Contacts of the helix formed by residues 528 - 540 (chain B) in PDB entry 2A19
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 ASN 528 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406B HIS* 6.0 0.2 - - - +
467B LYS* 3.3 33.5 - - + +
471B LEU* 3.9 8.7 - - + -
526B ARG 3.6 2.4 + - - -
527B PRO* 1.3 75.4 - - - +
529B THR* 1.3 60.3 + - - +
530B SER* 3.3 15.2 + - - -
531B GLU* 2.9 37.3 + - - +
532B ILE* 3.0 11.8 + - - +
534B ARG* 4.8 1.4 + - - -
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Residues in contact with THR 529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399B THR* 4.0 7.4 - - + +
402B VAL* 3.9 18.8 - - + -
403B ASP* 2.3 55.9 + - - +
406B HIS* 4.5 7.8 + - - +
471B LEU* 4.1 10.0 - - + +
474B LEU* 4.0 18.4 - - + -
528B ASN* 1.3 72.5 - - - +
530B SER* 1.3 60.0 + - - +
532B ILE* 3.8 8.7 - - - +
533B LEU* 2.9 33.8 + - - +
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Residues in contact with SER 530 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403B ASP* 3.6 8.9 + - - -
528B ASN* 3.3 15.6 + - - -
529B THR* 1.3 81.2 + - - +
531B GLU* 1.3 56.8 + - - +
533B LEU* 3.3 6.3 + - - +
534B ARG* 3.0 49.0 + - - +
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Residues in contact with GLU 531 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514B LEU* 6.2 0.2 - - - -
517B LYS* 3.7 23.9 + - - +
527B PRO* 3.3 30.6 - - + +
528B ASN* 2.9 15.6 + - - +
530B SER* 1.3 75.5 - - - +
532B ILE* 1.3 65.4 + - - +
534B ARG* 3.2 27.9 + - + +
535B THR* 2.9 37.4 + - - +
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Residues in contact with ILE 532 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B PHE* 3.7 30.7 - - + -
399B THR* 3.7 11.2 - - + -
471B LEU* 4.8 1.6 - - + -
474B LEU* 4.0 26.2 - - + -
514B LEU* 4.8 14.6 - - + -
518B LEU* 3.8 28.9 - - + -
527B PRO* 3.9 17.5 - - + +
528B ASN 3.0 12.6 + - - +
529B THR* 3.8 12.6 - - + +
530B SER 3.4 0.2 - - - -
531B GLU* 1.3 74.9 - - - +
533B LEU* 1.3 57.6 + - - +
535B THR* 3.1 8.4 + - - -
536B LEU* 3.0 31.2 + - + +
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Residues in contact with LEU 533 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B GLU* 4.2 11.7 - - + +
399B THR* 3.4 30.7 - - + +
400B LYS* 4.2 24.5 - - + +
403B ASP* 3.8 32.8 - - + +
529B THR 2.9 20.4 + - - +
530B SER* 3.5 6.1 - - - +
532B ILE* 1.3 73.8 - - - +
534B ARG* 1.3 65.2 + - - +
536B LEU* 3.4 13.6 + - + +
537B THR* 3.1 26.0 + - - -
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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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528B ASN* 4.8 1.6 + - - -
530B SER* 3.0 35.4 + - - +
531B GLU* 3.6 40.0 - - + +
533B LEU* 1.3 76.3 - - + +
535B THR* 1.3 58.4 + - - +
537B THR* 3.4 7.7 + - - -
538B VAL* 3.1 32.5 + - + +
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Residues in contact with THR 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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510B LYS 5.8 0.4 - - - +
514B LEU* 4.6 19.5 - - + +
531B GLU* 2.9 29.6 + - - +
532B ILE* 3.1 8.0 + - - -
534B ARG* 1.3 76.6 - - - +
536B LEU* 1.3 60.1 + - + +
538B VAL* 3.4 8.2 + - + +
539B TRP* 3.1 57.6 + - + +
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Residues in contact with LEU 536 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B LEU* 4.8 10.5 - - + +
395B PHE* 3.8 31.4 - - + -
396B GLU* 3.7 48.9 - - + +
399B THR* 4.7 0.2 - - - +
514B LEU* 5.3 2.7 - - + -
532B ILE* 3.0 21.0 + - + +
533B LEU* 3.9 13.5 - - + +
534B ARG 3.4 0.2 - - - -
535B THR* 1.3 75.1 - - - +
537B THR* 1.3 63.4 + - - +
539B TRP* 3.5 36.3 + - + +
540B LYS* 3.2 29.4 + - - +
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Residues in contact with THR 537 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B GLU* 5.3 2.6 + - - -
533B LEU 3.1 14.3 + - - -
534B ARG* 3.6 10.9 - - - -
535B THR 3.3 0.2 - - - -
536B LEU* 1.3 75.9 - - - +
538B VAL* 1.3 65.4 + - + +
540B LYS* 3.2 31.9 + - + +
541B LYS* 3.7 13.5 - - + +
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Residues in contact with VAL 538 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510B LYS* 6.2 1.3 - - + -
534B ARG* 3.1 17.7 + - + +
535B THR* 3.7 11.2 - - + +
536B LEU 3.4 0.2 - - - -
537B THR* 1.3 75.7 - - + +
539B TRP* 1.3 67.6 - - + +
541B LYS* 3.2 42.0 + - - +
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Residues in contact with TRP 539 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B LEU* 4.3 27.1 - - + -
478B LEU* 4.6 9.6 - - + -
510B LYS* 3.5 76.4 + - + +
511B GLU* 3.9 26.9 - - + -
514B LEU* 3.8 27.8 - - + -
535B THR* 3.1 34.4 + - + +
536B LEU* 3.6 31.4 - - + +
537B THR 3.3 0.2 - - - -
538B VAL* 1.3 78.6 - - + +
540B LYS* 1.3 58.1 + - + +
541B LYS* 3.0 15.5 + - - -
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Residues in contact with LYS 540 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B GLU* 5.8 1.7 + - - -
396B GLU* 2.9 42.1 + - - -
536B LEU* 3.2 16.4 - - - +
537B THR* 3.2 23.9 + - + +
539B TRP* 1.3 76.0 - - - +
541B LYS* 1.3 59.7 + - + +
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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