Contacts of the helix formed by residues 501 - 517 (chain A) in PDB entry 3LJK
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 501 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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346A GLU* 4.5 18.2 - - + +
498A GLN* 3.4 29.8 - - + +
500A GLY* 1.3 79.3 - - - +
502A GLU* 1.3 68.4 + - + +
503A LEU 3.4 0.6 + - - -
504A GLY* 3.7 4.6 + - - -
505A LYS* 3.6 44.8 + - - +
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Residues in contact with GLU 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 GLN 5.0 2.2 - - - +
499A TRP* 3.3 53.8 + - + +
501A VAL* 1.3 81.8 - - + +
503A LEU* 1.3 64.1 + - - +
505A LYS* 3.1 22.0 + - + +
506A LYS* 3.2 13.2 + - - +
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Residues in contact with LEU 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 TRP 4.7 0.6 + - - -
500A GLY 4.3 7.5 + - - +
501A VAL 3.4 1.0 - - - -
502A GLU* 1.3 78.0 - - - +
504A GLY* 1.3 57.7 + - - +
506A LYS* 3.1 30.2 + - - +
507A LEU* 2.9 58.3 + - + +
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Residues in contact with GLY 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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500A GLY 5.1 1.4 + - - -
501A VAL 3.7 6.6 + - - -
502A GLU 3.3 0.6 - - - -
503A LEU* 1.3 79.0 - - - +
505A LYS* 1.3 54.8 + - - +
507A LEU* 3.9 8.1 - - - +
508A GLY* 3.0 26.3 + - - -
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Residues in contact with LYS 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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203A THR* 5.9 6.8 + - - +
501A VAL* 3.6 37.2 + - - +
502A GLU* 3.1 13.6 + - + +
504A GLY* 1.3 76.0 - - - +
506A LYS* 1.3 62.3 + - - +
508A GLY* 3.4 2.2 + - - -
509A LYS* 3.2 33.1 + - - +
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Residues in contact with LYS 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 GLU 3.2 8.3 + - - +
503A LEU* 3.1 31.1 + - - +
505A LYS* 1.3 79.1 - - - +
507A LEU* 1.3 70.3 + - - +
509A LYS* 3.2 21.2 + - - +
510A ASN* 3.2 25.2 + - - +
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Residues in contact with LEU 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A LEU* 2.9 51.5 + - + +
504A GLY* 4.1 6.5 - - - +
506A LYS* 1.3 82.3 - - - +
508A GLY* 1.3 56.6 + - - +
510A ASN* 3.2 21.3 + - + +
511A ILE* 2.9 42.9 + - + +
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Residues in contact with GLY 508 (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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204A GLU* 6.6 0.4 - - - -
504A GLY 3.0 18.1 + - - -
505A LYS* 3.8 2.5 - - - -
506A LYS 3.2 0.2 - - - -
507A LEU* 1.3 77.2 - - - +
509A LYS* 1.3 55.5 + - - +
511A ILE* 3.4 8.0 + - - +
512A LEU* 3.0 35.4 + - - +
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Residues in contact with LYS 509 (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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204A GLU* 6.6 0.2 - - - -
505A LYS* 3.2 20.2 + - - +
506A LYS* 3.2 12.8 + - - +
508A GLY* 1.3 74.6 - - - +
510A ASN* 1.3 63.9 - - - +
512A LEU* 3.4 12.8 + - + +
513A LYS* 3.1 41.8 + - - +
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Residues in contact with ASN 510 (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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506A LYS* 3.2 23.9 + - - +
507A LEU* 3.2 27.3 + - + +
509A LYS* 1.3 80.7 - - - +
511A ILE* 1.3 59.2 + - + +
513A LYS* 3.2 9.8 + - - +
514A ALA* 3.0 23.3 + - - +
522A GLU* 3.5 30.7 - - + +
526A LEU* 5.6 4.3 - - + -
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Residues in contact with ILE 511 (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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507A LEU* 2.9 30.9 + - + +
508A GLY* 3.9 7.9 - - - +
510A ASN* 1.3 74.8 - - + +
512A LEU* 1.3 58.4 + - - +
514A ALA* 3.2 7.0 + - - +
515A MSE 2.8 47.2 + - - +
526A LEU* 4.1 10.3 - - + -
530A THR* 3.8 28.7 - - + +
534A ILE* 4.1 15.3 - - + -
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Residues in contact with LEU 512 (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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204A GLU* 3.6 24.2 - - - +
508A GLY 3.0 17.2 + - - +
509A LYS* 3.5 15.3 - - + +
511A ILE* 1.3 75.6 - - - +
513A LYS* 1.3 64.4 + - + +
515A MSE 3.3 18.3 + - + +
516A ASN* 3.0 40.4 + - - +
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Residues in contact with LYS 513 (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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509A LYS* 3.1 31.9 + - - +
510A ASN* 3.5 11.9 + - - +
512A LEU* 1.3 80.4 - - + +
514A ALA* 1.3 62.3 + - - +
516A ASN* 3.1 7.6 + - - +
517A ASP* 3.1 25.1 + - - +
520A SER* 4.1 3.9 + - - -
522A GLU* 3.7 35.0 - - + +
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Residues in contact with ALA 514 (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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510A ASN 3.0 13.8 + - - +
511A ILE* 3.2 10.1 + - - +
513A LYS* 1.3 76.7 - - - +
515A MSE 1.3 60.6 + - - +
516A ASN 3.2 0.5 + - - -
517A ASP 3.4 10.2 + - - -
518A ASP* 4.0 1.2 + - - +
520A SER* 3.9 11.4 - - - -
522A GLU* 4.0 2.4 - - - +
523A TYR* 3.6 45.3 - - + +
526A LEU* 4.0 18.6 - - + -
534A ILE* 4.4 2.9 - - + +
538A LYS* 4.4 2.8 + - - -
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Residues in contact with MSE 515 (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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511A ILE* 2.8 38.1 + - - +
512A LEU* 3.6 19.7 - - + +
513A LYS 3.3 0.2 - - - -
514A ALA* 1.3 71.6 - - - +
516A ASN* 1.3 66.0 + - - +
534A ILE* 3.8 29.8 - - + +
537A VAL* 4.4 26.7 - - + -
538A LYS* 2.7 41.5 + - + +
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Residues in contact with ASN 516 (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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512A LEU* 3.0 34.6 + - - +
513A LYS* 3.1 6.9 + - - +
514A ALA 3.1 0.8 - - - -
515A MSE 1.3 83.9 - - - +
517A ASP* 1.3 62.2 + - + +
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Residues in contact with ASP 517 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513A LYS 3.1 9.5 + - - +
514A ALA 3.4 8.0 + - - +
515A MSE 3.5 0.4 - - - -
516A ASN* 1.3 83.6 - - + +
518A ASP* 1.3 59.0 + - - +
519A SER* 2.9 31.4 + - - -
520A SER* 2.6 44.6 + - - -
523A TYR* 3.7 0.5 - - - +
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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