Contacts of the helix formed by residues 571 - 582 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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387I TRP* 3.2 26.9 - - - -
438I ALA* 3.5 11.5 - - - +
441I GLU* 3.6 9.5 + - - -
567I ARG* 3.2 25.4 - - - -
568I ILE 3.1 10.0 + - - -
569I ILE 3.6 0.2 - - - -
570I GLN* 1.3 78.6 - - - +
572I GLY* 1.3 64.8 + - - +
573I ILE* 3.3 9.2 + - - +
574I ALA* 3.2 16.9 + - - +
575I LEU* 3.6 3.1 + - - +
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Residues in contact with GLY 572 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368I LEU* 4.6 2.4 - - - +
438I ALA* 3.4 23.3 + - - +
441I GLU* 2.8 21.1 + - - +
442I LEU* 3.6 26.3 - - - +
571I SER* 1.3 69.7 - - - +
573I ILE* 1.3 67.3 + - - +
575I LEU* 3.3 2.6 + - - +
576I LEU* 3.1 18.0 + - - +
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Residues in contact with ILE 573 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368I LEU* 3.3 49.6 - - + +
371I ARG* 4.1 19.7 - - + +
372I MET* 3.5 34.1 - - + -
375I MET* 4.4 12.1 - - + -
376I PHE* 4.7 0.2 - - + -
387I TRP* 3.6 26.5 - - + -
441I GLU* 4.7 4.5 - - - +
571I SER* 3.2 7.4 - - - +
572I GLY* 1.3 78.3 - - - +
574I ALA* 1.3 62.0 + - - +
576I LEU* 3.3 6.5 + - - +
577I LEU* 3.2 22.1 + - + +
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Residues in contact with ALA 574 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387I TRP* 3.9 11.9 - - + +
391I VAL* 3.8 9.5 - - + +
394I LEU* 3.9 16.8 - - + +
568I ILE* 3.0 40.8 - - + +
571I SER* 3.2 9.1 + - - +
572I GLY 3.1 0.2 - - - -
573I ILE* 1.3 77.0 - - - +
575I LEU* 1.3 65.8 + - - +
577I LEU* 3.2 18.5 + - - +
578I MET* 3.2 8.8 + - - +
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Residues in contact with LEU 575 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394I LEU* 4.0 18.8 - - + -
401I MET* 5.5 0.4 - - + -
405I VAL* 4.7 4.3 - - + -
435I LEU* 4.3 15.7 - - + -
438I ALA* 3.5 35.9 - - + +
439I LEU* 3.5 34.3 - - + +
442I LEU* 3.6 20.0 - - + -
571I SER 3.6 1.1 + - - +
572I GLY 3.3 5.0 + - - +
574I ALA* 1.3 76.5 - - - +
576I LEU* 1.3 59.5 + - - +
578I MET* 3.0 32.3 + - + +
579I LEU* 2.9 34.4 + - - +
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Residues in contact with LEU 576 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365I PHE* 3.5 40.4 - - + +
368I LEU* 3.5 27.4 - - + -
369I LEU* 3.5 17.0 - - + -
372I MET* 3.5 27.6 - - - -
442I LEU* 3.8 10.0 - - + +
572I GLY 3.1 12.6 + - - +
573I ILE* 3.4 10.8 - - - +
575I LEU* 1.3 78.0 - - - +
577I LEU* 1.3 60.9 + - - +
579I LEU* 3.0 5.8 + - + +
580I ILE* 3.0 44.8 + - + +
588I PHE* 5.4 1.1 - - + -
596I ILE* 6.0 0.7 - - + -
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Residues in contact with LEU 577 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372I MET* 3.4 33.0 - - + -
376I PHE* 4.6 2.2 - - + -
384I ILE* 4.3 9.6 - - + -
387I TRP* 3.6 35.4 - - + +
388I MET* 3.5 33.5 - - + +
391I VAL* 3.9 4.0 - - + -
573I ILE 3.2 10.8 + - - +
574I ALA* 3.2 9.7 + - - +
576I LEU* 1.3 78.6 - - - +
578I MET* 1.3 56.9 + - - +
580I ILE* 3.5 8.4 + - + +
581I TRP* 3.1 30.3 + - - +
599I TRP* 4.9 0.7 - - + -
603I LEU* 3.6 27.4 - - + +
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Residues in contact with MET 578 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391I VAL* 3.5 38.3 - - + +
394I LEU* 4.4 11.0 - - - -
395I HIS* 4.5 6.1 - - - -
401I MET* 3.5 25.4 - - + -
402I ASP* 3.7 22.5 - - + +
405I VAL* 3.5 33.2 - - + -
574I ALA 3.2 9.4 + - - +
575I LEU* 3.0 28.4 + - + +
577I LEU* 1.3 78.5 - - - +
579I LEU* 1.3 61.1 + - + +
581I TRP* 3.9 1.8 - - - -
582I TYR* 3.4 29.6 + - + +
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Residues in contact with LEU 579 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365I PHE* 3.5 28.9 - - + -
402I ASP* 4.5 5.2 - - - +
405I VAL* 3.5 29.8 - - + -
406I TYR* 4.6 2.2 - - + +
409I LEU* 3.9 14.8 - - + -
442I LEU* 3.8 29.8 - - + -
575I LEU 2.9 12.7 + - - +
576I LEU* 3.0 7.6 + - + +
578I MET* 1.3 81.2 - - + +
580I ILE* 1.3 57.7 + - - +
581I TRP 3.3 0.2 - - - -
583I ARG* 3.2 49.4 + - + +
588I PHE* 3.4 17.3 - - + -
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Residues in contact with ILE 580 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369I LEU* 3.9 28.7 - - + -
372I MET* 5.4 0.4 - - - -
576I LEU* 3.0 32.4 + - + +
577I LEU* 4.1 11.2 - - + +
579I LEU* 1.3 77.6 - - - +
581I TRP* 1.3 58.2 + - - +
583I ARG 4.6 1.1 - - - -
588I PHE* 4.4 12.3 - - + -
596I ILE* 3.6 38.8 - - + +
599I TRP* 4.1 21.8 - - + -
600I LYS* 2.7 42.0 + - + +
603I LEU* 5.0 5.2 - - + -
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Residues in contact with TRP 581 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388I MET* 3.5 25.6 - - + -
391I VAL* 5.2 2.0 - - + -
577I LEU 3.1 19.2 + - - +
578I MET* 4.1 1.3 - - - +
579I LEU 3.3 0.4 - - - -
580I ILE* 1.3 79.9 - - - +
582I TYR* 1.3 90.9 + + + +
600I LYS* 4.2 4.3 + - - -
603I LEU* 3.6 40.6 - - + +
604I ASP* 5.1 8.3 - - - -
607I PHE* 3.8 26.9 - - + -
608I SER 3.8 9.2 - - - -
609I LEU* 4.6 17.7 - - + +
612I TYR* 3.4 47.3 - + + -
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Residues in contact with TYR 582 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391I VAL* 4.5 0.4 - - + -
395I HIS* 3.4 27.7 - + - -
402I ASP* 3.2 33.0 - - + +
578I MET* 3.4 23.8 + - + +
581I TRP* 1.3 97.5 - + + +
583I ARG* 1.3 68.4 + - - +
584I PRO* 3.4 7.1 - - - +
600I LYS* 4.6 1.7 + - - -
612I TYR* 2.8 43.3 + + - -
613I GLN* 5.1 1.5 + - - -
616I 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