Contacts of the helix formed by residues 473 - 482 (chain A) in PDB entry 1SIW
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 473 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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335A ASP* 3.1 28.9 - - - +
336A MET* 3.2 8.5 + - + +
338A MET 3.0 15.5 + - - +
340A VAL* 3.8 11.0 - - + -
354A MET* 3.7 21.1 - - + -
472A THR* 1.3 71.8 - - - +
474A TYR* 1.3 52.5 + - - +
476A LEU* 3.2 8.4 + - - +
477A THR* 2.7 50.4 + - - +
1044A LEU* 4.2 15.9 - - + -
1045A TYR* 3.8 26.7 - - + -
1058A LEU* 4.9 2.5 - - + -
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Residues in contact with TYR 474 (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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314A LEU* 6.0 0.4 - - + -
318A HIS* 4.1 32.3 + + - +
319A LEU* 4.1 10.0 - - - +
330A VAL* 5.1 1.1 - - + -
336A MET* 2.7 56.8 + - + +
417A LEU* 3.4 42.5 - - + +
418A SER* 3.5 37.0 - - - -
472A THR* 3.4 0.2 - - - +
473A VAL* 1.3 77.2 - - - +
475A ASP* 1.3 62.7 + - - +
477A THR* 3.1 5.2 + - - -
478A LEU* 3.1 51.3 + - + +
485A ARG* 4.5 1.8 - - - -
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Residues in contact with ASP 475 (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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418A SER* 2.4 31.7 + - - -
419A LEU* 3.1 23.3 + - - +
455A LEU* 3.4 20.7 - - + +
456A PRO* 3.9 10.9 - - + +
471A THR* 3.5 21.2 + - - +
472A THR* 2.7 24.4 + - - +
474A TYR* 1.3 74.4 - - - +
476A LEU* 1.3 63.4 + - - +
478A LEU* 3.3 3.0 + - - +
479A ALA* 3.0 19.2 + - - +
485A ARG* 2.7 21.5 + - - +
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Residues in contact with LEU 476 (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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340A VAL* 4.0 28.9 - - + -
342A LEU* 4.8 7.2 - - + -
351A ALA* 3.8 26.5 - - + -
429A VAL* 4.9 2.0 - - + -
431A PHE* 3.4 21.3 - - + -
455A LEU* 3.8 22.0 - - + -
471A THR* 3.3 27.6 - - + -
472A THR 3.0 8.3 + - - +
473A VAL* 3.5 9.2 - - - +
475A ASP* 1.3 76.4 - - - +
477A THR* 1.3 56.7 + - - +
479A ALA* 3.6 0.8 + - - -
480A ASN* 3.0 30.0 + - - +
1045A TYR* 4.3 11.7 - - + -
1058A LEU* 3.6 10.3 - - + +
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Residues in contact with THR 477 (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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314A LEU* 4.6 0.9 - - + -
336A MET* 3.8 22.7 - - + -
473A VAL* 2.7 37.5 + - - +
474A TYR 3.4 5.8 - - - -
475A ASP 3.1 0.2 - - - -
476A LEU* 1.3 72.8 - - - +
478A LEU* 1.3 69.2 + - + +
480A ASN* 3.3 5.6 + - - +
481A TYR* 3.1 36.6 + - + -
559A ASN* 5.9 0.4 - - - +
563A PHE* 3.9 20.4 - - + -
1044A LEU* 4.1 9.1 - - + +
1058A LEU* 4.3 12.2 - - + +
1059A LEU* 6.0 0.9 - - + -
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Residues in contact with LEU 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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314A LEU* 4.4 22.2 - - + -
319A LEU* 3.8 31.4 - - + -
336A MET* 4.9 0.2 - - + -
474A TYR* 3.1 46.8 + - + +
475A ASP 3.3 4.2 + - - +
477A THR* 1.3 81.0 - - + +
479A ALA* 1.3 62.4 + - - +
481A TYR* 3.4 2.1 + - - -
482A GLY 3.2 4.2 + - - -
483A LEU* 3.1 39.8 + - + +
485A ARG* 3.5 46.7 - - - +
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Residues in contact with ALA 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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431A PHE* 3.8 7.2 - - + -
453A HIS* 3.2 30.4 + - + -
454A LYS 5.4 1.8 - - - +
455A LEU* 3.8 28.7 - - + -
475A ASP 3.0 16.9 + - - +
476A LEU 3.7 4.5 - - - +
478A LEU* 1.3 74.9 - - - +
480A ASN* 1.3 60.4 + - - +
482A GLY* 2.8 18.9 + - - -
483A LEU 4.9 5.2 - - - +
485A ARG* 5.7 0.8 - - - +
492A CYS* 5.4 2.2 - - - -
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Residues in contact with ASN 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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307A LEU* 5.1 3.0 - - - +
431A PHE* 3.5 30.3 - - + +
432A PRO* 5.3 0.5 - - - +
453A HIS* 4.9 2.7 + - - -
476A LEU 3.0 19.8 + - - +
477A THR* 3.6 5.8 - - - +
479A ALA* 1.3 76.1 - - - +
481A TYR* 1.3 64.1 + - - +
482A GLY 3.5 0.2 + - - -
501A ALA* 3.8 2.9 - - - +
502A TYR* 3.5 21.5 - - - -
1058A LEU* 3.8 17.5 - - + +
1059A LEU* 2.7 44.3 + - - +
1060A VAL* 3.8 13.0 - - - +
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Residues in contact with TYR 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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306A ALA 5.1 0.7 + - - -
307A LEU* 3.2 42.5 - - + +
310A GLY* 3.9 8.7 - - - -
311A HIS* 3.0 39.7 + - + -
314A LEU* 3.7 11.4 - - + -
477A THR* 3.1 39.9 + - + +
479A ALA 3.1 0.4 - - - -
480A ASN* 1.3 81.4 - - - +
482A GLY* 1.3 57.5 + - - +
483A LEU* 3.3 21.1 - - + -
501A ALA 3.3 9.2 - - - +
502A TYR* 3.6 11.9 + - + +
556A GLY* 4.9 2.1 + - - -
559A ASN* 3.2 27.1 + - - +
560A MET* 6.1 0.2 - - - +
563A PHE* 3.7 12.1 - + - -
1059A LEU* 3.4 31.5 - - + +
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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
----------------------------------------------------------
311A HIS* 3.5 11.8 - - - -
453A HIS* 4.5 4.0 - - - -
479A ALA 2.8 16.6 + - - -
480A ASN 3.2 1.0 - - - -
481A TYR* 1.3 79.8 - - - +
483A LEU* 1.3 60.0 + - - +
484A GLU 3.6 0.3 + - - -
491A ASN 4.9 0.9 - - - -
492A CYS* 4.1 14.8 - - - -
493A ALA* 3.1 25.5 + - - +
500A LYS* 5.9 0.4 - - - -
501A ALA 3.6 12.3 - - - -
503A THR* 6.3 0.2 - - - -
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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