Contacts of the helix formed by residues 571 - 582 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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387F TRP* 3.2 26.5 - - - -
438F ALA* 3.5 11.3 - - - +
441F GLU* 3.5 9.4 + - - -
567F ARG* 3.2 24.9 - - - -
568F ILE 3.1 9.4 + - - -
569F ILE 3.6 0.4 - - - -
570F GLN* 1.3 78.8 - - - +
572F GLY* 1.3 66.0 + - - +
573F ILE* 3.3 9.0 + - - +
574F ALA* 3.2 16.1 + - - +
575F LEU* 3.6 2.8 + - - +
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Residues in contact with GLY 572 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368F LEU* 4.6 2.9 - - - +
438F ALA* 3.4 23.5 + - - +
441F GLU* 2.8 20.9 + - - +
442F LEU* 3.6 26.3 - - - +
571F SER* 1.3 70.3 - - - +
573F ILE* 1.3 66.9 + - - +
574F ALA 3.3 0.2 + - - -
575F LEU* 3.3 2.8 + - - +
576F LEU* 3.1 17.8 + - - +
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Residues in contact with ILE 573 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368F LEU* 3.3 50.3 - - + +
371F ARG* 4.1 18.8 - - + +
372F MET* 3.5 33.4 - - + -
375F MET* 4.4 12.1 - - + -
376F PHE* 4.7 0.4 - - + -
387F TRP* 3.6 24.7 - - + -
441F GLU* 4.7 3.8 - - - +
571F SER* 3.2 8.4 - - - +
572F GLY* 1.3 76.7 - - - +
574F ALA* 1.3 62.9 + - - +
576F LEU* 3.3 5.9 + - - +
577F LEU* 3.2 21.7 + - + +
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Residues in contact with ALA 574 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387F TRP* 3.9 11.3 - - + +
391F VAL* 3.8 9.3 - - + +
394F LEU* 3.9 17.2 - - + +
568F ILE* 3.0 40.6 - - + +
571F SER* 3.2 9.9 + - - +
572F GLY 3.1 0.2 - - - -
573F ILE* 1.3 76.6 - - - +
575F LEU* 1.3 66.8 + - - +
577F LEU* 3.2 18.6 + - - +
578F MET* 3.2 9.0 + - - +
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Residues in contact with LEU 575 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394F LEU* 4.0 18.6 - - + -
401F MET* 5.5 0.2 - - + -
405F VAL* 4.7 4.0 - - + -
435F LEU* 4.2 15.9 - - + -
438F ALA* 3.5 34.5 - - + +
439F LEU* 3.5 35.4 - - + +
442F LEU* 3.6 20.0 - - + -
571F SER 3.6 1.1 + - - +
572F GLY 3.3 5.0 + - - +
574F ALA* 1.3 75.9 - - - +
576F LEU* 1.3 60.2 + - - +
578F MET* 3.1 31.9 + - + +
579F LEU* 2.9 33.8 + - - +
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Residues in contact with LEU 576 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365F PHE* 3.5 39.9 - - + +
368F LEU* 3.5 28.5 - - + -
369F LEU* 3.5 17.0 - - + -
372F MET* 3.5 27.1 - - - -
442F LEU* 3.8 10.5 - - + +
572F GLY 3.1 12.4 + - - +
573F ILE* 3.4 11.7 - - - +
574F ALA 3.1 0.8 - - - -
575F LEU* 1.3 77.4 - - - +
577F LEU* 1.3 61.9 - - - +
579F LEU* 3.0 6.2 + - + +
580F ILE* 3.0 44.8 + - + +
588F PHE* 5.4 0.9 - - + -
596F ILE* 6.0 0.9 - - + -
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Residues in contact with LEU 577 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372F MET* 3.4 32.3 - - + -
376F PHE* 4.6 2.2 - - + -
384F ILE* 4.3 9.0 - - + -
387F TRP* 3.6 35.4 - - + +
388F MET* 3.5 33.2 - - + +
391F VAL* 3.9 3.8 - - + -
573F ILE 3.2 11.0 + - - +
574F ALA* 3.2 9.3 + - - +
576F LEU* 1.3 79.2 - - - +
578F MET* 1.3 57.6 - - - +
580F ILE* 3.5 8.7 + - + +
581F TRP* 3.1 29.3 + - - +
599F TRP* 4.9 0.4 - - + -
603F LEU* 3.6 28.2 - - + +
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Residues in contact with MET 578 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391F VAL* 3.5 37.9 - - + +
394F LEU* 4.4 11.0 - - - -
395F HIS* 4.5 5.8 - - - -
401F MET* 3.5 25.8 - - + -
402F ASP* 3.7 22.8 - - + +
405F VAL* 3.5 33.4 - - + -
574F ALA 3.2 9.6 + - - +
575F LEU* 3.1 28.2 + - + +
577F LEU* 1.3 78.5 - - - +
579F LEU* 1.3 62.8 + - + +
581F TRP* 3.9 2.0 - - - -
582F TYR* 3.4 29.3 + - + +
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Residues in contact with LEU 579 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365F PHE* 3.5 28.7 - - + -
402F ASP* 4.5 4.7 - - - +
405F VAL* 3.5 30.3 - - + -
406F TYR* 4.6 3.1 - - + +
409F LEU* 3.9 14.8 - - + -
442F LEU* 3.8 25.4 - - + -
575F LEU 2.9 18.5 + - - +
576F LEU* 3.0 7.8 + - + +
578F MET* 1.3 80.0 - - + +
580F ILE* 1.3 58.6 + - + +
581F TRP 3.4 0.2 - - - -
583F ARG* 3.2 48.8 + - + +
588F PHE* 3.4 17.7 - - + -
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Residues in contact with ILE 580 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369F LEU* 3.9 28.9 - - + -
372F MET* 5.4 0.2 - - - -
576F LEU* 3.0 31.6 + - + +
577F LEU* 3.5 11.6 + - + +
579F LEU* 1.3 76.7 - - - +
581F TRP* 1.3 57.7 + - - +
583F ARG 4.6 0.9 - - - -
588F PHE* 4.4 12.3 - - + -
596F ILE* 3.6 39.5 - - + +
599F TRP* 4.1 21.8 - - + +
600F LYS* 2.7 40.8 + - + +
603F LEU* 5.0 6.3 - - + -
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Residues in contact with TRP 581 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388F MET* 3.5 27.4 - - + -
391F VAL* 5.2 2.5 - - + -
577F LEU 3.1 19.1 + - - +
578F MET* 4.4 0.7 - - - -
579F LEU 3.4 0.2 - - - -
580F ILE* 1.3 82.3 - - - +
582F TYR* 1.3 91.2 - + + +
600F LYS* 4.2 4.2 + - - -
603F LEU* 3.6 39.3 - - + -
604F ASP* 5.0 8.5 - - - -
607F PHE* 3.8 26.5 - - + -
608F SER 3.8 9.6 - - - -
609F LEU* 4.6 16.6 - - + +
612F TYR* 3.4 47.6 - + + -
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Residues in contact with TYR 582 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391F VAL* 4.5 0.2 - - + -
395F HIS* 3.3 26.0 - + - -
402F ASP* 3.2 32.8 - - + +
578F MET* 3.4 25.6 + - + +
581F TRP* 1.3 98.0 - + + +
583F ARG* 1.3 67.8 + - - +
584F PRO* 3.4 7.3 - - - +
600F LYS* 4.6 2.3 + - - -
612F TYR* 2.8 43.3 + + - -
613F GLN* 5.1 1.5 + - - -
616F LYS* 3.3 18.8 + - - -
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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