Contacts of the helix formed by residues 533 - 543 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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532D LEU* 1.3 78.2 - - - +
534D ARG* 1.3 66.1 + - - +
535D LEU* 3.7 8.1 + - - +
536D LYS* 2.9 34.3 + - - +
537D ALA* 2.9 22.1 + - - +
558D GLU* 3.6 22.2 - - - -
605F ARG* 3.4 13.0 - - - +
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Residues in contact with ARG 534 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532D LEU 3.7 1.6 + - - -
533D SER* 1.3 72.0 - - - +
535D LEU* 1.3 57.6 + - - +
537D ALA* 3.4 2.1 + - - +
538D ALA* 2.9 29.0 + - + +
555D ARG* 3.7 21.6 - - - +
558D GLU* 4.9 5.1 + - - +
576D HIS* 3.3 35.4 + - + +
812J ASP* 2.6 50.6 + - - +
813J PTR 2.7 64.9 + - - +
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Residues in contact with LEU 535 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533D SER* 3.1 8.6 + - - +
534D ARG* 1.3 77.2 - - - +
536D LYS* 1.3 68.5 + - + +
538D ALA* 3.3 8.2 + - + +
539D GLN* 3.0 50.1 + - + +
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Residues in contact with LYS 536 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532D LEU* 4.0 21.1 - - + -
533D SER* 2.9 28.3 + - - +
535D LEU* 1.3 80.5 - - + +
537D ALA* 1.3 64.3 + - - +
539D GLN* 3.0 27.4 + - - +
540D LEU* 2.9 29.2 + - + +
606F VAL* 5.5 11.9 - - - +
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Residues in contact with ALA 537 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532D LEU* 3.8 16.2 - - + +
533D SER 2.9 15.1 + - - +
534D ARG 3.5 4.9 - - - +
536D LYS* 1.3 76.8 - - - +
538D ALA* 1.3 63.4 + - - +
540D LEU* 3.2 4.0 + - - +
541D VAL* 3.1 27.0 + - - +
553D LEU* 4.1 6.7 - - + -
555D ARG* 3.6 29.4 - - - +
567D THR* 3.8 15.3 - - + +
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Residues in contact with ALA 538 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534D ARG* 2.9 18.0 + - + +
535D LEU* 3.6 10.8 - - + +
537D ALA* 1.3 75.0 - - - +
539D GLN* 1.3 63.7 + - + +
541D VAL* 3.4 3.9 - - - +
542D LEU* 3.1 33.7 + - + +
567D THR* 4.1 3.0 - - - +
574D ALA* 3.6 27.4 - - + -
576D HIS* 4.3 7.2 - - + +
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Residues in contact with GLN 539 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535D LEU* 3.0 52.7 + - + +
536D LYS* 3.0 29.0 + - - +
538D ALA* 1.3 77.9 - - + +
540D LEU* 1.3 63.9 + - + +
542D LEU* 3.3 7.2 + - - +
543D GLU* 3.3 20.1 + - - +
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Residues in contact with LEU 540 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529D HIS* 4.1 15.5 - - + +
532D LEU* 3.8 31.0 - - + -
536D LYS* 2.9 16.4 + - + +
537D ALA 3.2 6.7 + - - +
539D GLN* 1.3 79.8 - - + +
541D VAL* 1.3 60.9 + - - +
542D LEU 3.4 0.5 + - - -
543D GLU* 3.4 20.2 + - - +
551D VAL* 4.9 0.7 - - - +
553D LEU* 4.1 3.4 - - + -
625D VAL* 3.6 34.9 - - + +
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Residues in contact with VAL 541 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537D ALA 3.1 11.8 + - - +
538D ALA* 3.4 13.2 - - - +
540D LEU* 1.3 76.2 - - - +
542D LEU* 1.3 62.5 + - + +
543D GLU 3.3 1.1 - - - -
548D SER* 4.0 7.1 - - - -
551D VAL* 3.9 19.9 - - - +
552D PHE* 4.1 10.8 - - - -
553D LEU* 4.1 16.8 - - + -
567D THR* 3.7 29.6 - - + +
568D PHE 3.9 19.5 - - - +
569D ASN* 3.0 25.4 + - - +
574D ALA* 4.4 7.2 - - + -
625D VAL* 4.1 6.1 - - + -
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Residues in contact with LEU 542 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538D ALA* 3.1 25.1 + - + +
539D GLN* 3.8 6.5 - - - +
540D LEU 3.2 0.4 - - - -
541D VAL* 1.3 78.2 - - - +
543D GLU* 1.3 65.9 + - - +
544D GLY 2.9 4.7 + - - -
545D GLY* 2.9 17.3 + - - -
569D ASN* 3.7 11.7 - - + +
572D GLY* 3.1 36.6 - - - +
573D LYS* 3.7 12.1 - - - +
574D ALA* 4.2 18.4 - - + +
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Residues in contact with GLU 543 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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539D GLN 3.3 10.1 + - - +
540D LEU* 3.4 18.9 - - + +
541D VAL 3.3 1.3 - - - +
542D LEU* 1.3 76.4 - - - +
544D GLY* 1.3 56.6 + - - +
548D SER* 2.9 15.4 + - - -
551D VAL* 5.6 1.2 - - - +
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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