Contacts of the helix formed by residues 530 - 540 (chain A) in PDB entry 5E92
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 530 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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447A VAL* 4.3 5.8 - - - -
528A ARG 5.4 1.6 - - - +
529A LEU* 1.3 78.0 - - - +
531A ALA* 1.4 62.2 + - - +
532A GLN* 3.5 11.1 + - - +
533A CYS* 3.0 33.1 + - - +
534A VAL* 3.2 22.6 + - - +
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Residues in contact with ALA 531 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355A ALA* 3.8 8.2 - - - +
358A ILE* 3.7 21.1 - - + -
359A ALA* 3.6 30.7 - - - +
362A HIS* 4.4 8.7 + - - +
447A VAL* 3.9 9.4 - - + +
450A MET* 4.4 17.9 - - - -
530A THR* 1.4 71.7 - - - +
532A GLN* 1.4 56.6 + - - +
534A VAL* 3.4 3.1 + - - +
535A ALA* 3.0 28.4 + - - +
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Residues in contact with GLN 532 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359A ALA* 3.8 20.5 - - + +
530A THR* 3.2 9.5 + - - +
531A ALA* 1.4 75.6 - - - +
533A CYS* 1.4 64.9 + - - +
535A ALA* 3.3 8.3 + - - +
536A GLU* 3.0 56.7 + - - +
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Residues in contact with CYS 533 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529A LEU* 4.0 22.9 - - + -
530A THR* 3.0 46.5 + - - +
532A GLN* 1.4 75.3 - - - +
534A VAL* 1.4 57.8 + - - +
536A GLU* 3.2 16.7 + - - +
537A ARG* 2.9 34.8 + - + +
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Residues in contact with VAL 534 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355A ALA* 3.8 11.9 - - + -
450A MET* 3.7 18.4 - - + -
454A LEU* 4.2 7.0 - - + -
516A THR* 4.0 15.9 - - + -
520A CYS* 3.5 31.0 - - - -
529A LEU* 4.1 4.7 - - + -
530A THR 3.2 13.6 + - - +
531A ALA 3.7 7.0 - - - +
532A GLN 3.3 0.2 - - - -
533A CYS* 1.4 75.3 - - - +
535A ALA* 1.3 55.1 + - - +
537A ARG* 3.2 7.7 + - - +
538A PHE* 3.0 53.7 + - + -
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Residues in contact with ALA 535 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352A SER* 5.0 3.5 - - - +
355A ALA* 3.7 17.2 - - + +
356A ARG* 4.1 26.6 - - + +
359A ALA* 5.1 0.7 - - + -
531A ALA 3.0 13.3 + - - +
532A GLN* 3.3 18.4 + - - +
534A VAL* 1.3 73.7 - - - +
536A GLU* 1.3 56.2 + - - +
538A PHE* 3.4 7.3 + - - +
539A SER* 3.1 26.5 + - - -
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Residues in contact with GLU 536 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532A GLN* 3.0 45.9 + - - +
533A CYS* 3.4 17.7 - - - +
535A ALA* 1.3 72.9 - - - +
537A ARG* 1.4 63.9 + - + +
539A SER* 2.7 26.1 + - - +
540A GLU* 3.2 20.5 + - - +
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Residues in contact with ARG 537 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512A MET* 4.9 14.1 + - + +
515A GLU* 4.4 4.2 + - - +
516A THR* 3.2 41.5 + - + +
519A GLU* 2.8 38.1 + - - -
529A LEU* 3.5 19.7 - - - +
533A CYS* 2.9 19.1 + - + +
534A VAL* 3.2 10.3 + - - +
536A GLU* 1.4 75.1 - - + +
538A PHE* 1.3 60.6 + - + +
540A GLU* 3.4 29.4 + - - +
541A LEU* 3.7 13.2 + - - +
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Residues in contact with PHE 538 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347A LEU* 4.0 11.0 - - + -
348A ARG* 3.7 14.1 - - - +
351A GLY* 3.7 28.0 - - - -
352A SER* 3.5 32.1 - - - -
355A ALA* 4.9 0.2 - - + -
454A LEU* 3.8 20.9 - - + -
513A VAL* 4.0 33.9 - - + -
516A THR* 5.1 6.7 - - + -
534A VAL* 3.0 46.4 + - + +
535A ALA 3.7 3.4 - - - +
536A GLU 3.3 0.2 - - - -
537A ARG* 1.3 76.8 - - + +
539A SER* 1.4 61.8 + - - +
541A LEU* 3.3 34.9 + - + +
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Residues in contact with SER 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352A SER* 5.3 1.1 - - - -
535A ALA 3.1 13.0 + - - -
536A GLU* 2.7 24.2 + - - +
538A PHE* 1.4 74.4 - - - +
540A GLU* 1.3 62.6 + - - +
541A LEU 3.2 2.4 + - - -
542A GLU* 4.4 5.9 + - - +
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Residues in contact with GLU 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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536A GLU* 3.2 18.6 + - - +
537A ARG* 3.4 21.3 - - - +
538A PHE 3.3 0.2 - - - -
539A SER* 1.3 79.8 + - - +
541A LEU* 1.4 50.6 + - - +
542A GLU* 2.8 22.4 + - - +
543A HIS 4.5 1.9 + - - -
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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