Contacts of the helix formed by residues 438 - 454 (chain B) in PDB entry 1LDK
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 GLU 438 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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436B ASN 4.1 0.9 + - - +
437B PRO* 1.3 76.4 - - - +
439B GLU* 1.3 70.8 + - - +
440B ALA* 3.5 1.3 - - + +
441B GLU* 2.9 39.3 + - + +
442B LEU 3.1 3.8 + - - -
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Residues in contact with GLU 439 (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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437B PRO* 3.5 5.3 + - - -
438B GLU* 1.3 73.4 - - - +
440B ALA* 1.3 71.9 + - - +
442B LEU* 3.2 6.0 + - - +
443B GLU* 3.1 23.3 + - + +
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Residues in contact with ALA 440 (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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438B GLU* 3.5 1.5 - - + +
439B GLU* 1.3 85.3 - - - +
441B GLU* 1.3 56.0 + - - +
443B GLU* 4.2 8.1 - - - -
444B ASP* 2.4 42.3 + - + +
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Residues in contact with GLU 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B PRO* 5.6 2.0 - - + -
438B GLU* 2.9 38.7 + - + +
440B ALA* 1.3 77.7 - - - +
442B LEU* 1.3 52.3 + - + +
444B ASP* 3.6 4.0 - - - +
445B THR* 2.6 59.7 + - - +
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Residues in contact with LEU 442 (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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429B LEU* 2.9 39.0 - - + +
430B LEU* 3.4 18.4 - - + -
437B PRO* 3.9 28.7 - - + -
438B GLU 3.1 1.8 + - - -
439B GLU* 3.6 7.6 - - - +
441B GLU* 1.3 78.4 - - - +
443B GLU* 1.3 62.4 + - - +
445B THR* 2.8 8.2 + - - -
446B LEU* 2.4 48.9 + - + +
481B SER* 4.5 5.4 - - - -
484B ALA* 3.0 35.9 - - + -
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Residues in contact with GLU 443 (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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439B GLU* 3.1 14.0 + - + +
440B ALA* 3.5 10.1 - - - +
442B LEU* 1.3 82.3 - - - +
444B ASP* 1.5 55.4 + - - +
446B LEU* 3.4 15.4 + - - +
447B ASN* 3.4 21.7 + - - +
484B ALA* 4.9 4.0 - - - +
487B SER* 3.0 27.3 + - - -
491B LYS* 3.6 23.8 + - - -
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Residues in contact with ASP 444 (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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440B ALA* 2.4 36.9 + - + +
441B GLU* 3.6 4.5 - - - +
443B GLU* 1.5 53.7 - - - +
445B THR* 1.3 60.7 + - - +
447B ASN* 3.4 28.3 + - - +
448B GLN* 3.7 8.6 + - - +
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Residues in contact with THR 445 (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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425B TYR* 3.8 15.7 - - + +
429B LEU* 3.2 31.4 - - + -
441B GLU* 2.6 46.3 + - - +
442B LEU* 2.8 13.7 + - - -
444B ASP* 1.3 70.0 - - - +
446B LEU* 1.3 61.4 + - - -
448B GLN* 3.0 37.0 + - - +
449B VAL* 3.4 4.7 + - - +
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Residues in contact with LEU 446 (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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426B CYS* 4.5 10.3 - - - -
429B LEU* 3.9 18.4 - - + -
430B LEU* 4.4 16.8 - - + -
442B LEU* 2.4 74.8 + - + +
443B GLU* 3.7 12.3 - - - +
444B ASP 3.4 0.2 - - - -
445B THR* 1.3 69.3 - - - +
447B ASN* 1.3 68.3 + - - +
449B VAL* 3.1 16.2 + - + +
450B MET* 3.2 15.3 + - - +
484B ALA* 5.9 2.2 - - + +
488B MET* 3.5 37.6 - - + +
491B LYS* 5.5 8.1 - - + -
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Residues in contact with ASN 447 (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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443B GLU* 3.4 22.0 + - - +
