Contacts of the helix formed by residues 494 - 503 (chain A) in PDB entry 1SL1
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 GLY 494 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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485A ALA 5.6 0.2 - - - -
489A ALA* 3.7 16.3 - - - +
492A ASP* 2.9 8.2 + - - -
493A ASN* 1.3 76.9 - - - +
495A GLU* 1.3 59.5 + - - +
496A TYR 3.4 2.2 - - - -
497A ALA* 3.3 12.7 + - - +
498A HIS* 2.8 30.5 + - - +
687A ARG* 4.7 7.0 - - - -
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Residues in contact with GLU 495 (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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492A ASP* 3.3 25.2 + - + +
493A ASN 3.4 1.0 + - - -
494A GLY* 1.3 77.4 - - - +
496A TYR* 1.3 65.4 + - - +
498A HIS* 3.1 8.5 + - - +
499A GLU* 3.0 22.7 + - - +
508A LYS* 5.8 4.5 - - - -
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Residues in contact with TYR 496 (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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481A LEU* 3.7 23.8 - - + +
484A LEU* 4.2 7.6 - - + +
485A ALA* 4.1 17.0 - - + +
488A MET* 3.4 38.4 - - + -
492A ASP* 2.7 21.5 + - - +
495A GLU* 1.3 72.8 - - - +
497A ALA* 1.3 63.3 + - - +
499A GLU* 3.3 6.9 + - - +
500A ILE* 3.2 27.1 + - + +
505A ILE* 3.3 22.4 - - + +
508A LYS* 3.8 24.2 - - - +
509A ASN* 2.6 40.0 + - - -
525A ILE* 4.1 7.1 - - - +
555A PHE* 4.3 1.7 - - - -
559A THR* 4.3 9.6 - - + -
562A ILE* 4.9 1.1 - - + -
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Residues in contact with ALA 497 (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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485A ALA* 3.6 21.2 + - + +
494A GLY* 3.3 13.3 + - - +
495A GLU 3.2 0.6 - - - -
496A TYR* 1.3 78.7 - - - +
498A HIS* 1.3 61.8 + - - +
500A ILE* 3.4 1.9 + - - +
501A LEU* 3.3 31.9 + - + +
687A ARG 3.6 24.5 - - - +
688A CYS* 3.7 18.8 - - + -
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Residues in contact with HIS 498 (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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494A GLY 2.8 17.0 + - - +
495A GLU* 3.1 8.5 + - - +
497A ALA* 1.3 75.7 - - - +
499A GLU* 1.3 62.7 + - - +
500A ILE 3.4 0.2 + - - -
501A LEU* 3.4 2.5 + - - -
502A ASN* 2.9 64.3 + - + +
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Residues in contact with GLU 499 (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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495A GLU 3.0 11.9 + - - +
496A TYR* 3.3 10.1 + - - +
498A HIS* 1.3 83.9 - - - +
500A ILE* 1.3 56.1 + - - +
502A ASN 4.9 0.2 - - - -
503A GLY* 2.7 41.3 + - - +
504A ASP* 2.7 34.1 + - - +
505A ILE* 3.8 18.5 + - + +
508A LYS* 3.4 34.1 - - + +
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Residues in contact with ILE 500 (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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481A LEU* 3.7 44.4 - - + +
482A ARG* 4.2 23.7 + - + +
485A ALA* 3.8 18.4 - - + -
496A TYR* 3.2 14.7 + - + +
497A ALA 3.6 6.3 - - - +
498A HIS 3.2 0.4 - - - -
499A GLU* 1.3 79.6 - - - +
501A LEU* 1.3 73.2 + - + +
503A GLY 4.2 5.4 + - - +
505A ILE* 3.9 29.6 + - + +
688A CYS* 4.5 1.3 - - - -
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Residues in contact with LEU 501 (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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482A ARG* 4.1 20.0 - - - +
497A ALA 3.3 19.3 + - - +
498A HIS* 4.1 1.3 - - - +
500A ILE* 1.3 88.8 - - + +
502A ASN* 1.3 75.8 + - - +
503A GLY 3.8 0.2 - - - -
688A CYS* 3.7 19.7 - - - -
689A LEU* 3.2 44.6 - - + +
691A ASP* 5.2 1.8 - - - +
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Residues in contact with ASN 502 (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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498A HIS* 2.9 49.9 + - + +
499A GLU* 4.9 0.2 - - - -
501A LEU* 1.3 91.6 - - - +
503A GLY* 1.3 58.7 + - - +
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Residues in contact with GLY 503 (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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499A GLU* 2.7 32.8 + - - +
500A ILE 4.5 5.2 - - - +
501A LEU 3.8 1.0 - - - -
502A ASN* 1.3 75.3 - - - +
504A ASP* 1.3 61.6 + - - +
505A ILE 4.0 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