 9.0 - - - +
480A ASP* 1.3 77.5 - - - +
482A GLY* 1.3 62.0 + - - +
484A ASP* 3.3 23.3 + - - +
485A LYS* 3.4 13.5 + - - +
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Residues in contact with GLY 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444A ILE* 3.7 18.2 - - - +
478A ILE 2.9 16.7 + - - -
479A ARG 3.1 3.3 + - - -
481A ASP* 1.3 72.9 - - - +
483A LEU* 1.3 60.7 + - - +
485A LYS* 3.0 7.8 + - - +
486A VAL* 3.0 22.3 + - - +
496A VAL* 3.6 25.9 - - - +
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Residues in contact with LEU 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413A LEU* 3.6 29.2 - - + +
414A PHE* 3.5 26.2 - - + -
479A ARG* 2.7 54.0 + - + +
480A ASP* 3.3 13.0 + - - +
482A GLY* 1.3 68.1 - - - +
484A ASP* 1.3 66.5 + - - +
486A VAL* 3.3 6.0 + - + +
487A ARG* 3.0 19.4 + - - +
493A LEU* 3.5 31.4 - - + -
496A VAL* 4.0 10.3 - - + +
497A MSE 4.5 4.5 - - - -
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Residues in contact with ASP 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A THR* 5.4 6.6 - - + +
480A ASP* 2.9 20.2 + - - +
481A ASP* 3.4 16.2 - - - +
482A GLY 3.2 0.2 - - - -
483A LEU* 1.3 76.9 - - - +
485A LYS* 1.3 58.8 + - + +
487A ARG* 3.2 15.1 - - - +
488A GLN* 2.8 43.2 + - - +
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Residues in contact with LYS 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A GLY* 2.8 31.4 + - - -
242A THR* 5.3 7.4 - - + -
393A VAL* 5.7 0.7 - - + -
442A THR* 3.3 31.5 + - + +
443A GLY 3.0 18.9 + - - -
444A ILE* 4.2 11.0 - - + -
481A ASP* 3.6 18.2 - - - +
482A GLY* 3.0 9.1 + - - +
484A ASP* 1.3 77.6 - - + +
486A VAL* 1.3 61.1 + - - +
488A GLN* 3.3 13.1 + - - +
489A GLY 3.2 2.8 + - - -
490A ILE* 2.9 52.3 + - + +
491A THR* 3.6 10.3 + - + -
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Residues in contact with VAL 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414A PHE* 3.9 19.3 - - + -
424A LEU* 4.2 19.5 - - + +
425A TYR 5.1 1.0 + - - +
482A GLY 3.0 15.3 + - - +
483A LEU* 3.3 11.9 + - - +
485A LYS* 1.3 73.4 - - - +
487A ARG* 1.3 58.6 + - - +
489A GLY* 2.6 28.2 + - - -
491A THR* 3.5 13.3 - - + +
492A SER* 3.5 22.9 - - - +
493A LEU* 3.9 30.3 - - + +
496A VAL* 3.7 15.3 - - + -
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Residues in contact with ARG 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414A PHE* 4.0 35.9 + - + +
422A LEU* 3.7 32.9 - - + +
423A ILE 4.2 11.8 - - - +
424A LEU* 4.2 10.5 - - - -
483A LEU 3.0 12.7 + - - +
484A ASP* 3.2 19.1 - - - +
486A VAL* 1.3 77.7 - - - +
488A GLN* 1.3 63.3 + - + +
489A GLY* 3.2 1.2 + - - -
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Residues in contact with GLN 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401A LYS* 5.2 2.3 + - - -
425A TYR* 5.6 1.5 - - - -
484A ASP* 2.8 37.2 + - - +
485A LYS* 3.7 12.8 - - - +
486A VAL 3.1 1.2 - - - -
487A ARG* 1.3 78.1 - - + +
489A GLY* 1.3 61.7 + - - +
490A ILE* 3.4 27.6 + - + +
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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