Contacts of the helix formed by residues 534 - 548 (chain T) in PDB entry 2P8Z
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 GLY 534 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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484T SER* 5.3 1.3 - - - -
489T VAL* 3.7 12.6 - - - -
532T GLY 3.3 0.4 - - - -
533T THR* 1.3 82.3 - - - +
535T GLU* 1.3 70.4 + - - -
536T LEU* 3.2 3.6 - - - -
537T HIS* 3.1 6.3 + - - +
538T LEU* 2.9 22.7 + - - +
781T THR* 5.9 1.8 - - - -
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Residues in contact with GLU 535 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489T VAL* 3.7 22.3 - - + +
534T GLY* 1.3 74.8 - - - +
536T LEU* 1.3 62.5 + - - +
538T LEU* 3.5 3.0 + - - +
539T GLU* 3.1 22.3 + - - +
779T GLY* 5.3 5.7 - - - -
781T THR* 3.6 30.1 + - + +
782T GLY* 4.2 12.6 - - - -
785T ARG* 5.1 6.0 + - - -
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Residues in contact with LEU 536 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59S ARG* 3.2 37.5 - - - +
61S ILE* 5.9 1.6 - - + -
63S ILE* 5.2 17.7 - - + -
534T GLY* 3.2 0.8 - - - -
535T GLU* 1.3 75.6 - - - +
537T HIS* 1.3 66.8 + - - +
539T GLU* 3.1 25.5 + - - +
540T ILE* 3.1 41.4 + - + +
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Residues in contact with HIS 537 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108T HIS* 6.2 6.5 - + + -
515T ASP* 3.0 28.6 + - - -
517T CYS* 3.6 39.3 - - + +
518T VAL* 4.0 2.7 - - - -
532T GLY* 3.6 4.9 - - - -
533T THR* 3.0 27.5 + - + -
534T GLY* 3.1 17.5 + - - +
536T LEU* 1.3 77.7 - - - +
538T LEU* 1.3 63.9 + - - +
540T ILE* 3.2 11.9 + - + +
541T CYS* 3.0 38.5 + - - -
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Residues in contact with LEU 538 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489T VAL* 3.6 35.0 - - + +
490T GLN* 4.4 0.2 - - - -
491T VAL* 4.0 25.8 - - + -
530T VAL* 3.7 37.9 - - + +
531T ALA 4.2 0.4 - - - -
532T GLY* 3.9 18.2 - - - +
534T GLY 2.9 15.5 + - - +
535T GLU* 3.7 4.9 - - - +
537T HIS* 1.3 78.0 + - - +
539T GLU* 1.3 58.2 + - - +
541T CYS* 3.4 5.1 + - + +
542T LEU* 2.9 42.6 + - + +
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Residues in contact with GLU 539 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535T GLU 3.1 14.3 + - - +
536T LEU* 3.1 28.5 + - - +
538T LEU* 1.3 74.9 - - - +
540T ILE* 1.3 68.9 + - + +
542T LEU* 3.3 8.0 + - - +
543T GLN* 2.9 52.3 + - + +
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Residues in contact with ILE 540 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55S GLU* 4.2 32.1 - - + +
63S ILE* 4.7 14.1 - - + -
64S ASN* 5.4 5.6 - - - +
536T LEU* 3.1 37.9 + - + +
537T HIS* 3.6 11.0 - - + +
539T GLU* 1.3 77.1 - - - +
541T CYS* 1.3 56.6 + - - +
543T GLN* 3.0 19.9 + - - +
544T ASP* 2.8 58.6 + - - +
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Residues in contact with CYS 541 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511T LEU* 4.1 21.6 - - + +
515T ASP* 3.8 9.6 - - - -
518T VAL* 3.6 26.5 - - + -
530T VAL* 4.8 2.0 - - + -
532T GLY* 5.6 0.4 - - - -
537T HIS* 3.0 42.4 + - - -
538T LEU* 3.5 16.2 - - + +
540T ILE* 1.3 77.4 - - - +
542T LEU* 1.3 53.6 + - - +
544T ASP* 3.4 5.6 + - - +
545T LEU* 2.8 36.1 + - - +
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Residues in contact with LEU 542 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491T VAL* 3.7 23.6 - - + -
493T VAL* 3.9 27.1 - - + -
530T VAL* 4.2 17.5 - - + -
538T LEU* 2.9 34.5 + - + +
539T GLU* 3.9 6.5 - - - +
541T CYS* 1.3 70.6 - - - +
543T GLN* 1.3 66.3 + - + +
545T LEU* 3.7 11.0 - - + +
546T GLU* 2.9 27.9 + - - +
554T LEU* 4.7 1.8 - - + +
556T ILE* 4.0 26.5 - - + -
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Residues in contact with GLN 543 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55S GLU* 4.3 12.6 - - - +
539T GLU* 2.9 45.8 + - + +
540T ILE* 3.4 28.0 - - - +
542T LEU* 1.3 77.1 - - + +
544T ASP* 1.3 61.7 + - - +
546T GLU* 3.8 4.2 - - - +
547T HIS* 2.8 34.9 + - + +
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Residues in contact with ASP 544 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55S GLU* 5.7 1.9 - - - +
511T LEU* 5.3 1.1 - - + -
540T ILE* 2.8 43.0 + - - +
541T CYS* 3.8 5.3 + - - +
543T GLN* 1.3 75.0 - - - +
545T LEU* 1.3 57.1 + - - +
547T HIS* 4.9 0.7 - - - -
548T ASP* 2.9 42.0 + - - +
549T HIS* 3.0 30.2 + - + +
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Residues in contact with LEU 545 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493T VAL* 4.1 12.6 - - + -
504T LEU* 4.2 3.4 - - + -
507T GLY* 3.5 36.1 - - - +
508T LEU* 3.6 28.5 - - + +
511T LEU* 4.0 11.4 - - + -
530T VAL* 4.4 8.7 - - + -
541T CYS 2.8 22.1 + - - +
542T LEU* 3.7 10.3 - - + +
544T ASP* 1.3 74.3 - - - +
546T GLU* 1.3 60.9 + - - +
549T HIS* 3.6 9.6 - - + -
550T ALA* 2.7 37.2 + - + +
554T LEU* 3.5 22.2 - - + -
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Residues in contact with GLU 546 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496T LYS* 5.4 1.0 - - - -
542T LEU 2.9 18.5 + - - +
543T GLN* 3.9 3.3 - - - +
545T LEU* 1.3 78.4 - - - +
547T HIS* 1.3 59.5 + - + +
551T GLY* 2.9 25.6 + - - +
552T VAL 3.1 16.0 + - - +
553T PRO* 3.3 8.1 - - - +
554T LEU* 2.8 54.1 + - + +
556T ILE* 5.9 2.1 - - - +
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Residues in contact with HIS 547 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543T GLN 2.8 21.8 + - - +
544T ASP* 4.9 0.2 - - - -
546T GLU* 1.3 76.5 - - + +
548T ASP* 1.3 83.4 + - - +
551T GLY* 3.4 13.5 - - - -
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Residues in contact with ASP 548 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510T ARG* 4.6 4.3 + - - -
544T ASP* 2.9 31.1 + - - +
547T HIS* 1.3 101.7 + - - +
549T HIS* 1.3 75.6 + - + +
550T ALA 3.0 5.1 + - - -
551T GLY* 3.2 8.7 + - - -
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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