Contacts of the helix formed by residues 479 - 490 (chain A) in PDB entry 3SHW
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 ILE 479 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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441A ASN* 3.9 15.0 - - + +
478A ILE* 1.3 76.0 - - - +
480A ARG* 1.3 68.4 + - - +
481A GLU* 3.8 25.1 - - + +
482A GLU* 3.0 41.1 + - + +
483A ALA* 3.1 10.7 + - - +
517A ASP* 3.4 9.6 - - - +
519A PHE* 3.7 26.0 - - + -
548A THR* 3.9 15.7 - - + +
557A TRP* 4.0 17.7 - - + -
635A ARG* 3.9 19.5 - - - +
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Residues in contact with ARG 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A LEU* 3.8 30.6 + - + -
438A ALA* 4.0 9.9 - - - -
439A GLY 2.8 34.6 + - - +
440A GLY* 4.0 1.0 - - - -
445A ILE* 3.8 13.2 - - + -
478A ILE 3.7 1.0 + - - -
479A ILE* 1.3 70.7 - - - +
481A GLU* 1.3 55.0 + - - +
483A ALA* 3.0 3.3 + - - +
484A VAL* 2.8 37.0 + - + +
516A GLY* 5.6 3.6 - - - -
517A ASP* 3.2 20.8 + - - +
546A VAL 5.6 0.2 + - - -
547A ASP* 2.8 35.4 + - - +
548A THR* 3.5 1.3 + - - +
549A LEU* 3.4 42.5 + - + +
552A GLY* 5.4 2.2 - - - +
1138B VAL* 5.8 0.2 - - - +
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Residues in contact with GLU 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479A ILE* 3.8 6.2 - - + +
480A ARG* 1.3 75.3 - - - +
482A GLU* 1.3 56.6 + - - +
484A VAL* 3.8 5.4 - - - +
485A LEU* 2.9 43.1 + - + +
548A THR* 3.0 37.3 + - - +
549A LEU* 4.6 5.5 - - - +
554A LEU* 4.0 24.3 - - + +
555A GLY 4.1 3.8 + - - -
557A TRP* 3.4 26.6 + - - -
576A ASN* 2.9 32.9 + - - +
577A LYS* 4.9 2.6 + - - +
578A ASN* 5.7 0.3 + - - +
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Residues in contact with GLU 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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478A ILE* 3.4 28.5 - - + +
479A ILE* 3.0 36.9 + - + +
481A GLU* 1.3 79.4 - - - +
483A ALA* 1.3 56.5 + - - +
485A LEU* 3.8 5.2 - - - +
486A PHE* 2.9 31.9 + - - +
635A ARG* 4.9 7.3 + - - -
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Residues in contact with ALA 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A LEU* 4.0 11.2 - - + -
445A ILE* 3.8 20.4 - - + -
475A PHE* 3.6 31.2 - - + -
478A ILE* 3.8 6.7 - - + +
479A ILE 3.1 9.6 + - - +
480A ARG 3.0 8.6 + - - +
482A GLU* 1.3 74.5 - - - +
484A VAL* 1.3 64.9 + - - +
486A PHE* 3.4 1.4 + - - +
487A LEU* 3.1 29.6 + - - +
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Residues in contact with VAL 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A LEU* 3.7 24.9 - - + +
480A ARG* 2.8 23.2 + - + +
481A GLU* 3.8 4.5 - - - +
483A ALA* 1.3 73.2 - - - +
485A LEU* 1.3 58.4 + - + +
487A LEU* 3.3 1.6 + - - +
488A LEU* 3.0 27.1 + - + +
549A LEU* 3.5 30.5 - - + -
554A LEU* 4.9 14.1 - - + -
1138B VAL* 4.2 21.5 - - + +
1140B ILE* 3.8 27.1 - - + +
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Residues in contact with LEU 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A GLU* 2.9 41.5 + - + +
482A GLU* 4.1 4.7 - - - +
484A VAL* 1.3 73.0 - - + +
486A PHE* 1.3 60.6 + - - +
488A LEU* 3.5 15.3 - - + +
489A ASP* 2.9 30.7 + - - +
554A LEU* 4.0 32.3 - - + -
576A ASN* 6.0 0.4 - - - +
578A ASN* 6.3 1.1 - - - +
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Residues in contact with PHE 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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470A VAL* 3.6 32.8 - - + -
471A ASN* 4.5 8.1 - - + -
473A VAL* 3.6 38.4 - - + -
475A PHE* 3.7 21.5 - + + -
478A ILE* 5.0 3.6 - - + -
482A GLU 2.9 21.2 + - - +
483A ALA* 3.7 6.1 - - - +
485A LEU* 1.3 75.8 - - - +
487A LEU* 1.3 64.2 + - - +
489A ASP* 3.3 14.0 + - + +
490A LEU* 3.3 35.5 + - + +
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Residues in contact with LEU 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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429A LYS* 3.3 22.0 - - - -
433A VAL* 4.4 15.3 - - + +
435A LEU* 5.0 5.2 - - + -
437A LEU* 3.6 31.2 - - + -
467A ILE* 5.1 3.4 - - + -
470A VAL* 3.8 36.6 - - + -
475A PHE* 4.2 13.2 - - + -
483A ALA 3.1 18.9 + - - +
484A VAL 3.9 2.7 - - - +
486A PHE* 1.3 77.0 - - + +
488A LEU* 1.3 66.1 + - - +
490A LEU* 3.5 17.4 - - + +
496A VAL* 5.4 0.2 - - + -
498A ILE* 5.2 8.5 - - + -
1140B ILE* 3.7 23.0 - - + +
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Residues in contact with LEU 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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429A LYS* 3.8 4.3 + - - +
431A ASP 5.8 1.6 - - - +
484A VAL* 3.0 18.6 + - + +
485A LEU* 3.5 21.8 - - + +
487A LEU* 1.3 79.1 - - - +
489A ASP* 1.3 61.7 + - - +
490A LEU 3.2 2.9 + - - +
492A LYS* 3.4 27.3 + - - +
554A LEU* 5.3 9.0 - - + -
1140B ILE* 3.6 29.3 - - + +
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Residues in contact with ASP 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A LEU 2.9 19.3 + - - +
486A PHE* 3.7 8.0 - - + +
487A LEU 3.3 0.4 - - - -
488A LEU* 1.3 74.2 - - - +
490A LEU* 1.3 65.9 + - - +
491A PRO* 3.4 5.9 - - - +
492A LYS* 5.3 1.5 + - - +
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Residues in contact with LEU 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A LYS* 3.3 25.4 + - + +
433A VAL* 4.7 4.7 - - + -
470A VAL* 4.4 4.3 - - + -
471A ASN* 4.0 15.3 - - - +
486A PHE* 3.3 41.9 + - + +
487A LEU* 3.5 31.9 - - + +
488A LEU 3.2 3.5 + - - +
489A ASP* 1.3 79.3 - - + +
491A PRO* 1.4 73.3 - - + +
492A LYS* 3.7 5.4 + - - -
495A GLU 5.8 0.2 - - - +
496A VAL* 3.7 40.4 - - + -
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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