Contacts of the helix formed by residues 493 - 506 (chain A) in PDB entry 1L8A
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 493 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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492A ILE* 1.3 80.5 - - - +
494A THR* 1.3 60.1 + - - +
495A THR* 3.7 2.3 - - - -
496A ILE* 3.2 25.6 + - - +
497A ALA* 3.0 25.1 + - - +
692A LEU* 3.2 22.6 + - - -
693A ASN* 4.3 2.1 - - - -
694A GLU 3.2 25.4 - - - -
695A ASN* 3.1 11.5 + - - +
698A MET* 3.7 6.9 - - - +
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Residues in contact with THR 494 (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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493A SER* 1.3 73.4 - - - +
495A THR* 1.3 55.8 + - - +
497A ALA* 3.5 9.5 - - - +
498A PHE* 2.9 25.1 + - - +
660A PRO* 3.8 13.6 + - - +
661A ALA 3.5 32.3 - - - +
662A TYR 4.0 7.0 - - - -
666A VAL* 3.8 22.5 - - + +
691A THR* 3.5 13.3 - - - +
692A LEU* 2.8 40.1 + - + +
694A GLU 4.9 0.2 + - - -
696A TYR* 4.4 0.2 - - - +
698A MET* 3.9 4.1 - - + +
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Residues in contact with THR 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A SER* 3.1 3.9 + - - -
494A THR* 1.3 78.4 + - - +
496A ILE* 1.3 66.9 + - + +
498A PHE* 3.0 5.5 + - - +
499A VAL* 2.9 23.5 + - + +
525A THR 5.5 0.2 - - - +
526A PHE* 3.6 33.8 - - + +
597A ILE* 3.9 23.1 - - + -
626A GLY* 4.8 2.4 - - - -
627A THR 4.9 0.7 + - - -
691A THR* 3.0 21.5 + - - -
692A LEU 2.6 27.5 + - - -
693A ASN* 5.3 0.9 - - - -
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Residues in contact with ILE 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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491A GLU 5.2 0.4 - - - +
492A ILE* 3.9 20.9 - - + -
493A SER* 3.2 16.8 + - - +
495A THR* 1.3 79.3 - - + +
497A ALA* 1.3 57.6 + - - +
499A VAL* 3.4 9.2 + - + +
500A ARG* 2.9 54.8 + - + +
526A PHE 6.0 0.2 - - - -
527A GLY* 6.3 2.7 - - - -
695A ASN* 3.7 29.8 - - - +
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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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484A LEU* 3.6 15.7 - - + +
492A ILE* 4.6 2.0 - - + -
493A SER 3.0 11.2 + - - +
494A THR* 3.5 11.2 - - - +
496A ILE* 1.3 78.5 - - - +
498A PHE* 1.3 55.7 + - - +
500A ARG* 3.2 3.3 + - - +
501A ALA* 2.9 29.1 + - - +
663A ALA* 3.5 40.4 - - + +
666A VAL* 4.1 10.5 - - + -
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Residues in contact with PHE 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 THR 2.9 15.2 + - - +
495A THR* 3.3 12.8 - - + +
497A ALA* 1.3 77.5 - - - +
499A VAL* 1.3 77.2 + - + +
501A ALA* 3.0 5.0 + - - +
502A LEU* 2.9 38.6 + - + +
528A MET* 3.9 20.2 - - + -
595A PHE* 3.8 27.6 - + + -
597A ILE* 3.7 32.8 - - + -
624A ILE* 3.6 33.2 - - + -
666A VAL* 3.9 13.0 - - + +
670A MET* 3.7 18.8 - - + +
691A THR* 4.2 9.2 - - + -
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Residues in contact with VAL 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495A THR 2.9 18.7 + - - +
496A ILE* 3.7 9.0 - - - +
498A PHE* 1.3 89.3 - - + +
500A ARG* 1.3 64.2 + - + +
502A LEU* 3.1 9.5 + - - +
503A ASN* 3.0 32.4 + - - +
526A PHE 3.6 22.2 - - - +
527A GLY 3.9 17.3 - - - +
528A MET* 4.0 10.5 - - - -
531A LEU* 4.5 19.3 - - + -
