Contacts of the helix formed by residues 400 - 415 (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 LYS 400 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138 GLN* 4.2 25.8 + - + +
395H HIS* 4.6 9.2 - - - -
398H LEU 3.2 1.8 + - - -
399H PRO* 1.3 76.3 - - + +
401H MET* 1.3 66.1 + - - +
402H ASP* 3.4 7.6 - - - -
403H SER* 3.1 30.2 + - - +
404H VAL* 3.0 23.3 + - + +
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Residues in contact with MET 401 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394H LEU* 3.2 33.2 - - + +
395H HIS* 3.8 12.9 + - - -
397H LEU* 3.5 33.4 - - + -
398H LEU* 3.1 39.3 + - + +
399H PRO 4.3 1.1 - - - -
400H LYS* 1.3 74.8 - - - +
402H ASP* 1.3 65.2 + - - +
404H VAL* 3.0 22.6 + - - +
405H VAL* 3.0 19.8 + - - +
435H LEU* 3.8 27.8 - - + -
575H LEU* 5.5 0.2 - - + -
578H MET* 3.5 19.1 - - + -
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Residues in contact with ASP 402 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395H HIS* 2.9 24.0 + - + -
400H LYS* 3.9 5.4 - - - -
401H MET* 1.3 76.2 - - - +
403H SER* 1.3 71.6 + - - +
405H VAL* 3.3 12.0 + - - +
406H TYR* 3.3 13.0 + - - +
578H MET* 3.7 35.8 - - + +
579H LEU* 4.5 5.2 - - + +
582H TYR* 3.2 40.8 - - + +
583H ARG* 3.7 19.2 + - + +
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Residues in contact with SER 403 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400H LYS* 3.1 45.2 + - - +
402H ASP* 1.3 85.8 + - - +
404H VAL* 1.3 56.1 + - - +
406H TYR* 3.4 6.2 + - - +
407H ASP* 2.7 32.8 + - - +
583H ARG* 2.8 31.1 + - - +
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Residues in contact with VAL 404 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398H LEU* 5.7 5.4 - - + -
399H PRO 4.0 11.7 - - - +
400H LYS* 3.0 17.7 + - + +
401H MET* 3.0 14.3 + - - +
403H SER* 1.3 74.9 - - - +
405H VAL* 1.3 60.4 + - + +
407H ASP* 3.1 11.0 + - - +
408H PHE* 2.9 27.7 + - + +
422H TRP* 3.5 30.1 - - + -
543H LYS* 5.1 10.1 - - - -
545H ILE* 4.2 13.2 - - + -
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Residues in contact with VAL 405 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401H MET* 3.0 24.4 + - + +
402H ASP 3.4 6.5 - - - +
404H VAL* 1.3 77.4 - - + +
406H TYR* 1.3 56.9 + - - +
408H PHE* 3.3 7.5 + - + +
409H LEU* 2.9 36.5 + - + +
435H LEU* 5.5 0.7 - - + -
439H LEU* 4.5 14.8 - - + -
442H LEU* 3.7 26.2 - - + -
575H LEU* 4.7 6.5 - - + -
578H MET* 3.5 24.5 - - + -
579H LEU* 3.5 23.8 - - + -
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Residues in contact with TYR 406 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402H ASP 3.3 4.1 + - - +
403H SER 3.7 8.5 - - - +
404H VAL 3.3 0.4 - - - -
405H VAL* 1.3 78.4 - - - +
407H ASP* 1.3 72.0 + - - +
409H LEU* 3.5 17.6 + - + +
410H LYS* 3.2 63.0 + - + +
579H LEU* 4.6 1.5 - - + +
583H ARG* 3.9 33.7 - - + +
587H GLU* 3.1 59.7 + - + +
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Residues in contact with ASP 407 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403H SER* 2.7 24.9 - - - +
404H VAL* 3.1 10.4 + - - +
406H TYR* 1.3 82.8 - - - +
408H PHE* 1.3 60.7 + - - +
410H LYS* 3.5 4.0 + - - +
411H CYS* 2.8 31.4 + - - +
422H TRP* 4.2 15.4 - - + -
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Residues in contact with PHE 408 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404H VAL* 2.9 16.9 + - + +
