Contacts of the helix formed by residues 493 - 506 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492B ILE* 1.3 80.2 - - - +
494B THR* 1.3 64.2 + - - +
495B THR* 3.6 2.4 - - - -
496B ILE* 3.0 27.6 + - - +
497B ALA* 3.1 19.9 + - - +
692B LEU 3.2 21.2 + - - -
693B ASN* 4.2 2.7 - - - -
694B GLU 3.3 24.9 - - - -
695B ASN* 3.0 10.3 + - - -
698B MET* 3.6 6.2 - - - +
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Residues in contact with THR 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493B SER* 1.3 73.4 - - - +
495B THR* 1.3 58.2 + - - +
497B ALA* 3.4 9.3 - - - +
498B PHE* 2.9 24.9 + - - +
660B PRO* 3.8 13.1 + - - +
661B ALA 3.4 33.9 - - - +
662B TYR 4.1 2.5 - - - +
666B VAL* 3.8 23.6 - - + +
691B THR* 3.5 12.2 - - - +
692B LEU* 2.8 39.8 + - + +
694B GLU 4.7 0.2 + - - -
696B TYR* 5.5 0.2 + - - -
698B MET* 3.8 7.8 - - + +
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Residues in contact with THR 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493B SER* 3.1 4.1 + - - -
494B THR* 1.3 76.8 - - - +
496B ILE* 1.3 66.8 + - + +
497B ALA 3.1 0.2 - - - -
498B PHE* 3.1 6.0 + - + +
499B VAL* 3.0 22.4 + - - +
525B THR 5.5 0.4 - - - +
526B PHE* 3.5 34.0 - - + +
597B ILE* 3.9 22.4 - - + -
626B GLY* 4.7 2.8 - - - -
627B THR 4.8 1.0 + - - -
691B THR* 2.8 22.6 + - - -
692B LEU 2.6 27.1 + - - -
693B ASN* 5.3 0.9 - - - -
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Residues in contact with ILE 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490B LYS* 4.3 12.1 - - - +
492B ILE* 3.8 20.4 - - + -
493B SER* 3.0 21.7 + - - +
495B THR* 1.3 77.4 - - + +
497B ALA* 1.3 58.3 + - - +
499B VAL* 3.3 7.8 + - + +
500B ARG* 3.0 53.6 + - + +
526B PHE 5.9 0.2 - - - -
527B GLY* 6.2 4.5 - - - -
695B ASN* 3.6 26.5 - - - +
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Residues in contact with ALA 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484B LEU* 3.9 7.5 - - + +
492B ILE* 4.5 5.2 - - + -
493B SER 3.1 11.9 + - - +
494B THR* 3.4 12.1 - - - +
495B THR 3.1 0.2 - - - -
496B ILE* 1.3 74.7 - - - +
498B PHE* 1.3 60.5 + - - +
500B ARG* 3.3 8.8 + - - +
501B ALA* 2.9 28.4 + - - +
663B ALA* 3.5 43.1 - - + +
666B VAL* 4.2 7.3 - - + +
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Residues in contact with PHE 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494B THR 2.9 14.3 + - - +
495B THR* 3.1 13.2 + - + +
497B ALA* 1.3 77.2 - - - +
499B VAL* 1.3 69.5 + - + +
501B ALA* 3.1 3.1 + - - +
502B LEU* 2.9 38.9 + - + +
528B MET* 4.0 20.0 - - + -
595B PHE* 3.8 27.6 - + + -
597B ILE* 3.7 33.7 - - + -
624B ILE* 3.7 34.8 - - + -
666B VAL* 3.9 14.6 - - + +
670B MET* 3.6 19.1 - - + -
691B THR* 4.3 7.6 - - + -
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Residues in contact with VAL 499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495B THR 3.0 18.4 + - - +
496B ILE* 3.8 8.5 - - - +
498B PHE* 1.3 82.9 - - + +
500B ARG* 1.3 64.8 + - + +
502B LEU* 3.2 8.5 + - - +
503B ASN* 3.0 31.9 + - - +
526B PHE 3.6 21.8 - - - +
527B GLY 3.9 16.2 - - - +
528B MET* 3.8 19.3 - - - -
530B GLY* 6.6 0.2 - - - -
531B LEU* 4.4 17.5 - - + -
