Contacts of the helix formed by residues 400 - 415 (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 LYS 400 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139 GLN 5.7 6.5 + - - +
149 ILE* 6.0 2.0 - - - +
395I HIS* 4.6 10.8 - - - -
398I LEU 3.2 1.8 + - - -
399I PRO* 1.3 75.1 - - + +
401I MET* 1.3 66.2 + - - +
402I ASP* 3.4 8.1 - - - -
403I SER* 3.1 30.4 + - - +
404I VAL* 3.0 23.3 + - + +
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Residues in contact with MET 401 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394I LEU* 3.2 34.1 - - + +
395I HIS* 3.8 13.4 + - + -
397I LEU* 3.5 33.2 - - + -
398I LEU* 3.1 37.5 + - + +
399I PRO 4.3 0.9 - - - -
400I LYS* 1.3 74.8 - - - +
402I ASP* 1.3 65.0 + - - +
404I VAL* 3.0 22.2 + - - +
405I VAL* 3.0 19.5 + - - +
435I LEU* 3.8 27.8 - - + -
575I LEU* 5.5 0.2 - - + -
578I MET* 3.5 19.1 - - + -
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Residues in contact with ASP 402 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395I HIS* 2.9 24.7 + - + -
400I LYS* 3.9 5.0 - - - -
401I MET* 1.3 76.5 - - - +
403I SER* 1.3 72.2 + - - +
405I VAL* 3.3 12.2 + - - +
406I TYR* 3.3 12.8 + - - +
578I MET* 3.7 34.5 - - + +
579I LEU* 4.5 3.9 - - + +
582I TYR* 3.2 41.7 - - + +
583I ARG* 3.6 20.5 + - + -
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Residues in contact with SER 403 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400I LYS* 3.1 45.4 + - - +
402I ASP* 1.3 85.4 + - - +
404I VAL* 1.3 57.1 + - - +
406I TYR* 3.4 5.9 + - - +
407I ASP* 2.7 32.3 + - - +
583I ARG* 2.9 30.0 + - - +
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Residues in contact with VAL 404 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398I LEU* 5.7 6.1 - - + -
399I PRO 3.9 11.2 - - - +
400I LYS* 3.0 17.2 + - + +
401I MET* 3.0 14.8 + - - +
403I SER* 1.3 74.8 - - - +
405I VAL* 1.3 60.6 + - + +
407I ASP* 3.1 10.4 + - - +
408I PHE* 2.9 27.8 + - + +
422I TRP* 3.5 30.1 - - + -
435I LEU* 6.4 1.1 - - + -
543I LYS* 5.1 10.8 - - - -
545I ILE* 4.2 13.0 - - + -
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Residues in contact with VAL 405 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401I MET* 3.0 23.7 + - + +
402I ASP 3.5 6.3 - - - +
403I SER 3.3 0.2 - - - -
404I VAL* 1.3 76.5 - - - +
406I TYR* 1.3 56.3 + - - +
408I PHE* 3.3 6.4 + - - +
409I LEU* 2.9 36.8 + - + +
435I LEU* 5.5 0.7 - - + -
439I LEU* 4.5 14.6 - - + -
442I LEU* 3.7 26.5 - - + -
575I LEU* 4.7 6.3 - - + -
578I MET* 3.5 25.1 - - + -
579I LEU* 3.5 23.8 - - + -
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Residues in contact with TYR 406 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402I ASP 3.3 4.8 + - - +
403I SER 3.7 8.3 - - - +
404I VAL 3.3 0.6 - - - -
405I VAL* 1.3 78.0 - - - +
407I ASP* 1.3 69.3 + - - +
409I LEU* 3.5 16.4 + - + +
410I LYS* 3.2 63.0 + - + +
579I LEU* 4.6 2.0 - - + +
583I ARG* 3.9 32.5 - - + +
587I GLU* 3.1 59.2 + - + +
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Residues in contact with ASP 407 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403I SER* 2.7 24.8 - - - +
404I VAL* 3.1 9.8 + - - +
406I TYR* 1.3 82.3 - - - +
408I PHE* 1.3 59.3 + - - +
410I LYS* 3.5 4.0 + - - +
411I CYS* 2.8 31.6 + - - +
422I TRP* 4.2 16.1 - - + -
583I ARG* 5.9 0.6 + - - -
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Residues in contact with PHE 408 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404I VAL* 2.9 16.9 + - + +