405H VAL* 3.7 6.5 - - - +
407H ASP* 1.3 72.5 - - - +
409H LEU* 1.3 68.9 + - + +
411H CYS* 3.0 3.4 + - - +
412H MET* 2.9 63.5 + - + +
422H TRP* 3.9 39.2 - + + -
424H PHE* 6.1 0.4 - + - -
439H LEU* 4.4 25.4 - - + -
443H CYS* 3.9 15.3 - - - -
469H LEU* 3.7 22.7 - - + -
524H GLY 4.3 2.7 - - - -
525H ILE* 3.5 40.2 - - + -
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Residues in contact with LEU 409 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361H LEU* 4.2 10.2 - - + +
365H PHE* 3.9 26.9 - - + -
405H VAL* 2.9 26.4 + - + +
406H TYR* 3.6 22.0 - - + +
408H PHE* 1.3 78.2 - - + +
410H LYS* 1.3 61.5 + - + +
412H MET* 3.0 22.4 + - - +
413H VAL* 3.0 17.6 + - + +
442H LEU* 4.3 7.9 - - + -
443H CYS* 3.5 28.5 - - - -
579H LEU* 3.9 28.7 - - + -
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Residues in contact with LYS 410 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358H GLU* 3.3 30.7 + - - +
406H TYR* 3.2 58.3 + - + +
407H ASP* 4.0 3.8 - - - +
409H LEU* 1.3 77.9 - - + +
411H CYS* 1.3 57.9 + - - +
413H VAL* 3.8 13.0 - - + +
414H TYR* 2.7 63.8 + - + +
587H GLU 4.0 11.1 + - - -
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Residues in contact with CYS 411 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407H ASP 2.8 21.2 + - - +
408H PHE 3.0 6.7 + - - +
410H LYS* 1.3 75.6 - - - +
412H MET* 1.3 63.6 + - + +
414H TYR* 4.3 5.0 - - - +
415H ASN* 3.4 17.0 + - - -
416H ILE* 4.7 5.3 + - - +
419H LYS 4.2 14.6 - - - +
420H ARG* 3.9 15.8 - - - +
422H TRP* 3.2 33.2 - - + +
542H VAL* 4.4 11.2 - - - -
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Residues in contact with MET 412 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357H ARG* 2.8 32.6 + - - +
408H PHE* 2.9 57.7 + - + +
409H LEU* 3.2 8.5 - - - +
411H CYS* 1.3 83.7 - - - +
413H VAL* 1.3 57.0 + - - +
415H ASN* 3.7 5.4 + - - +
420H ARG* 3.2 27.8 - - - +
443H CYS* 5.2 0.7 - - - -
468H PHE* 3.7 25.8 - - + -
469H LEU* 4.0 12.1 - - + -
523H PRO* 3.6 33.2 - - + +
524H GLY 4.0 7.2 - - - +
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Residues in contact with VAL 413 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357H ARG* 3.7 24.3 - - + +
358H GLU* 3.5 42.6 - - + +
361H LEU* 3.5 25.4 - - + -
409H LEU* 3.1 16.2 - - + +
410H LYS* 2.9 21.3 + - + +
412H MET* 1.3 76.1 - - - +
414H TYR* 1.3 73.7 + - + +
415H ASN* 3.2 1.2 + - - +
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Residues in contact with TYR 414 (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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410H LYS* 2.7 56.6 + - + +
411H CYS* 4.3 4.9 - - - +
413H VAL* 1.3 78.9 - - + +
415H ASN* 1.3 71.5 + - - +
416H ILE* 4.0 25.7 - - + +
561I GLU* 5.9 3.1 - - + -
565I GLU* 3.7 57.5 + - + +
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Residues in contact with ASN 415 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357H ARG* 3.7 36.5 + - - +
411H CYS 3.4 10.9 + - - -
412H MET* 4.0 3.8 - - - +
413H VAL 3.1 1.6 - - - -
414H TYR* 1.3 85.5 - - - +
416H ILE* 1.3 58.9 + - - +
417H PRO* 3.6 3.3 - - - +
420H ARG* 3.0 37.6 + - - +
520H ILE* 5.3 2.4 - - - +
523H PRO* 5.1 3.0 - - - +
564I LEU 4.3 2.6 - - - +
565I GLU 5.1 0.2 - - - +
567I ARG* 2.9 38.0 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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