Contacts of the helix formed by residues 522 - 534 (chain B) in PDB entry 4DHZ
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 522 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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520B SER 3.5 2.8 + - - +
521B ASP* 1.3 76.9 - - - +
523B ILE* 1.3 65.5 + - - +
524B GLU* 3.3 15.8 + - - +
525B ASN* 3.0 41.6 + - - +
526B VAL* 3.3 11.5 + - - +
552B ASP 4.5 2.2 - - - -
553B GLY 4.4 10.1 - - - +
554B ARG 3.4 10.5 - - - -
555B THR* 3.9 12.8 - - + -
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Residues in contact with ILE 523 (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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522B THR* 1.3 73.9 - - - +
524B GLU* 1.3 62.9 + - - +
526B VAL* 3.3 6.9 + - + +
527B LYS* 3.0 37.2 + - - +
543B LEU* 3.8 22.0 - - + -
550B LEU* 3.7 43.3 - - + -
551B GLU 3.1 30.5 - - - +
552B ASP* 4.4 1.7 + - - -
554B ARG 3.2 11.0 + - - +
555B THR 4.6 4.9 - - - -
556B LEU* 4.5 17.5 - - + -
559B TYR* 4.2 15.0 - - + -
567B LEU* 6.2 0.2 - - + -
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Residues in contact with GLU 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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522B THR* 3.0 12.3 + - - +
523B ILE* 1.3 79.4 - - - +
525B ASN* 1.3 60.3 + - - +
527B LYS* 3.4 8.6 + - + +
528B ALA* 2.9 27.5 + - - +
538B PRO* 5.1 8.9 - - + +
552B ASP* 3.5 40.6 + - - +
553B GLY* 5.5 0.2 - - - -
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Residues in contact with ASN 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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521B ASP* 4.0 21.6 - - - +
522B THR* 3.0 36.1 + - - +
524B GLU* 1.3 75.9 - - - +
526B VAL* 1.3 56.6 + - - +
528B ALA* 3.1 9.2 + - - +
529B LYS* 2.7 42.8 + - + +
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Residues in contact with VAL 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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503B ILE* 4.4 2.9 - - + -
515B LEU* 3.8 20.4 - - + +
517B VAL* 4.6 6.3 - - + -
521B ASP* 4.6 5.6 - - + -
522B THR 3.5 13.7 - - - +
523B ILE* 3.3 13.7 + - + +
525B ASN* 1.3 74.0 - - - +
527B LYS* 1.3 59.4 + - - +
529B LYS* 3.2 11.3 + - - +
530B ILE* 3.0 34.4 + - + +
543B LEU* 4.0 11.0 - - + -
556B LEU* 4.3 30.3 - - + -
567B LEU* 4.0 24.0 - - + -
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Residues in contact with LYS 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 ILE* 3.0 31.5 + - + +
524B GLU* 3.5 11.9 - - + +
526B VAL* 1.3 72.4 - - - +
528B ALA* 1.3 64.5 + - - +
530B ILE* 3.2 4.6 + - - +
531B GLN* 3.0 18.4 + - - +
538B PRO* 3.6 29.5 + - + +
541B GLN* 3.3 63.7 + - + +
542B ARG* 4.9 1.8 - - - +
543B LEU* 3.8 21.3 - - + +
549B GLN* 5.5 1.6 - - - +
550B LEU 4.8 6.3 + - - -
552B ASP* 3.1 31.8 + - - +
572B ARG* 4.7 6.1 - - - +
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Residues in contact with ALA 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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524B GLU 2.9 15.5 + - - +
525B ASN* 3.3 14.8 - - - +
527B LYS* 1.3 74.8 - - - +
529B LYS* 1.3 61.4 + - + +
531B GLN* 3.1 22.9 - - - +
532B ASP* 3.2 15.0 + - - +
538B PRO* 4.3 14.0 - - + +
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Residues in contact with LYS 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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515B LEU* 4.0 17.4 - - + +
516B GLU 3.0 23.8 + - - +
517B VAL* 3.7 19.0 - - + +
521B ASP* 3.1 24.0 + - - -
525B ASN* 2.7 25.5 + - - +
526B VAL* 3.5 5.6 - - - +
528B ALA* 1.3 70.7 - - - +
530B ILE* 1.3 65.6 + - - +
532B ASP* 3.1 26.9 + - + +
533B LYS* 3.3 12.5 + - - +
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Residues in contact with ILE 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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505B VAL* 3.9 19.1 - - + -
513B ILE* 4.3 16.8 - - + -
515B LEU* 4.0 18.4 - - + +
526B VAL* 3.0 20.7 + - + +
527B LYS* 3.2 8.3 + - - +
529B LYS* 1.3 74.6 - - - +
531B GLN* 1.3 54.6 + - - +
533B LYS* 3.1 3.0 + - - +
534B GLU* 2.7 45.6 + - + +
536B ILE* 5.1 4.3 - - + +
541B GLN* 3.6 26.0 - - - +
543B LEU* 3.8 18.4 - - + -
569B LEU* 3.8 24.5 - - + -
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Residues in contact with GLN 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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244A TRP* 5.2 2.8 - - - -
527B LYS 3.0 10.8 + - - +
528B ALA* 3.1 16.0 + - - +
530B ILE* 1.3 77.6 - - - +
532B ASP* 1.3 59.0 + - - +
535B GLY* 2.9 34.0 + - - +
536B ILE 3.2 21.0 + - - +
537B PRO* 3.5 23.6 - - - +
538B PRO* 3.1 23.8 - - + +
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Residues in contact with ASP 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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528B ALA* 3.2 19.6 + - - +
529B LYS* 3.1 17.7 + - + +
531B GLN* 1.3 80.7 - - - +
533B LYS* 1.3 63.1 + - + +
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Residues in contact with LYS 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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513B ILE* 4.4 25.4 - - + +
514B THR* 3.0 44.5 + - - +
515B LEU* 4.1 11.4 - - + -
529B LYS 3.3 9.4 + - - +
530B ILE 3.1 5.1 + - - +
532B ASP* 1.3 83.6 - - + +
534B GLU* 1.3 68.3 + - + +
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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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507B THR* 4.7 13.8 + - + +
509B THR* 5.2 1.4 + - - -
511B LYS* 3.3 44.3 + - - +
513B ILE* 4.1 25.0 - - + +
530B ILE* 2.7 23.4 + - + +
533B LYS* 1.3 81.1 - - - +
535B GLY* 1.3 56.4 + - - +
536B ILE* 3.5 25.0 - - + +
569B LEU* 6.4 0.9 - - + -
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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