444B ASP* 3.4 19.8 + - - +
445B THR 3.2 0.8 - - - -
446B LEU* 1.3 77.5 - - - +
448B GLN* 1.3 63.9 + - - +
450B MET* 2.9 19.7 + - - +
451B VAL* 2.9 14.3 + - - +
454B LYS* 5.4 0.7 + - - -
491B LYS* 4.2 23.3 + - - +
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Residues in contact with GLN 448 (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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368A GLN* 4.4 14.9 + - - +
371A LEU* 3.1 44.2 - - + +
375A LYS* 4.0 16.6 - - - +
425B TYR* 5.2 3.6 + - + -
444B ASP* 3.7 8.4 + - - +
445B THR* 3.0 25.1 + - + +
447B ASN* 1.3 78.3 - - - +
449B VAL* 1.3 66.3 + - + +
451B VAL* 2.7 21.6 + - - +
452B VAL* 2.8 12.3 + - - +
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Residues in contact with VAL 449 (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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371A LEU* 4.9 0.7 - - - -
422B LEU* 3.3 30.0 - - + +
425B TYR* 3.4 36.6 - - + -
426B CYS* 3.7 27.4 - - - -
429B LEU* 4.3 10.3 - - + -
445B THR 3.4 8.9 + - - +
446B LEU* 3.1 11.1 + - + +
448B GLN* 1.3 78.2 - - - +
450B MET* 1.3 59.9 + - + +
452B VAL* 3.0 14.6 - - - +
453B PHE* 2.8 23.4 + - + +
462B PHE* 4.9 2.2 - - + -
488B MET* 5.6 2.5 - - + -
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Residues in contact with MET 450 (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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446B LEU 3.2 11.6 + - - +
447B ASN* 2.9 15.9 + - - +
448B GLN 2.8 0.8 + - - -
449B VAL* 1.3 76.3 - - + +
451B VAL* 1.3 56.3 + - - -
452B VAL 2.9 1.6 - - - -
453B PHE* 2.4 53.3 + - + +
454B LYS* 3.0 47.1 + - + +
462B PHE* 5.9 0.4 - - - -
488B MET* 4.9 5.6 - - - +
491B LYS* 3.0 55.0 - - + +
492B LEU* 3.5 25.1 - - + +
494B GLN 4.8 4.3 - - - +
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Residues in contact with VAL 451 (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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371A LEU* 4.4 12.1 - - + -
374A HIS* 3.5 37.9 - - + +
375A LYS* 5.0 9.6 - - - +
447B ASN 2.9 10.5 + - - +
448B GLN* 2.7 16.2 + - - +
450B MET* 1.3 72.5 - - - +
452B VAL* 1.3 69.8 + - + +
454B LYS* 4.0 16.0 + - + +
455B TYR* 3.6 18.1 - - + -
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Residues in contact with VAL 452 (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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366A TYR* 6.2 2.9 - - + -
367A VAL* 3.9 16.6 - - + +
370A VAL* 5.0 15.5 - - + -
371A LEU* 3.3 42.0 - - + -
403A ILE* 4.4 9.1 - - + +
422B LEU* 3.4 26.7 - - + -
448B GLN 2.8 7.7 + - - +
449B VAL* 3.0 12.1 - - - +
451B VAL* 1.3 83.1 - - + +
453B PHE* 1.3 63.3 + - - +
455B TYR* 3.2 24.7 - - - +
456B ILE* 3.5 9.3 - - + +
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Residues in contact with PHE 453 (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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422B LEU* 3.7 9.4 - - + -
449B VAL 2.8 13.1 + - - +
450B MET* 2.4 58.0 + - + +
452B VAL* 1.3 68.9 - - - +
454B LYS* 1.3 65.8 + - + +
455B TYR 2.3 20.5 + - - -
456B ILE* 2.4 37.1 + - + +
459B LYS* 3.7 33.7 - - + -
462B PHE* 3.7 38.1 - + + -
492B LEU* 4.8 3.8 - - + -
496B CYS* 3.7 39.0 - - + -
500B TYR* 4.2 10.3 - + - -
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Residues in contact with LYS 454 (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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447B ASN* 5.4 0.4 + - - -
450B MET* 3.2 51.5 - - + +
451B VAL* 4.5 10.9 - - + +
452B VAL 3.4 0.2 - - - -
453B PHE* 1.3 83.8 - - + +
455B TYR* 1.3 67.7 + - - +
459B LYS* 3.3 25.1 + - - +
491B LYS* 5.5 1.2 - - - +
494B GLN 6.1 0.4 - - - -
495B ALA* 6.5 0.7 - - + -
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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