Contacts of the helix formed by residues 571 - 582 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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387K TRP* 3.2 26.4 - - - -
438K ALA* 3.5 11.5 - - - +
441K GLU* 3.5 10.1 + - - -
567K ARG* 3.2 24.7 - - - -
568K ILE 3.1 9.9 + - - -
570K GLN* 1.3 79.0 - - - +
572K GLY* 1.3 65.2 + - - +
573K ILE* 3.3 9.4 + - - +
574K ALA* 3.2 16.9 + - - +
575K LEU 3.6 2.8 + - - -
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Residues in contact with GLY 572 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368K LEU* 4.6 2.9 - - - +
438K ALA* 3.4 23.1 + - - +
441K GLU* 2.8 20.8 + - - +
442K LEU* 3.6 26.4 - - - +
571K SER* 1.3 70.5 - - - +
573K ILE* 1.3 68.0 - - - +
575K LEU* 3.3 2.8 + - - -
576K LEU* 3.1 17.5 + - - +
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Residues in contact with ILE 573 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368K LEU* 3.3 50.0 - - + +
371K ARG* 4.1 18.2 - - + +
372K MET* 3.5 34.5 - - + -
375K MET* 4.4 11.7 - - + -
376K PHE* 4.7 0.4 - - + -
387K TRP* 3.6 25.4 - - + -
441K GLU* 4.6 4.5 - - - +
571K SER* 3.2 7.8 - - - +
572K GLY* 1.3 77.7 - - - +
574K ALA* 1.3 63.7 + - - +
576K LEU* 3.3 5.8 + - - +
577K LEU* 3.2 21.7 + - + +
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Residues in contact with ALA 574 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387K TRP* 3.9 11.0 - - + +
390K GLY 5.6 0.4 - - - -
391K VAL* 3.8 9.6 - - + +
394K LEU* 3.9 16.1 - - + +
568K ILE* 3.0 41.3 - - + +
571K SER* 3.2 9.9 + - - +
572K GLY 3.1 0.6 - - - -
573K ILE* 1.3 76.7 - - - +
575K LEU* 1.3 63.4 + - - +
577K LEU* 3.2 18.2 + - - +
578K MET* 3.2 9.7 + - - +
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Residues in contact with LEU 575 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394K LEU* 4.0 18.4 - - + -
401K MET* 5.5 0.2 - - + -
405K VAL* 4.7 4.7 - - + -
435K LEU* 4.2 15.7 - - + -
438K ALA* 3.5 35.2 - - + +
439K LEU* 3.5 34.1 - - + +
442K LEU* 3.6 20.2 - - + -
571K SER 3.6 0.9 + - - +
572K GLY 3.3 5.0 + - - +
574K ALA* 1.3 76.4 - - - +
576K LEU* 1.3 60.2 + - - +
578K MET* 3.0 32.3 + - + +
579K LEU* 2.9 34.2 + - - +
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Residues in contact with LEU 576 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365K PHE* 3.5 39.3 - - + +
368K LEU* 3.5 28.7 - - + +
369K LEU* 3.5 16.8 - - + -
372K MET* 3.5 27.6 - - - -
442K LEU* 3.8 9.4 - - + +
572K GLY 3.1 13.6 + - - +
573K ILE* 3.4 11.0 - - - +
574K ALA 3.1 0.2 - - - -
575K LEU* 1.3 77.2 - - - +
577K LEU* 1.3 61.7 + - - +
579K LEU* 3.1 6.3 + - + +
580K ILE* 3.0 44.3 + - + +
588K PHE* 5.4 0.7 - - + -
596K ILE* 6.0 0.9 - - + -
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Residues in contact with LEU 577 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372K MET* 3.4 32.5 - - + -
376K PHE* 4.6 2.2 - - + -
384K ILE* 4.3 9.4 - - + -
387K TRP* 3.6 35.4 - - + +
388K MET* 3.5 33.2 - - + +
391K VAL* 3.9 4.0 - - + -
573K ILE 3.2 9.9 + - - +
574K ALA* 3.2 9.5 + - - +
576K LEU* 1.3 79.2 - - - +
578K MET* 1.3 57.0 + - - +
580K ILE* 3.9 7.3 - - + +
581K TRP* 3.1 29.6 + - - +
599K TRP* 4.9 0.7 - - + -
603K LEU* 3.7 28.5 - - + +
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Residues in contact with MET 578 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391K VAL* 3.5 38.8 - - + +
394K LEU* 4.4 11.0 - - + -
395K HIS* 4.5 5.8 - - - -
401K MET* 3.5 26.5 - - + -
402K ASP* 3.7 22.4 - - + +
405K VAL* 3.5 33.0 - - + -
574K ALA 3.2 9.6 + - - +
575K LEU* 3.0 27.9 + - + +
577K LEU* 1.3 78.7 - - - +
579K LEU* 1.3 60.6 + - + +
581K TRP* 4.4 1.8 - - - -
582K TYR* 3.4 29.0 + - + +
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Residues in contact with LEU 579 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365K PHE* 3.5 29.8 - - + -
402K ASP* 4.5 4.7 - - - +
405K VAL* 3.5 29.4 - - + -
406K TYR* 4.6 3.8 - - + +
409K LEU* 3.9 13.7 - - + -
442K LEU* 3.8 29.6 - - + -
575K LEU 2.9 14.7 + - - +
576K LEU* 3.1 8.3 + - + +
578K MET* 1.3 80.5 - - + +
580K ILE* 1.3 57.4 + - - +
583K ARG* 3.2 49.1 + - + +
588K PHE* 3.4 17.8 - - + -
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Residues in contact with ILE 580 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369K LEU* 3.9 28.7 - - + -
372K MET* 5.4 0.4 - - - -
576K LEU* 3.0 32.2 + - + +
577K LEU* 4.1 11.9 - - + +
579K LEU* 1.3 77.6 - - - +
581K TRP* 1.3 59.0 + - - +
583K ARG 4.6 1.1 - - - -
588K PHE* 4.4 11.7 - - + -
596K ILE* 3.6 37.5 - - + +
599K TRP* 4.1 20.6 - - + +
600K LYS* 2.7 41.7 + - + +
603K LEU* 5.0 5.6 - - + -
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Residues in contact with TRP 581 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388K MET* 3.5 26.5 - - + -
391K VAL* 5.2 1.8 - - + -
577K LEU 3.1 19.1 + - - +
578K MET* 4.1 1.1 - - - +
579K LEU 3.4 0.4 - - - -
580K ILE* 1.3 81.3 - - - +
582K TYR* 1.3 91.6 + + + +
600K LYS* 4.2 4.2 + - - -
603K LEU* 3.6 40.4 - - + +
604K ASP* 5.0 8.3 - - - -
607K PHE* 3.8 26.7 - - + -
608K SER 3.8 9.9 - - - -
609K LEU* 4.6 17.2 - - + +
612K TYR* 3.4 45.2 - + + -
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Residues in contact with TYR 582 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391K VAL* 4.5 0.4 - - + -
395K HIS* 3.3 27.4 - + - -
402K ASP* 3.2 32.3 - - + +
578K MET* 3.4 24.3 + - + +
581K TRP* 1.3 96.5 - + + +
583K ARG* 1.3 69.1 + - - +
584K PRO* 3.4 7.1 - - - +
600K LYS* 4.6 1.9 + - - -
612K TYR* 2.8 43.2 + + - -
613K GLN* 5.1 1.3 + - - -
616K LYS* 3.3 19.0 + - - -
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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