405I VAL* 3.3 7.4 + - + +
407I ASP* 1.3 73.5 - - - +
409I LEU* 1.3 70.1 + - + +
411I CYS* 3.0 3.3 + - - +
412I MET* 2.9 61.8 + - + +
422I TRP* 3.9 40.1 - + + -
424I PHE* 6.1 0.2 - + - -
439I LEU* 4.4 25.1 - - + -
443I CYS* 3.9 15.7 - - - -
469I LEU* 3.7 22.0 - - + -
524I GLY 4.3 1.1 - - - -
525I ILE* 3.5 40.8 - - + -
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Residues in contact with LEU 409 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361I LEU* 4.2 11.1 - - + +
365I PHE* 3.9 26.2 - - + -
405I VAL* 2.9 27.3 + - + +
406I TYR* 3.6 22.0 - - + +
407I ASP 3.3 0.2 - - - -
408I PHE* 1.3 77.6 - - + +
410I LYS* 1.3 60.9 + - + +
412I MET* 3.0 23.0 + - - +
413I VAL* 3.0 17.7 + - + +
442I LEU* 4.3 8.3 - - + -
443I CYS* 3.5 28.9 - - - -
579I LEU* 3.9 29.4 - - + -
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Residues in contact with LYS 410 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358I GLU* 3.3 30.9 + - - +
406I TYR* 3.2 57.1 + - + +
407I ASP* 4.0 3.8 - - - +
409I LEU* 1.3 77.0 - - + +
411I CYS* 1.3 58.7 + - - +
413I VAL* 3.8 12.8 - - + +
414I TYR* 2.7 62.1 + - + -
587I GLU 4.0 10.9 + - - -
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Residues in contact with CYS 411 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407I ASP 2.8 20.6 + - - +
408I PHE 3.2 7.4 - - - +
410I LYS* 1.3 76.6 - - - +
412I MET* 1.3 63.1 + - + +
414I TYR* 4.3 5.2 - - - +
415I ASN* 3.4 17.2 + - - -
416I ILE* 4.7 5.0 + - - +
419I LYS 4.2 14.8 - - - +
420I ARG* 3.9 15.5 - - - +
422I TRP* 3.2 31.6 - - + +
542I VAL* 4.4 10.5 - - - -
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Residues in contact with MET 412 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357I ARG* 2.8 33.1 + - - +
408I PHE* 2.9 57.7 + - + +
409I LEU* 3.2 10.5 - - - +
411I CYS* 1.3 82.1 - - - +
413I VAL* 1.3 54.3 + - - +
415I ASN* 3.7 5.9 + - - +
420I ARG* 3.2 28.7 - - - +
443I CYS* 5.2 0.2 - - - -
468I PHE* 3.7 24.7 - - + -
469I LEU* 4.0 11.7 - - + -
523I PRO* 3.6 31.9 - - + +
524I GLY 4.0 7.4 - - - +
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Residues in contact with VAL 413 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357I ARG* 3.7 23.9 - - + +
358I GLU* 3.5 42.6 - - + +
361I LEU* 3.5 25.1 - - + -
409I LEU* 3.1 16.2 - - + +
410I LYS* 2.9 22.6 + - + +
412I MET* 1.3 77.2 - - - +
414I TYR* 1.3 71.7 + - + +
415I ASN* 3.2 0.9 + - - +
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Residues in contact with TYR 414 (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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410I LYS* 2.7 57.9 + - + +
411I CYS* 4.3 4.9 - - - +
413I VAL* 1.3 79.1 - - + +
415I ASN* 1.3 71.2 + - - +
416I ILE* 4.0 21.1 - - + -
561J GLU* 5.6 3.8 - - + -
565J GLU* 3.2 64.3 - - + +
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Residues in contact with ASN 415 (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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357I ARG* 3.7 36.6 + - - +
411I CYS 3.4 9.6 + - - -
412I MET* 4.0 4.3 - - - +
413I VAL 3.1 1.6 - - - +
414I TYR* 1.3 84.0 - - - +
416I ILE* 1.3 59.3 + - - +
417I PRO* 3.6 0.7 - - - +
420I ARG* 3.0 32.7 + - - +
520I ILE* 5.3 1.9 - - - +
523I PRO* 5.1 3.0 - - - +
564J LEU 3.7 4.2 - - - +
565J GLU 4.3 1.6 - - - +
567J ARG* 2.9 43.3 + - - +
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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