Contacts of the helix formed by residues 523 - 535 (chain B) in PDB entry 3LLK
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 ASP 523 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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511B ALA 3.7 13.2 - - - +
512B CYS 2.8 16.8 + - - +
514B ASN* 3.7 22.5 - - - +
522B TRP* 1.3 69.8 - - - +
524B VAL* 1.3 57.4 + - - +
525B GLU* 3.2 16.3 + - - +
526B ALA* 2.9 25.1 + - - +
527B THR* 2.9 28.8 + - - -
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Residues in contact with VAL 524 (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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475B LEU* 3.5 30.4 - - + +
478B TRP* 5.1 10.1 - - + -
520B PRO* 6.1 2.5 - - + -
522B TRP* 3.5 15.1 + - + +
523B ASP* 1.3 71.8 + - - +
525B GLU* 1.3 62.4 + - + +
527B THR* 3.7 6.1 - - - -
528B LEU* 2.9 27.8 + - + +
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Residues in contact with GLU 525 (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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523B ASP* 3.2 10.1 + - - +
524B VAL* 1.3 79.7 - - + +
526B ALA* 1.3 64.8 + - - +
528B LEU* 3.1 9.4 + - - +
529B ASN* 3.1 30.6 + - - +
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Residues in contact with ALA 526 (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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509B CYS* 4.9 0.5 - - - -
511B ALA* 3.4 39.5 - - + +
512B CYS* 4.1 2.9 - - - +
523B ASP* 2.9 20.8 + - - +
525B GLU* 1.3 76.6 - - - +
527B THR* 1.3 57.8 + - - +
529B ASN* 3.3 12.8 + - - +
530B PHE* 2.9 27.4 + - - +
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Residues in contact with THR 527 (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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475B LEU* 4.6 1.3 - - + -
478B TRP* 3.5 41.1 - - + +
504B PRO* 4.8 4.7 - - + -
512B CYS* 3.5 33.1 + - - +
522B TRP* 3.8 7.3 - - - +
523B ASP 2.9 19.7 + - - -
524B VAL* 3.7 8.5 - - - -
526B ALA* 1.3 75.6 - - - +
528B LEU* 1.3 59.6 + - - +
530B PHE* 3.3 1.8 + - + +
531B LEU* 2.9 39.1 + - + +
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Residues in contact with LEU 528 (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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471B ASN* 3.9 41.7 - - + +
474B VAL* 4.1 24.7 - - + -
475B LEU* 4.2 19.0 - - + +
524B VAL* 2.9 18.9 + - + +
525B GLU* 3.1 7.8 + - - +
527B THR* 1.3 75.0 - - - +
529B ASN* 1.3 67.6 + - - +
531B LEU* 3.3 3.5 + - - +
532B LYS* 3.0 46.2 + - + +
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Residues in contact with ASN 529 (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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525B GLU* 3.1 21.8 + - - +
526B ALA* 3.5 10.6 - - - +
528B LEU* 1.3 82.4 - - - +
530B PHE* 1.3 62.7 + - - +
532B LYS* 3.4 10.0 + - - +
533B ALA* 3.1 23.0 + - - +
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Residues in contact with PHE 530 (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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503B TRP* 3.4 26.0 - + - -
504B PRO* 3.6 21.1 - - + -
508B LEU* 3.6 44.6 - - + -
509B CYS* 3.7 19.1 - - + -
512B CYS* 3.6 13.7 - - - -
526B ALA 2.9 13.7 + - - +
527B THR 3.6 7.2 - - - +
528B LEU 3.3 0.2 - - - -
529B ASN* 1.3 77.6 - - - +
531B LEU* 1.3 66.4 + - + +
533B ALA* 3.2 6.1 + - + +
534B HIS* 2.8 49.6 + - + +
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Residues in contact with LEU 531 (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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412B HIS* 5.9 0.9 - - - +
416B VAL* 4.4 1.8 - - - -
474B VAL* 3.7 30.5 - - + -
475B LEU* 4.1 10.1 - - + -
478B TRP* 3.9 34.5 - - + +
503B TRP* 3.7 30.7 - - + -
527B THR* 2.9 29.1 + - + +
528B LEU* 3.6 4.3 - - - +
530B PHE* 1.3 81.9 - - + +
532B LYS* 1.3 57.7 + - - +
534B HIS* 4.4 0.7 - - - +
535B PHE* 3.0 53.4 + - + +
550B FAD 4.4 2.2 - - + -
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Residues in contact with LYS 532 (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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416B VAL* 3.6 15.8 - - + +
419B ALA* 3.6 24.4 + - + -
420B ARG* 3.6 33.5 + - + +
471B ASN* 2.8 35.1 + - - +
474B VAL* 5.6 1.3 - - + -
528B LEU* 3.0 39.0 + - + +
529B ASN* 3.9 9.6 - - - +
531B LEU* 1.3 77.6 - - + +
533B ALA* 1.3 59.1 + - - +
536B SER* 3.5 17.3 - - - -
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Residues in contact with ALA 533 (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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529B ASN 3.1 17.0 + - - +
530B PHE* 3.6 6.5 - - + +
531B LEU 3.1 0.6 - - - -
532B LYS* 1.3 78.3 - - - +
534B HIS* 1.3 63.5 + - - +
535B PHE 3.4 0.2 - - - -
536B SER* 3.5 15.1 - - - -
538B SER* 5.0 1.6 + - - -
539B ASN* 3.6 11.4 - - - +
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Residues in contact with HIS 534 (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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296B ARG 3.7 17.9 - - - -
297B SER* 3.5 29.3 + - - -
298B LYS 4.2 1.8 - - - -
299B ILE* 3.5 19.8 - - + +
503B TRP* 3.7 22.4 - + - -
508B LEU* 4.9 1.1 - - + +
530B PHE* 2.8 44.8 + + + +
531B LEU* 4.0 2.7 - - - +
533B ALA* 1.3 74.3 - - - +
535B PHE* 1.3 89.3 + + + +
536B SER 3.3 4.3 + - - -
539B ASN* 2.7 29.4 + - - +
550B FAD 4.7 4.8 + - - -
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Residues in contact with PHE 535 (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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299B ILE* 3.4 19.7 - - + -
409B VAL* 4.1 15.7 - - + -
412B HIS* 3.5 31.0 - + + -
413B PHE* 3.4 35.0 - + - -
416B VAL* 3.2 41.9 - - + +
417B GLN* 4.9 0.9 - - - +
420B ARG* 4.7 0.7 + - - -
503B TRP* 4.1 2.0 - + - -
531B LEU* 3.0 48.4 + - + +
532B LYS 4.1 2.2 - - - -
534B HIS* 1.3 94.7 - + - +
536B SER* 1.3 56.2 + - - +
537B PRO* 4.7 0.2 - - - +
550B FAD 3.6 25.4 - + - -
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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