Contacts of the helix formed by residues 571 - 582 (chain J) in PDB entry 4E2I
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 571 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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387J TRP* 3.2 27.4 - - - -
438J ALA* 3.5 11.7 - - - +
441J GLU* 3.6 9.2 + - - -
567J ARG* 3.2 24.5 - - - -
568J ILE 3.1 8.8 + - - -
570J GLN* 1.3 79.6 - - - +
572J GLY* 1.3 65.7 + - - +
573J ILE* 3.3 9.4 + - - +
574J ALA* 3.2 15.4 + - - +
575J LEU 3.6 2.6 + - - -
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Residues in contact with GLY 572 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368J LEU* 4.6 2.4 - - - +
438J ALA* 3.4 23.7 + - - -
441J GLU* 2.8 20.4 + - - +
442J LEU* 3.6 26.6 - - - +
571J SER* 1.3 69.4 - - - +
573J ILE* 1.3 67.1 + - - +
574J ALA 3.3 0.2 + - - -
575J LEU* 3.3 2.2 + - - +
576J LEU* 3.1 17.9 + - - +
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Residues in contact with ILE 573 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368J LEU* 3.3 49.8 - - + +
371J ARG* 4.1 18.8 - - + +
372J MET* 3.5 33.4 - - + -
375J MET* 4.4 12.1 - - + -
376J PHE* 4.7 0.2 - - + -
387J TRP* 3.6 25.8 - - + -
441J GLU* 4.6 4.5 - - - +
571J SER* 3.2 7.6 - - - +
572J GLY* 1.3 77.7 - - - +
574J ALA* 1.3 61.6 + - - +
576J LEU* 3.3 6.8 + - - +
577J LEU* 3.2 21.7 + - + +
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Residues in contact with ALA 574 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387J TRP* 3.9 10.8 - - + +
391J VAL* 3.8 9.4 - - + +
394J LEU* 3.9 16.8 - - + +
568J ILE* 3.0 41.5 - - + +
571J SER* 3.2 8.9 + - - +
572J GLY 3.1 0.2 - - - -
573J ILE* 1.3 77.7 - - - +
575J LEU* 1.3 64.8 + - - +
577J LEU* 3.2 19.5 + - - +
578J MET* 3.2 9.0 + - - +
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Residues in contact with LEU 575 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394J LEU* 4.0 18.4 - - + -
401J MET* 5.5 0.7 - - + -
405J VAL* 4.7 3.6 - - + -
435J LEU* 4.3 15.0 - - + -
438J ALA* 3.5 35.4 - - + +
439J LEU* 3.5 35.0 - - + +
442J LEU* 3.6 19.7 - - + -
571J SER 3.6 0.8 + - - +
572J GLY 3.3 5.5 + - - +
574J ALA* 1.3 76.1 - - - +
576J LEU* 1.3 59.6 + - - +
578J MET* 3.1 32.9 + - + +
579J LEU* 2.9 33.9 + - - +
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Residues in contact with LEU 576 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365J PHE* 3.5 39.3 - - + +
368J LEU* 3.5 26.9 - - + -
369J LEU* 3.5 17.0 - - + -
372J MET* 3.5 27.8 - - - -
442J LEU* 3.8 9.6 - - + +
572J GLY 3.1 13.1 + - - +
573J ILE* 3.4 10.1 - - - +
574J ALA 3.1 0.2 - - - -
575J LEU* 1.3 77.2 - - - +
577J LEU* 1.3 63.1 + - - +
579J LEU* 3.0 6.3 + - + +
580J ILE* 3.0 44.5 + - + +
588J PHE* 5.4 0.9 - - + -
596J ILE* 6.0 0.9 - - + -
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Residues in contact with LEU 577 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372J MET* 3.4 32.1 - - + -
376J PHE* 4.5 2.7 - - + -
384J ILE* 4.3 10.1 - - + -
387J TRP* 3.6 34.8 - - + +
388J MET* 3.5 32.1 - - + +
391J VAL* 3.9 4.0 - - + -
573J ILE 3.2 10.8 + - - +
574J ALA* 3.2 8.8 + - - +
576J LEU* 1.3 78.8 - - - +
578J MET* 1.3 57.7 + - - +
580J ILE* 3.5 9.0 + - + +
581J TRP* 3.1 30.5 + - - +
599J TRP* 4.9 0.7 - - + -
603J LEU* 3.6 27.3 - - + +
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Residues in contact with MET 578 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391J VAL* 3.5 39.5 - - + +
394J LEU* 4.4 11.4 - - + -
395J HIS* 4.5 5.8 - - - -
401J MET* 3.6 25.8 - - + -
402J ASP* 3.7 22.7 - - + +
405J VAL* 3.5 33.2 - - + -
574J ALA 3.2 9.4 + - - +
575J LEU* 3.1 28.4 + - + +
577J LEU* 1.3 77.6 - - - +
579J LEU* 1.3 60.5 + - + +
581J TRP* 3.9 2.5 - - - -
582J TYR* 3.4 29.6 + - + +
583J ARG* 5.3 0.2 - - - +
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Residues in contact with LEU 579 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365J PHE* 3.5 29.2 - - + -
402J ASP* 4.5 4.9 - - - +
405J VAL* 3.5 30.1 - - + -
406J TYR* 4.6 2.9 - - + +
409J LEU* 3.9 15.3 - - + -
442J LEU* 3.8 25.1 - - + -
575J LEU 2.9 20.1 + - - +
576J LEU* 3.0 7.4 + - - +
578J MET* 1.3 80.3 - - + +
580J ILE* 1.3 58.3 + - + +
581J TRP 3.4 0.2 - - - -
583J ARG* 3.2 49.8 + - + +
588J PHE* 3.4 17.1 - - + -
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Residues in contact with ILE 580 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369J LEU* 3.9 28.9 - - + -
372J MET* 5.4 0.2 - - - -
576J LEU* 3.0 31.1 + - + +
577J LEU* 3.5 11.4 + - + +
579J LEU* 1.3 76.5 - - - +
581J TRP* 1.3 58.5 + - - +
583J ARG 4.6 0.9 - - - -
588J PHE* 4.4 12.3 - - + -
596J ILE* 3.6 39.7 - - + +
599J TRP* 4.1 21.8 - - + -
600J LYS* 2.7 41.1 + - + +
603J LEU* 5.0 6.3 - - + -
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Residues in contact with TRP 581 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388J MET* 3.5 27.1 - - + -
391J VAL* 5.2 2.2 - - + -
577J LEU 3.1 19.8 + - - +
578J MET* 4.1 1.1 - - - +
580J ILE* 1.3 80.3 - - - +
582J TYR* 1.3 92.5 + + + +
600J LYS* 4.2 4.2 + - - -
603J LEU* 3.6 40.8 - - + +
604J ASP* 5.1 8.1 - - - -
607J PHE* 3.8 27.1 - - + -
608J SER 3.8 10.1 - - - -
609J LEU* 4.6 17.7 - - + +
612J TYR* 3.4 47.9 - + + -
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Residues in contact with TYR 582 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391J VAL* 4.5 0.4 - - + -
395J HIS* 3.3 28.2 - + - -
402J ASP* 3.2 31.6 - - + +
578J MET* 3.4 24.5 + - + +
581J TRP* 1.3 97.2 - + + +
583J ARG* 1.3 67.7 + - - +
584J PRO* 3.4 7.1 - - - +
600J LYS* 4.6 2.1 + - - -
612J TYR* 2.8 43.0 + + - -
613J GLN* 5.1 1.5 + - - -
616J LYS* 3.3 18.5 + - - -
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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