Contacts of the helix formed by residues 571 - 582 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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387A TRP* 3.2 27.7 - - - -
438A ALA* 3.5 11.1 - - - +
441A GLU* 3.6 9.0 + - - -
567A ARG* 3.2 24.9 - - - -
568A ILE 3.1 9.7 + - - -
569A ILE 3.6 0.6 - - - -
570A GLN* 1.3 80.3 - - - +
572A GLY* 1.3 66.4 + - - +
573A ILE* 3.3 8.7 + - - +
574A ALA* 3.2 17.0 + - - +
575A LEU 3.6 2.6 + - - -
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Residues in contact with GLY 572 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368A LEU* 4.6 2.6 - - - +
438A ALA* 3.4 24.3 + - - +
441A GLU* 2.8 20.2 + - - +
442A LEU* 3.6 25.9 - - - +
571A SER* 1.3 69.8 - - - +
573A ILE* 1.3 66.6 + - - +
574A ALA 3.3 0.2 + - - -
575A LEU* 3.3 2.5 + - - -
576A LEU* 3.1 17.8 + - - +
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Residues in contact with ILE 573 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A LEU* 3.3 50.0 - - + +
371A ARG* 4.1 18.8 - - + +
372A MET* 3.5 33.7 - - + -
375A MET* 4.4 11.7 - - + -
376A PHE* 4.7 0.7 - - + -
387A TRP* 3.6 25.1 - - + -
441A GLU* 4.6 4.3 - - - +
571A SER* 3.2 7.2 - - - +
572A GLY* 1.3 76.9 - - - +
574A ALA* 1.3 62.3 + - - +
576A LEU* 3.3 5.8 + - - +
577A LEU* 3.2 21.8 + - + +
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Residues in contact with ALA 574 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A TRP* 3.9 10.6 - - - +
390A GLY 5.5 0.7 - - - -
391A VAL* 3.8 9.8 - - + +
394A LEU* 3.9 16.2 - - + -
568A ILE* 3.0 41.5 - - + +
571A SER* 3.2 9.7 + - - +
572A GLY 3.1 0.2 - - - -
573A ILE* 1.3 78.7 - - - +
575A LEU* 1.3 64.7 + - - +
577A LEU* 3.2 18.3 + - - +
578A MET* 3.2 9.0 + - - +
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Residues in contact with LEU 575 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394A LEU* 4.0 18.4 - - + -
401A MET* 5.5 0.4 - - + -
405A VAL* 4.7 4.3 - - + -
435A LEU* 4.3 15.3 - - + -
438A ALA* 3.5 34.5 - - + +
439A LEU* 3.5 35.0 - - + +
442A LEU* 3.6 20.4 - - + -
571A SER 3.6 0.9 + - - +
572A GLY 3.3 5.6 + - - +
574A ALA* 1.3 76.2 - - - +
576A LEU* 1.3 60.2 + - - +
578A MET* 3.1 31.5 + - + +
579A LEU* 2.9 34.2 + - - +
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Residues in contact with LEU 576 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A PHE* 3.5 39.9 - - + +
368A LEU* 3.5 27.4 - - + +
369A LEU* 3.5 17.0 - - + -
372A MET* 3.5 28.0 - - - -
442A LEU* 3.8 10.0 - - + +
572A GLY 3.1 12.2 + - - +
573A ILE* 3.4 10.5 - - - +
575A LEU* 1.3 78.1 - - - +
577A LEU* 1.3 61.1 + - - +
579A LEU* 3.0 5.5 + - + +
580A ILE* 3.0 44.7 + - + +
588A PHE* 5.4 0.9 - - + -
596A ILE* 6.0 0.7 - - + -
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Residues in contact with LEU 577 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372A MET* 3.4 32.5 - - + -
376A PHE* 4.6 2.7 - - + -
384A ILE* 4.3 9.6 - - + -
387A TRP* 3.6 35.9 - - + +
388A MET* 3.5 33.2 - - + +
391A VAL* 3.9 4.5 - - + -
573A ILE 3.2 10.1 + - - +
574A ALA 3.2 9.0 + - - +
576A LEU* 1.3 79.2 - - - +
578A MET* 1.3 57.5 + - - +
580A ILE* 3.9 9.1 - - + +
581A TRP* 3.1 29.8 + - - +
599A TRP* 4.9 0.4 - - + -
603A LEU* 3.7 27.1 - - + +
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Residues in contact with MET 578 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391A VAL* 3.5 38.8 - - + +
394A LEU* 4.4 11.4 - - - -
395A HIS* 4.5 5.8 - - - -
401A MET* 3.5 24.7 - - + -
402A ASP* 3.7 23.2 - - + +
405A VAL* 3.5 33.4 - - + -
574A ALA 3.2 9.6 + - - +
575A LEU* 3.1 29.1 + - + +
577A LEU* 1.3 78.9 - - - +
579A LEU* 1.3 62.5 + - + +
581A TRP* 3.9 1.6 - - - -
582A TYR* 3.4 29.0 + - + +
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Residues in contact with LEU 579 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A PHE* 3.5 29.4 - - + -
402A ASP* 4.5 5.2 - - - +
405A VAL* 3.5 29.4 - - + -
406A TYR* 4.6 3.1 - - + +
409A LEU* 3.9 14.1 - - + -
442A LEU* 3.8 25.4 - - + -
575A LEU 2.9 17.0 + - - +
576A LEU* 3.0 8.0 + - + +
578A MET* 1.3 80.3 - - + +
580A ILE* 1.3 57.1 + - - +
581A TRP 3.4 0.2 - - - -
583A ARG* 3.2 48.2 + - + +
588A PHE* 3.4 17.7 - - + -
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Residues in contact with ILE 580 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A LEU* 3.9 28.7 - - + -
372A MET* 5.4 0.2 - - - -
576A LEU* 3.0 31.7 + - + +
577A LEU* 4.1 11.0 - - + +
579A LEU* 1.3 77.8 - - - +
581A TRP* 1.3 58.3 + - - +
583A ARG 4.6 0.9 - - - -
588A PHE* 4.4 12.3 - - + -
596A ILE* 3.6 37.9 - - + +
599A TRP* 4.1 21.8 - - + +
600A LYS* 2.7 42.9 + - + +
603A LEU* 5.0 6.1 - - + -
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Residues in contact with TRP 581 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388A MET* 3.5 26.9 - - + -
391A VAL* 5.2 2.2 - - + -
577A LEU 3.1 18.4 + - - +
578A MET* 3.7 1.5 + - - -
579A LEU 3.4 0.2 - - - -
580A ILE* 1.3 80.7 - - - +
582A TYR* 1.3 91.3 + + + +
600A LYS* 4.2 4.9 + - - -
603A LEU* 3.6 40.2 - - + -
604A ASP* 5.0 8.3 - - - -
607A PHE* 3.8 26.2 - - + -
608A SER 3.8 10.1 - - - -
609A LEU* 4.6 17.4 - - + +
612A TYR* 3.4 47.9 - + + -
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Residues in contact with TYR 582 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391A VAL* 4.5 0.2 - - + -
395A HIS* 3.3 27.5 - + - -
402A ASP* 3.2 32.5 - - + +
578A MET* 3.4 24.4 + - + +
581A TRP* 1.3 97.8 - + + +
583A ARG* 1.3 68.9 + - - +
584A PRO* 3.4 7.1 - - - +
600A LYS* 4.6 2.3 + - - -
612A TYR* 2.8 42.4 + + - -
613A GLN* 5.1 1.5 + - - -
616A LYS* 3.3 19.2 + - - -
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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