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Residues in contact with ARG 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484B LEU* 3.8 23.6 - - + +
488B GLN* 2.6 33.1 + - - +
489B SER 5.9 0.6 - - - +
490B LYS* 4.8 10.7 - - - +
492B ILE* 3.8 28.3 - - - +
496B ILE* 3.0 39.6 + - + +
497B ALA* 3.6 6.1 - - - +
499B VAL* 1.3 77.0 - - + +
501B ALA* 1.3 62.2 + - - +
503B ASN* 3.3 11.5 + - - +
504B VAL* 3.2 23.7 + - - +
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Residues in contact with ALA 501 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481B PHE* 3.5 16.1 - - + -
484B LEU* 3.7 17.0 - - + +
497B ALA 2.9 12.4 + - - +
498B PHE 3.1 8.5 + - - +
500B ARG* 1.3 74.4 - - - +
502B LEU* 1.3 66.0 + - - +
504B VAL* 3.1 13.7 + - - +
505B MET* 3.2 16.9 + - - +
666B VAL* 4.9 2.5 - - + -
667B ALA* 5.0 2.0 - - - -
670B MET* 3.4 28.7 - - + -
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Residues in contact with LEU 502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498B PHE* 2.9 39.2 + - + +
499B VAL* 3.3 10.5 - - - +
501B ALA* 1.3 76.4 - - - +
503B ASN* 1.3 57.2 + - - +
505B MET* 3.2 11.4 + - - +
506B LEU* 2.9 37.4 + - + +
515B LEU* 4.6 8.5 - - + -
517B PRO* 4.6 14.1 - - + -
528B MET* 4.3 7.9 - - + -
531B LEU* 3.9 27.4 - - + -
595B PHE* 3.6 46.9 - - + -
670B MET* 4.3 0.8 - - - +
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Residues in contact with ASN 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499B VAL* 3.0 22.0 + - - +
500B ARG* 3.4 13.3 - - - +
501B ALA 3.1 0.4 - - - -
502B LEU* 1.3 74.9 - - - +
504B VAL* 1.3 65.1 + - + +
506B LEU* 3.3 15.0 + - - +
507B LYS* 3.4 29.4 + - - +
531B LEU* 3.3 19.8 - - - +
534B GLN* 3.3 34.6 + - - +
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Residues in contact with VAL 504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476B PRO* 4.6 3.1 - - + +
480B ASP* 3.4 37.2 - - + +
481B PHE* 3.5 38.6 - - + -
483B ALA* 6.4 1.8 - - + -
484B LEU* 4.9 7.6 - - + -
500B ARG 3.2 14.6 + - - +
501B ALA* 3.1 9.2 + - - +
503B ASN* 1.3 75.8 - - - +
505B MET* 1.3 64.6 + - - +
507B LYS* 3.1 22.0 + - - +
508B ASN* 3.6 5.7 + - - +
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Residues in contact with MET 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476B PRO* 4.5 2.2 - - + -
481B PHE* 3.9 22.9 - - + -
501B ALA 3.2 8.7 + - - +
502B LEU* 3.4 12.1 - - - +
504B VAL* 1.3 74.2 - - - +
506B LEU* 1.3 55.6 + - - +
507B LYS 3.0 5.4 - - - -
508B ASN* 3.0 30.1 + - - +
511B ILE* 3.9 10.8 - - + +
512B LYS* 3.8 6.2 - - - -
515B LEU* 3.6 15.9 - - + -
595B PHE* 3.5 32.3 - - + -
670B MET* 3.7 41.3 - - + +
674B LEU* 3.7 32.3 - - + -
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Residues in contact with LEU 506 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502B LEU* 2.9 24.7 + - + +
503B ASN* 3.6 12.3 - - - +
504B VAL 3.2 0.6 - - - -
505B MET* 1.3 74.2 - - - +
507B LYS* 1.3 60.1 + - + +
508B ASN 3.5 0.2 - - - -
512B LYS* 3.4 38.7 + - + +
515B LEU* 3.3 21.1 - - + -
517B PRO* 5.7 1.3 - - + -
531B LEU* 3.7 31.6 - - + -
534B GLN* 4.1 6.7 - - - +
535B ILE* 4.1 33.2 - - + -
563B GLN* 4.0 11.0 - - - +
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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