Contacts of the helix formed by residues 525 - 534 (chain B) in PDB entry 2HA7
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 ARG 525 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330B VAL* 5.7 0.6 - - - +
332B LYS 4.1 18.0 + - - -
400B ALA* 5.5 9.1 - - - +
404B ASP* 3.0 39.9 + - - -
408B VAL* 4.1 21.0 - - + +
429B ILE* 4.8 15.4 - - - +
510B TYR* 5.2 1.0 + - - -
523B GLY 3.2 5.8 + - - -
524B LEU* 1.3 78.6 - - - +
526B ALA* 1.3 55.3 + - - +
527B GLN 3.5 2.0 - - - -
528B THR* 3.3 16.6 + - - -
529B CYS* 2.7 43.3 + - - +
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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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508B GLN* 4.2 20.2 - - - +
523B GLY* 4.1 15.2 + - - +
524B LEU 3.2 4.2 - - - +
525B ARG* 1.3 75.5 - - - +
527B GLN* 1.3 70.5 + - - +
529B CYS* 4.1 2.3 - - - +
530B ALA* 3.2 23.0 + - - +
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Residues in contact with GLN 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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381B HIS* 4.9 6.9 - - + -
525B ARG 3.5 0.2 - - - -
526B ALA* 1.3 81.4 - - + +
528B THR* 1.3 64.6 + - - +
530B ALA* 3.2 18.4 + - - +
531B PHE* 3.3 10.0 + - - +
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Residues in contact with THR 528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B HIS* 4.0 20.1 + - - +
382B TYR* 3.1 34.6 - - + +
404B ASP* 3.6 14.4 - - + +
409B CYS* 4.8 0.7 - - - -
525B ARG* 3.3 21.3 + - - +
527B GLN* 1.3 79.2 - - - +
529B CYS* 1.3 57.0 + - - +
531B PHE* 3.1 22.5 + - - +
532B TRP* 3.3 12.5 + - + -
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Residues in contact with CYS 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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408B VAL* 4.3 3.6 - - - -
409B CYS* 2.1 58.1 - - + -
412B ALA* 4.4 6.3 - - + -
524B LEU 3.9 9.2 - - - +
525B ARG* 2.7 39.3 + - - +
526B ALA* 4.4 2.7 - - - +
528B THR* 1.3 70.8 - - - +
530B ALA* 1.3 56.0 + - - +
532B TRP 4.3 0.4 - - - +
533B ASN* 2.7 47.6 + - - +
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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 3.2 14.7 + - - +
527B GLN* 3.2 13.9 + - - +
529B CYS* 1.3 75.1 - - - +
531B PHE* 1.3 58.0 + - - +
533B ASN* 5.1 0.7 - - - -
534B ARG* 2.9 52.0 + - - +
535B PHE* 3.2 8.4 + - - +
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Residues in contact with PHE 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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377B ALA* 3.9 19.3 - - + -
378B VAL* 3.8 37.5 - - + -
381B HIS* 4.0 36.8 - + + -
382B TYR* 4.8 1.6 - + - -
527B GLN 3.3 3.0 + - - +
528B THR 3.1 11.0 + - - +
530B ALA* 1.3 80.2 - - - +
532B TRP* 1.3 84.8 + + - +
535B PHE* 3.4 23.1 + + + -
536B LEU* 2.9 59.4 + - + +
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Residues in contact with TRP 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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367B VAL* 3.6 27.8 - - + -
378B VAL* 3.8 16.6 - - + -
382B TYR* 2.8 42.2 + + - -
401B VAL* 3.9 13.2 - - + -
404B ASP* 3.8 3.9 - - + +
405B HIS* 3.3 49.1 - + + +
409B CYS* 3.8 22.7 - - + -
528B THR* 3.3 21.6 + - + -
529B CYS 3.2 5.4 + - - +
531B PHE* 1.3 86.6 - + - +
533B ASN* 1.3 67.1 + - - +
536B LEU* 3.7 34.6 - - + +
537B PRO* 3.5 18.1 - - - +
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Residues in contact with ASN 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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409B CYS* 3.2 36.0 + - - +
410B PRO* 4.6 2.1 - - - +
412B ALA* 4.8 0.8 - - - +
413B GLN* 3.8 31.9 + - - +
529B CYS* 2.7 35.5 + - - +
530B ALA* 5.1 0.2 - - - -
532B TRP* 1.3 79.0 - - - +
534B ARG* 1.3 65.9 + - + +
537B PRO* 3.7 14.1 - - - +
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Residues in contact with ARG 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 31.7 + - - +
533B ASN* 1.3 85.0 - - + +
535B PHE* 1.3 63.0 + - + +
536B LEU 3.8 0.2 - - - -
537B PRO* 4.0 5.7 - - - +
538B LYS* 3.6 27.1 + - - +
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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