Contacts of the helix formed by residues 571 - 582 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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387G TRP* 3.2 26.8 - - - -
438G ALA* 3.5 11.4 - - - +
441G GLU* 3.6 9.0 + - - -
567G ARG* 3.2 24.9 - - - -
568G ILE 3.1 9.4 + - - -
569G ILE 3.6 0.6 - - - -
570G GLN* 1.3 79.4 - - - +
572G GLY* 1.3 66.3 + - - +
573G ILE* 3.3 9.5 + - - +
574G ALA* 3.1 16.8 + - - +
575G LEU 3.6 2.3 + - - -
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Residues in contact with GLY 572 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368G LEU* 4.6 2.9 - - - +
438G ALA* 3.4 23.5 + - - -
441G GLU* 2.8 21.5 + - - +
442G LEU* 3.6 26.3 - - - +
571G SER* 1.3 70.5 - - - +
573G ILE* 1.3 66.3 + - - +
575G LEU 3.3 2.2 + - - -
576G LEU* 3.1 18.4 + - - +
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Residues in contact with ILE 573 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368G LEU* 3.3 49.8 - - + +
371G ARG* 4.1 19.1 - - + +
372G MET* 3.5 33.0 - - + -
375G MET* 4.4 11.7 - - + -
376G PHE* 4.7 0.4 - - + -
387G TRP* 3.5 26.7 - - + -
441G GLU* 4.6 4.5 - - - +
571G SER* 3.2 7.4 - - - +
572G GLY* 1.3 77.3 - - - +
574G ALA* 1.3 61.9 + - - +
576G LEU* 3.3 6.8 + - - +
577G LEU* 3.2 21.8 + - + +
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Residues in contact with ALA 574 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387G TRP* 3.9 11.2 - - - +
391G VAL* 3.8 9.3 - - + +
394G LEU* 3.9 17.2 - - + +
568G ILE* 3.0 40.2 - - + +
571G SER* 3.1 9.7 + - - +
572G GLY 3.1 0.6 - - - -
573G ILE* 1.3 76.0 - - - +
575G LEU* 1.3 66.3 + - - +
577G LEU* 3.2 18.7 + - - +
578G MET* 3.2 9.2 + - - +
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Residues in contact with LEU 575 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394G LEU* 4.0 18.2 - - + -
401G MET* 5.5 0.7 - - + -
405G VAL* 4.7 4.7 - - + -
435G LEU* 4.2 15.3 - - + -
438G ALA* 3.5 34.5 - - + +
439G LEU* 3.5 35.7 - - + +
442G LEU* 3.6 19.7 - - + -
571G SER 3.6 1.1 + - - +
572G GLY 3.3 4.8 + - - +
574G ALA* 1.3 76.2 - - - +
576G LEU* 1.3 61.2 + - - +
578G MET* 3.0 31.5 + - + +
579G LEU* 2.9 33.8 + - - +
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Residues in contact with LEU 576 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365G PHE* 3.6 40.4 - - + +
368G LEU* 3.5 27.6 - - + +
369G LEU* 3.5 16.8 - - + -
372G MET* 3.5 27.8 - - - -
442G LEU* 3.8 9.8 - - + +
572G GLY 3.1 12.6 + - - +
573G ILE* 3.4 10.5 - - - +
574G ALA 3.1 0.4 - - - -
575G LEU* 1.3 77.7 - - - +
577G LEU* 1.3 62.5 + - - +
579G LEU* 3.0 5.4 + - + +
580G ILE* 3.0 44.9 + - + +
588G PHE* 5.4 0.9 - - + -
596G ILE* 6.0 0.9 - - + -
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Residues in contact with LEU 577 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372G MET* 3.4 31.9 - - + -
376G PHE* 4.6 2.2 - - + -
384G ILE* 4.3 10.3 - - + -
387G TRP* 3.6 36.1 - - + +
388G MET* 3.5 33.2 - - + +
391G VAL* 3.9 3.8 - - + -
573G ILE 3.2 10.3 + - - +
574G ALA* 3.2 8.6 + - - +
576G LEU* 1.3 79.4 - - - +
578G MET* 1.3 57.8 + - - +
580G ILE* 3.9 8.3 - - + +
581G TRP* 3.0 30.1 + - - +
599G TRP* 4.9 0.7 - - + -
603G LEU* 3.6 27.5 - - + +
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Residues in contact with MET 578 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391G VAL* 3.5 37.0 - - + +
394G LEU* 4.4 11.2 - - + -
395G HIS* 4.5 5.8 - - - -
401G MET* 3.5 26.0 - - + -
402G ASP* 3.7 22.7 - - + +
405G VAL* 3.5 33.2 - - + -
574G ALA 3.2 9.4 + - - +
575G LEU* 3.0 28.1 + - + +
577G LEU* 1.3 78.3 - - - +
579G LEU* 1.3 60.8 + - + +
580G ILE 3.4 0.2 - - - -
581G TRP* 4.4 1.6 - - - -
582G TYR* 3.4 29.6 + - + +
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Residues in contact with LEU 579 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365G PHE* 3.5 28.3 - - + -
402G ASP* 4.5 5.4 - - - +
405G VAL* 3.5 28.9 - - + -
406G TYR* 4.6 3.1 - - + +
409G LEU* 3.9 14.4 - - + -
442G LEU* 3.8 29.6 - - + -
575G LEU 2.9 13.8 + - - +
576G LEU* 3.0 8.5 + - + +
578G MET* 1.3 80.1 - - + +
580G ILE* 1.3 58.4 + - + +
583G ARG* 3.2 48.4 + - + +
588G PHE* 3.4 18.2 - - + -
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Residues in contact with ILE 580 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369G LEU* 3.8 28.7 - - + -
372G MET* 5.4 0.2 - - - -
576G LEU* 3.0 31.3 + - + +
577G LEU* 4.1 12.1 - - + +
578G MET 3.4 0.2 - - - -
579G LEU* 1.3 77.6 - - - +
581G TRP* 1.3 57.9 + - - +
583G ARG 4.6 0.9 - - - -
588G PHE* 4.4 13.2 - - + -
596G ILE* 3.6 38.6 - - + +
599G TRP* 4.1 20.4 - - + +
600G LYS* 2.7 41.8 + - + +
603G LEU* 5.0 5.6 - - + -
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Residues in contact with TRP 581 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388G MET* 3.5 26.5 - - + -
391G VAL* 5.2 2.7 - - + -
577G LEU 3.0 19.3 + - - +
578G MET* 4.1 1.6 - - - +
579G LEU 3.3 0.2 - - - -
580G ILE* 1.3 81.3 - - - +
582G TYR* 1.3 91.6 + + + +
600G LYS* 4.2 4.2 + - - -
603G LEU* 3.6 39.5 - - + +
604G ASP* 5.0 8.5 - - - -
607G PHE* 3.8 26.9 - - + -
608G SER 3.8 9.6 - - - -
609G LEU* 4.5 17.0 - - + +
612G TYR* 3.4 48.5 - + + -
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Residues in contact with TYR 582 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391G VAL* 4.5 0.4 - - + -
395G HIS* 3.3 26.9 - + - -
402G ASP* 3.2 31.2 - - + +
578G MET* 3.4 24.2 + - + +
581G TRP* 1.3 95.9 - + + +
583G ARG* 1.3 68.6 + - + +
584G PRO* 3.4 7.3 - - - +
600G LYS* 4.6 1.7 + - - -
612G TYR* 2.8 42.4 + + - -
613G GLN* 5.1 2.3 + - - -
616G LYS* 3.3 19.4 + - - -
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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