Contacts of the helix formed by residues 508 - 520 (chain B) in PDB entry 5YDJ
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 THR 508 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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506B THR* 4.2 1.3 - - - +
507B VAL* 1.3 75.5 - - - +
509B ARG* 1.3 61.9 + - - +
510B GLU* 4.4 4.5 + - - +
511B GLU* 3.1 33.4 + - - +
512B PHE* 2.9 26.6 + - - +
542B ASP 5.8 0.7 - - - -
544B PRO* 4.8 19.3 - - + -
547B ASN* 4.6 0.7 - - - -
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Residues in contact with ARG 509 (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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508B THR* 1.3 74.8 - - - +
510B GLU* 1.3 64.3 + - + +
512B PHE* 3.3 15.6 + - - +
513B LEU* 2.9 56.2 + - + +
532B VAL* 4.4 10.3 + - - +
536B THR* 2.8 42.6 + - - +
538B TRP* 5.1 7.1 - - - -
541B PRO* 3.5 21.4 + - - +
542B ASP* 3.4 29.3 + - + +
547B ASN* 2.7 38.5 + - - +
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Residues in contact with GLU 510 (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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508B THR* 3.3 3.9 + - - +
509B ARG* 1.3 81.2 - - + +
511B GLU* 1.3 61.4 + - + +
513B LEU* 3.4 15.7 + - - +
514B GLN* 2.9 31.2 + - - +
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Residues in contact with GLU 511 (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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498B LEU* 3.5 36.0 - - + +
506B THR 4.1 3.6 - - - +
507B VAL* 3.7 12.4 - - + -
508B THR* 3.1 37.8 + - - +
510B GLU* 1.3 76.2 - - + +
512B PHE* 1.3 59.8 + - - +
514B GLN* 3.8 6.4 - - - +
515B ALA* 2.9 28.4 + - - +
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Residues in contact with PHE 512 (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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507B VAL* 3.5 9.1 - - + +
508B THR 2.9 11.4 + - - +
509B ARG* 3.4 30.1 - - - +
510B GLU 3.3 0.2 - - - -
511B GLU* 1.3 74.3 - - - +
513B LEU* 1.3 74.5 + - + +
515B ALA* 3.1 4.4 + - - +
516B VAL* 3.1 39.3 + - + +
531B ILE 5.1 0.2 - - - -
532B VAL* 3.9 29.8 - - + -
535B TYR* 3.1 30.3 - - + -
547B ASN* 3.3 33.9 - - - +
550B ALA* 3.7 16.8 - - + -
551B LEU* 3.6 22.0 - - + -
554B MET* 4.6 2.2 - - - -
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Residues in contact with LEU 513 (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 ARG* 2.9 56.2 + - + +
510B GLU* 3.6 20.2 - - - +
512B PHE* 1.3 85.2 - - + +
514B GLN* 1.3 56.0 + - - +
516B VAL* 3.2 20.4 - - + +
517B ARG* 3.7 25.5 + - - +
532B VAL* 4.2 21.8 - - + -
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Residues in contact with GLN 514 (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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510B GLU 2.9 17.8 + - - +
511B GLU* 3.9 7.2 - - - +
512B PHE 3.2 0.2 - - - -
513B LEU* 1.3 74.2 - - - +
515B ALA* 1.3 64.7 + - - +
516B VAL 3.4 0.2 - - - -
517B ARG* 3.4 26.8 + - - +
518B GLU* 3.5 32.1 + - - +
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Residues in contact with ALA 515 (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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495B LEU* 4.3 20.0 - - + -
498B LEU* 4.9 3.4 - - + -
511B GLU 2.9 20.0 + - - +
512B PHE 3.1 2.9 + - - +
514B GLN* 1.3 77.4 - - - +
516B VAL* 1.3 57.1 + - - +
518B GLU* 3.1 5.1 + - - +
519B LEU* 2.9 35.3 + - + +
551B LEU* 3.4 34.5 - - + -
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Residues in contact with VAL 516 (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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512B PHE* 3.1 38.7 + - + +
513B LEU* 3.2 23.3 - - + +
515B ALA* 1.3 75.2 - - - +
517B ARG* 1.3 61.1 + - + +
519B LEU 4.0 0.2 - - - -
520B ASN* 3.2 32.1 + - - +
528B ARG* 4.5 14.6 - - + +
531B ILE* 4.7 8.4 - - + +
532B VAL* 3.7 25.6 - - + -
551B LEU* 4.6 0.2 - - + -
554B MET* 3.8 30.1 - - + -
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Residues in contact with ARG 517 (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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513B LEU* 3.7 26.6 + - - +
514B GLN* 3.4 26.4 + - - +
515B ALA 3.2 0.4 - - - -
516B VAL* 1.3 78.9 - - + +
518B GLU* 1.3 59.1 + - + +
520B ASN 3.2 21.6 - - - +
521B PRO* 3.4 11.3 - - - +
528B ARG* 3.2 55.3 + - - +
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Residues in contact with GLU 518 (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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445B GLY* 5.7 0.2 - - - -
446B ILE* 4.9 2.3 + - - +
494B TYR* 3.8 22.3 + - + +
495B LEU* 3.3 34.1 - - + +
497B GLU* 4.0 9.1 - - - +
514B GLN* 3.5 33.3 + - - +
515B ALA* 3.1 7.1 + - - +
517B ARG* 1.3 76.7 - - + +
519B LEU* 1.3 63.4 + - - +
520B ASN 3.4 0.4 - - - -
521B PRO* 4.1 12.8 - - - +
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Residues in contact with LEU 519 (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 ILE* 3.6 49.9 - - + +
491B ILE* 4.7 9.2 - - + -
494B TYR* 4.4 1.3 - - + -
495B LEU* 3.8 26.9 - - + -
515B ALA* 2.9 18.2 + - + +
518B GLU* 1.3 76.6 - - - +
520B ASN* 1.3 68.0 + - - +
521B PRO* 3.8 6.0 - - - +
551B LEU* 3.8 33.2 - - + -
554B MET* 4.1 17.0 - - + -
555B VAL* 3.7 23.5 - - + +
559B HIS* 5.4 2.6 + - - -
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Residues in contact with ASN 520 (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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516B VAL 3.2 14.9 + - - +
517B ARG* 3.2 10.2 - - - +
519B LEU* 1.3 81.3 + - - +
521B PRO* 1.4 62.0 - - - +
522B TYR* 3.4 3.6 - - - +
523B VAL* 3.5 34.0 - - + +
528B ARG* 4.7 3.8 + - - -
531B ILE* 3.7 21.8 - - + +
554B MET* 3.1 34.1 + - - +
558B TYR* 4.8 14.7 - - - -
559B HIS* 5.8 0.2 + - - -
686B TRP* 3.9 16.1 - - - -
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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