Contacts of the helix formed by residues 536 - 545 (chain D) in PDB entry 2I0J
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 LEU 536 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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354D LEU* 4.2 10.8 - - + -
380D GLU* 5.0 9.6 - - + +
383D TRP* 3.7 40.8 - - + +
522D MET* 5.7 1.3 - - + -
537D TYR* 1.3 61.6 + - - +
538D ASP* 2.9 6.9 + - - +
539D LEU* 2.7 54.1 + - + +
540D LEU* 2.8 38.0 + - + +
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Residues in contact with TYR 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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373D HIS* 2.8 43.7 + + - -
376D VAL* 3.5 28.6 - - + +
377D HIS* 4.5 12.1 - + + -
380D GLU* 3.2 37.8 + - - +
536D LEU* 1.3 78.6 - - - +
538D ASP* 1.3 72.1 + - - +
540D LEU* 4.9 2.5 - - - -
541D LEU* 3.3 41.0 + - + +
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Residues in contact with ASP 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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536D LEU 2.9 3.6 + - - +
537D TYR* 1.3 95.6 - - - +
539D LEU* 1.3 58.9 + - - +
541D LEU* 4.0 11.6 - - - +
542D GLU* 3.2 26.9 + - - +
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Residues in contact with LEU 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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351D ASP* 6.0 3.1 - - - +
354D LEU* 4.7 12.6 - - + -
536D LEU* 2.7 42.4 + - + +
538D ASP* 1.3 72.7 - - - +
540D LEU* 1.3 60.5 + - + +
542D GLU* 3.6 8.8 + - + +
543D MET* 2.8 39.3 + - + +
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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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354D LEU* 4.3 25.1 - - + -
358D ILE* 4.2 13.6 - - + +
376D VAL* 3.8 15.5 - - + +
379D LEU* 4.0 13.7 - - + +
380D GLU* 3.3 46.9 - - + +
383D TRP* 5.3 2.9 - - + -
536D LEU* 2.8 38.3 + - + +
537D TYR* 4.3 3.1 - - - +
539D LEU* 1.3 76.0 - - + +
541D LEU* 1.3 58.8 - - - +
543D MET* 3.1 8.9 + - + +
544D LEU* 2.8 32.9 + - + +
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Residues in contact with LEU 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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372D LEU* 3.7 37.0 - - + +
373D HIS* 5.7 1.8 - - - +
376D VAL* 3.4 16.3 - - + +
537D TYR* 3.3 37.1 + - + +
538D ASP* 4.2 10.5 - - - +
540D LEU* 1.3 73.3 - - - +
542D GLU* 1.3 67.5 + - - +
543D MET 3.0 1.8 - - - -
544D LEU 4.4 0.2 - - - +
545D ASP* 2.9 35.2 + - + +
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Residues in contact with GLU 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 ASP 3.2 18.0 + - - +
539D LEU* 3.6 12.3 - - + +
540D LEU 3.3 0.2 - - - -
541D LEU* 1.3 79.5 - - - +
543D MET* 1.3 62.2 + - + +
545D ASP* 3.6 15.4 - - - +
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Residues in contact with MET 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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354D LEU 5.2 0.2 - - - -
355D VAL* 3.8 44.0 - - + +
358D ILE* 3.0 40.5 - - + +
362D LYS* 5.3 1.2 + - - -
539D LEU* 2.8 38.1 - - + +
540D LEU* 3.2 3.4 - - + +
541D LEU 3.0 0.2 - - - -
542D GLU* 1.3 81.7 - - + +
544D LEU* 1.3 67.4 + - - +
545D ASP 3.1 7.8 + - - +
546D ALA* 4.1 5.5 + - - +
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Residues in contact with LEU 544 (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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358D ILE* 3.4 26.7 - - + +
362D LYS* 3.2 38.5 + - + +
367D PHE* 4.8 2.7 - - + -
372D LEU* 3.6 18.8 - - + +
375D GLN* 3.5 25.1 - - + +
376D VAL* 3.1 44.9 - - + +
379D LEU* 4.0 17.0 - - + -
540D LEU 2.8 19.5 + - - +
541D LEU 4.1 1.1 - - - +
543D MET* 1.3 73.8 - - - +
545D ASP* 1.3 56.4 + - - +
546D ALA* 3.0 9.0 + - - +
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Residues in contact with ASP 545 (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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372D LEU* 3.7 26.0 - - + +
541D LEU* 2.9 23.9 + - + +
542D GLU* 3.6 15.8 - - - +
543D MET 3.1 2.2 + - - +
544D LEU* 1.3 72.7 - - - +
546D ALA* 1.3 65.2 + - - +
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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