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Residues in contact with ARG 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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483A ALA* 6.0 1.6 - - - +
484A LEU* 3.8 23.9 - - + +
488A GLN* 2.6 38.4 + - - +
490A LYS* 4.9 12.7 - - - +
492A ILE* 3.6 31.1 - - - +
496A ILE* 2.9 30.5 + - + +
497A ALA 3.4 8.5 - - - +
499A VAL* 1.3 77.7 - - + +
501A ALA* 1.3 61.8 + - - +
503A ASN* 3.1 13.2 + - - +
504A VAL* 3.1 23.7 + - - +
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Residues in contact with ALA 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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481A PHE* 3.7 18.0 - - + -
484A LEU* 3.6 15.2 - - + +
497A ALA 2.9 14.0 + - - +
498A PHE 3.0 8.3 + - - +
500A ARG* 1.3 76.4 - - - +
502A LEU* 1.3 62.2 + - - +
504A VAL* 3.2 4.6 + - - +
505A MET* 3.1 27.9 + - - +
666A VAL* 5.0 2.2 - - + -
667A ALA* 5.0 2.5 - - - -
670A MET* 3.5 28.0 - - + -
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Residues in contact with LEU 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 PHE* 2.9 43.3 + - + +
499A VAL* 3.1 11.4 + - - +
501A ALA* 1.3 77.7 - - - +
503A ASN* 1.3 56.0 + - - +
505A MET* 3.1 10.5 + - - +
506A LEU* 2.8 40.1 + - + +
515A LEU* 3.4 31.2 - - + -
517A PRO* 4.5 14.8 - - + -
528A MET* 4.4 7.0 - - + -
531A LEU* 3.8 25.6 - - + -
595A PHE* 4.1 21.5 - - + -
670A MET* 4.3 1.7 - - + +
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Residues in contact with ASN 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 VAL* 3.0 30.5 + - - +
500A ARG* 3.4 13.1 - - - +
502A LEU* 1.3 74.5 - - - +
504A VAL* 1.3 64.9 + - + +
506A LEU* 3.1 15.7 + - - +
507A LYS* 3.3 16.9 + - - +
531A LEU* 3.6 10.9 - - - +
534A GLN* 2.7 42.3 + - - +
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Residues in contact with VAL 504 (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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476A PRO* 4.9 3.3 - - + +
480A ASP* 3.3 38.8 - - + +
481A PHE* 3.7 33.0 - - + -
483A ALA* 6.5 0.9 - - + -
484A LEU* 5.1 4.7 - - + -
500A ARG 3.1 14.3 + - - +
501A ALA* 3.2 9.2 + - - +
503A ASN* 1.3 76.9 - - + +
505A MET* 1.3 62.4 + - - +
507A LYS* 3.2 21.8 + - - +
508A ASN* 3.6 6.6 + - - +
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Residues in contact with MET 505 (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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476A PRO* 4.7 2.9 - - + -
481A PHE* 4.1 18.6 - - + -
501A ALA 3.1 10.3 + - - +
502A LEU* 3.1 10.5 + - - +
504A VAL* 1.3 74.2 - - - +
506A LEU* 1.3 55.7 + - - +
507A LYS 3.0 4.9 - - - -
508A ASN* 3.1 27.6 + - - +
511A ILE* 3.9 9.8 - - + +
512A LYS* 3.7 11.8 + - - -
515A LEU* 3.5 14.6 - - + -
595A PHE* 3.5 32.1 - - + -
622A PHE* 5.3 0.2 - - + -
670A MET* 3.6 42.4 - - + +
674A LEU* 3.7 35.0 - - + -
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Residues in contact with LEU 506 (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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502A LEU* 2.8 32.1 + - + +
503A ASN* 3.1 15.0 + - - +
505A MET* 1.3 76.3 - - - +
507A LYS* 1.3 58.6 + - - +
508A ASN 3.4 0.2 - - - -
512A LYS* 3.2 42.8 + - + +
515A LEU* 3.5 23.1 - - + -
531A LEU* 3.7 30.3 - - + -
534A GLN* 4.8 4.7 - - - +
535A ILE* 4.1 28.7 - - + -
563A GLN* 4.2 7.2 - - - +
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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