Contacts of the helix formed by residues 533 - 543 (chain B) in PDB entry 2HDX
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 SER 533 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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532B LEU* 1.3 78.2 - - - +
534B ARG* 1.3 66.2 + - - +
535B LEU* 3.9 6.8 + - - +
536B LYS* 3.1 34.5 + - - +
537B ALA* 2.9 22.9 + - - +
558B GLU* 3.8 14.6 - - - -
605E ARG* 3.4 16.6 - - - +
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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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532B LEU 3.8 1.0 + - - -
533B SER* 1.3 72.9 - - - +
535B LEU* 1.3 62.8 + - - +
537B ALA* 3.3 2.6 + - - +
538B ALA* 2.9 23.8 + - + +
555B ARG* 3.7 20.9 - - - +
558B GLU* 5.0 4.8 + - - +
576B HIS* 3.4 36.1 + - + +
812H ASP* 2.7 39.7 + - - +
813H PTR 2.7 61.8 + - - +
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Residues in contact with LEU 535 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533B SER* 3.1 7.7 - - - +
534B ARG* 1.3 80.5 - - - +
536B LYS* 1.3 66.8 + - + +
538B ALA* 3.1 9.5 + - + +
539B GLN* 3.0 52.7 + - + +
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Residues in contact with LYS 536 (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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532B LEU* 3.7 28.5 - - + -
533B SER* 3.1 20.4 + - - +
535B LEU* 1.3 84.0 - - + +
537B ALA* 1.3 62.9 + - - +
539B GLN* 3.3 17.4 + - - +
540B LEU* 3.0 30.6 + - + +
605E ARG* 5.8 1.4 + - - +
606E VAL* 4.7 16.8 - - - +
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Residues in contact with ALA 537 (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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532B LEU* 3.8 12.0 - - + +
533B SER 2.9 11.2 + - - +
534B ARG 3.5 3.4 - - - +
536B LYS* 1.3 76.3 - - - +
538B ALA* 1.3 62.0 + - - +
540B LEU* 3.5 1.6 + - - +
541B VAL* 3.3 29.5 + - - +
553B LEU* 4.0 10.7 - - + +
555B ARG* 3.3 38.6 - - - +
567B THR* 3.7 12.1 - - + +
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Residues in contact with ALA 538 (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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534B ARG* 2.9 13.2 + - + +
535B LEU* 3.1 12.8 + - + +
537B ALA* 1.3 74.6 - - - +
539B GLN* 1.3 67.7 + - + +
541B VAL* 3.3 9.0 - - - +
542B LEU* 2.9 36.1 + - + +
567B THR* 4.2 2.4 - - - +
574B ALA* 3.7 21.8 - - + -
576B HIS* 4.3 7.6 - - + +
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Residues in contact with GLN 539 (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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535B LEU* 3.0 41.4 + - + +
536B LYS* 3.7 19.5 - - - +
538B ALA* 1.3 76.2 - - + +
540B LEU* 1.3 64.8 + - + +
542B LEU* 3.2 8.8 + - + +
543B GLU* 3.1 22.9 + - - +
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Residues in contact with LEU 540 (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 HIS* 4.0 17.3 - - + +
532B LEU* 3.8 28.7 - - + -
536B LYS* 3.0 18.5 + - + +
537B ALA 3.8 4.9 - - - +
538B ALA 3.3 0.2 - - - -
539B GLN* 1.3 81.2 - - + +
541B VAL* 1.3 59.7 + - - +
543B GLU* 3.6 16.4 + - - +
551B VAL* 5.1 0.5 - - - +
553B LEU* 3.9 15.0 - - + -
625B VAL* 3.6 24.1 - - + +
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Residues in contact with VAL 541 (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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537B ALA 3.3 13.9 + - - +
538B ALA* 3.3 15.5 - - - +
540B LEU* 1.3 76.3 - - - +
542B LEU* 1.3 60.3 + - + +
543B GLU 3.4 0.9 - - - -
548B SER* 3.8 7.4 - - - -
551B VAL* 4.2 7.5 - - + +
552B PHE* 4.1 6.7 - - - -
553B LEU* 3.8 18.8 - - + -
567B THR* 3.8 34.8 - - + +
568B PHE 4.0 14.6 - - - +
569B ASN* 3.0 33.2 + - - +
574B ALA* 4.4 6.7 - - + -
625B VAL* 4.0 12.1 - - + -
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Residues in contact with LEU 542 (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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538B ALA* 2.9 31.5 + - + +
539B GLN* 3.2 8.3 + - + +
541B VAL* 1.3 78.9 - - - +
543B GLU* 1.3 67.6 + - - +
545B GLY* 2.8 21.9 + - - +
569B ASN* 3.9 7.6 - - - +
572B GLY 3.4 30.1 - - - +
573B LYS* 3.9 1.6 - - - -
574B ALA* 3.6 31.9 - - + +
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Residues in contact with GLU 543 (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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539B GLN 3.1 10.9 + - - +
540B LEU* 3.7 15.1 - - - +
541B VAL 3.4 2.0 - - - +
542B LEU* 1.3 75.4 - - - +
544B GLY* 1.3 51.2 + - - +
548B SER* 2.5 26.0 + - - -
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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