Contacts of the helix formed by residues 571 - 582 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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387H TRP* 3.2 26.5 - - - -
438H ALA* 3.5 11.9 - - - +
441H GLU* 3.6 9.3 + - - -
567H ARG* 3.2 25.4 - - - -
568H ILE 3.1 9.8 + - - -
569H ILE 3.6 0.2 - - - -
570H GLN* 1.3 79.0 - - - +
572H GLY* 1.3 66.4 + - - +
573H ILE* 3.3 9.0 + - - +
574H ALA* 3.2 16.6 + - - +
575H LEU 3.6 2.6 + - - -
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Residues in contact with GLY 572 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368H LEU* 4.6 2.8 - - - +
438H ALA* 3.4 23.3 + - - +
441H GLU* 2.8 20.7 + - - +
442H LEU* 3.6 26.5 - - - +
571H SER* 1.3 70.7 - - - +
573H ILE* 1.3 66.2 + - - +
574H ALA 3.3 0.2 + - - -
575H LEU* 3.3 2.2 + - - -
576H LEU* 3.1 17.5 + - - +
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Residues in contact with ILE 573 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368H LEU* 3.3 48.9 - - + +
371H ARG* 4.1 19.1 - - + +
372H MET* 3.5 33.4 - - + -
375H MET* 4.4 12.1 - - + -
376H PHE* 4.7 0.4 - - + -
387H TRP* 3.5 26.0 - - + -
441H GLU* 4.6 4.5 - - - +
571H SER* 3.8 7.6 - - - +
572H GLY* 1.3 77.9 - - - +
574H ALA* 1.3 61.2 + - - +
576H LEU* 3.4 6.6 + - - +
577H LEU* 3.2 22.1 + - + +
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Residues in contact with ALA 574 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387H TRP* 3.9 10.4 - - + +
391H VAL* 3.8 10.5 - - + +
394H LEU* 3.9 16.8 - - + +
568H ILE* 3.0 40.6 - - + +
571H SER* 3.2 9.3 + - - +
572H GLY 3.1 0.2 - - - -
573H ILE* 1.3 77.7 - - - +
575H LEU* 1.3 64.9 + - - +
577H LEU* 3.2 18.8 + - - +
578H MET* 3.2 9.2 + - - +
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Residues in contact with LEU 575 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394H LEU* 4.0 18.6 - - + -
401H MET* 5.5 0.2 - - + -
405H VAL* 4.7 4.3 - - + -
435H LEU* 4.2 15.5 - - + -
438H ALA* 3.5 34.5 - - + +
439H LEU* 3.5 35.0 - - + +
442H LEU* 3.6 19.7 - - + -
571H SER 3.6 1.5 + - - +
572H GLY 3.3 5.7 + - - +
574H ALA* 1.3 76.8 - - - +
576H LEU* 1.3 60.4 + - - +
578H MET* 3.0 33.0 + - + +
579H LEU* 2.9 33.7 + - - +
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Residues in contact with LEU 576 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365H PHE* 3.5 40.2 - - + +
368H LEU* 3.5 27.6 - - + -
369H LEU* 3.5 17.0 - - + -
372H MET* 3.5 28.0 - - - -
442H LEU* 3.8 10.2 - - + +
572H GLY 3.1 12.8 + - - +
573H ILE* 3.4 10.8 - - - +
575H LEU* 1.3 77.3 - - - +
577H LEU* 1.3 62.2 + - - +
579H LEU* 3.0 5.5 + - + +
580H ILE* 3.0 45.0 + - + +
588H PHE* 5.4 1.1 - - + -
596H ILE* 6.0 0.9 - - + -
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Residues in contact with LEU 577 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372H MET* 3.4 31.6 - - + -
376H PHE* 4.5 2.2 - - + -
384H ILE* 4.3 9.6 - - + -
387H TRP* 3.6 35.9 - - + +
388H MET* 3.5 32.0 - - + +
391H VAL* 3.9 4.3 - - + -
573H ILE 3.2 10.7 + - - +
574H ALA 3.2 8.8 + - - +
576H LEU* 1.3 79.5 - - - +
578H MET* 1.3 57.9 + - - +
580H ILE* 3.5 8.9 + - + +
581H TRP* 3.1 30.3 + - - +
599H TRP* 4.9 0.7 - - + -
603H LEU* 3.6 27.3 - - + +
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Residues in contact with MET 578 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391H VAL* 3.5 39.5 - - + +
394H LEU* 4.4 11.0 - - + -
395H HIS* 4.5 6.1 - - - -
401H MET* 3.5 25.8 - - + -
402H ASP* 3.7 22.0 - - + +
405H VAL* 3.5 33.4 - - + -
574H ALA 3.2 8.3 + - - +
575H LEU* 3.0 27.7 + - + +
577H LEU* 1.3 77.8 - - - +
579H LEU* 1.3 61.1 + - + +
581H TRP* 3.9 1.6 - - - -
582H TYR* 3.4 29.0 + - + +
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Residues in contact with LEU 579 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365H PHE* 3.5 27.8 - - + -
402H ASP* 4.5 5.2 - - - +
405H VAL* 3.5 29.6 - - + -
406H TYR* 4.6 2.9 - - + +
409H LEU* 3.9 14.8 - - + -
442H LEU* 3.8 30.1 - - + -
575H LEU 2.9 12.9 + - - +
576H LEU* 3.0 8.3 + - + +
578H MET* 1.3 80.7 - - + +
580H ILE* 1.3 58.1 + - - +
583H ARG* 3.2 48.1 + - + +
588H PHE* 3.4 17.9 - - + -
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Residues in contact with ILE 580 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369H LEU* 3.9 28.9 - - + -
372H MET* 5.4 0.2 - - - -
576H LEU* 3.0 31.6 + - + +
577H LEU* 4.1 12.6 - - + +
578H MET 3.4 0.2 - - - -
579H LEU* 1.3 77.4 - - - +
581H TRP* 1.3 58.6 + - - +
583H ARG 4.6 0.9 - - - -
588H PHE* 4.4 12.3 - - + -
596H ILE* 3.6 37.7 - - + +
599H TRP* 4.1 20.4 - - + +
600H LYS* 2.7 40.3 + - + +
603H LEU* 5.0 5.4 - - + -
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Residues in contact with TRP 581 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388H MET* 3.5 26.0 - - + -
391H VAL* 5.2 1.8 - - + -
577H LEU 3.1 18.8 + - - +
578H MET* 4.4 1.1 - - - -
579H LEU 3.4 0.2 - - - -
580H ILE* 1.3 80.9 - - - +
582H TYR* 1.3 92.4 + + + +
600H LYS* 4.2 4.2 + - - -
603H LEU* 3.6 39.9 - - + +
604H ASP* 5.0 8.3 - - - -
607H PHE* 3.8 27.6 - - + -
608H SER 3.8 9.4 - - - -
609H LEU* 4.6 16.4 - - + +
612H TYR* 3.4 47.2 - + + -
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Residues in contact with TYR 582 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391H VAL* 4.5 0.4 - - + -
395H HIS* 3.3 27.0 - + - -
402H ASP* 3.2 32.8 - - + +
578H MET* 3.4 23.6 + - + +
581H TRP* 1.3 96.3 - + + +
583H ARG* 1.3 67.5 + - - +
584H PRO* 3.4 8.0 - - - +
600H LYS* 4.6 1.9 + - - -
612H TYR* 2.8 43.8 + + - -
613H GLN* 5.1 1.3 + - - -
616H 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