Contacts of the helix formed by residues 525 - 535 (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 GLY 525 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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523B VAL 3.6 3.2 + - - -
524B ASN* 1.3 77.6 + - - +
526B ALA* 1.3 62.4 + - - +
527B ALA 3.1 4.5 - - - +
528B ARG* 3.4 37.6 + - - +
529B GLN* 3.3 27.9 + - - +
807B SO4 3.7 0.8 + - - -
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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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524B ASN* 3.3 15.4 + - - +
525B GLY* 1.3 75.3 - - - +
527B ALA* 1.3 58.6 + - - +
529B GLN* 3.7 27.7 - - - +
530B ALA* 3.8 4.3 + - - +
693B LEU* 3.9 13.1 - - + +
697B THR* 3.8 23.8 - - + -
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Residues in contact with ALA 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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523B VAL* 3.8 25.6 - - + -
524B ASN* 3.8 10.5 + - - +
525B GLY 3.1 0.2 - - - -
526B ALA* 1.3 77.6 - - - +
528B ARG* 1.3 62.6 + - - +
529B GLN 3.3 0.4 - - - -
530B ALA* 3.2 4.9 + - - +
531B ILE* 3.1 27.2 + - - +
690B LEU* 3.9 16.8 - - + +
693B LEU* 3.9 13.2 - - + +
694B VAL* 4.2 16.2 - - + -
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Residues in contact with ARG 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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516B VAL* 4.5 13.4 - - + +
517B ARG* 3.2 67.6 + - - +
520B ASN 4.7 4.7 + - - +
521B PRO* 5.8 2.2 + - - +
523B VAL* 3.7 32.9 + - + +
525B GLY* 3.4 22.0 + - - +
527B ALA* 1.3 78.3 - - - +
529B GLN* 1.3 56.2 + - + +
531B ILE* 3.2 11.0 + - + +
532B VAL* 3.0 35.0 + - + +
807B SO4 2.7 31.4 + - - -
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Residues in contact with GLN 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 GLY 3.3 15.2 + - - +
526B ALA* 3.7 19.6 - - - +
527B ALA 3.3 0.8 - - - -
528B ARG* 1.3 76.8 - - + +
530B ALA* 1.3 57.2 + - - +
532B VAL* 3.2 24.6 - - + +
533B PHE* 3.2 16.1 + - - +
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Residues in contact with ALA 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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526B ALA 3.8 1.7 + - - +
527B ALA 3.2 11.2 + - - +
529B GLN* 1.3 78.0 - - - +
531B ILE* 1.3 58.5 + - - +
533B PHE* 3.5 8.7 + - - +
534B GLU* 2.9 22.9 + - - +
685B PHE* 3.3 28.1 - - + -
689B TYR* 4.2 10.1 - - + +
690B LEU* 4.1 1.6 - - + -
693B LEU* 3.9 25.1 - - + -
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Residues in contact with ILE 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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516B VAL* 4.7 8.1 - - + +
520B ASN* 3.7 27.1 - - + +
523B VAL* 4.5 7.9 - - + -
527B ALA 3.1 20.7 + - - +
528B ARG* 3.2 10.3 + - + +
530B ALA* 1.3 73.6 - - - +
532B VAL* 1.3 59.9 + - + +
534B GLU 3.3 0.2 + - - -
535B TYR* 2.8 45.8 + - + +
554B MET* 3.8 28.5 - - + -
685B PHE* 3.6 15.0 - - + -
686B TRP* 3.8 24.7 - - + -
690B LEU* 4.5 7.0 - - + -
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Residues in contact with VAL 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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509B ARG* 4.7 9.2 - - - +
512B PHE* 3.9 23.0 - - + -
513B LEU* 4.2 18.8 - - + -
516B VAL* 3.7 29.8 - - + -
528B ARG* 3.0 20.0 + - + +
529B GLN* 3.2 24.9 - - + +
531B ILE* 1.3 74.4 - - - +
533B PHE* 1.3 61.7 + - - +
535B TYR 3.3 0.9 - - - -
536B THR* 3.1 31.4 + - - +
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Residues in contact with PHE 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 GLN 3.2 20.3 + - - +
530B ALA* 3.7 8.5 - - - +
532B VAL* 1.3 80.6 - - + +
534B GLU* 1.3 78.2 + - + +
535B TYR 3.4 0.2 + - - -
536B THR* 3.5 9.7 + - - +
538B TRP* 3.3 54.7 + + + -
685B PHE* 6.0 0.7 - + - -
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Residues in contact with GLU 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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530B ALA 2.9 19.4 + - - +
531B ILE 3.9 3.1 - - - +
533B PHE* 1.3 90.1 - - + +
535B TYR* 1.3 77.1 + - + +
536B THR 3.6 2.7 + - - +
681B ARG* 2.7 49.1 + - - +
682B GLN* 3.7 16.4 + - + +
685B PHE* 3.7 41.8 - - + +
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Residues in contact with TYR 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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509B ARG* 4.9 0.2 + - - -
512B PHE* 3.1 26.3 - - + -
531B ILE* 2.8 25.6 + - + +
532B VAL 3.3 4.7 - - - -
534B GLU* 1.3 93.4 - - + +
536B THR* 1.3 56.0 + - - +
550B ALA* 3.2 25.8 - - + +
553B LYS* 3.8 13.7 - - + -
554B MET* 3.7 33.0 - - + -
557B ASP* 2.7 31.0 + - - +
679B ARG* 3.8 7.0 - - - -
682B GLN* 3.7 16.6 + - + +
685B PHE* 4.3 2.7 - + - -
686B TRP* 2.8 43.9 + + - -
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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