Contacts of the helix formed by residues 400 - 415 (chain K) 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 K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395K HIS* 4.6 10.5 - - - -
398K LEU 3.2 2.0 + - - -
399K PRO* 1.3 75.3 - - + +
401K MET* 1.3 66.5 - - - +
402K ASP* 3.4 8.3 - - - -
403K SER* 3.1 30.0 + - - +
404K VAL* 3.0 23.3 + - + +
583K ARG* 5.5 0.2 - - - +
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Residues in contact with MET 401 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394K LEU* 3.2 33.7 - - + +
395K HIS* 3.9 13.1 + - + -
397K LEU* 3.5 33.4 - - + -
398K LEU* 3.1 41.1 + - + +
399K PRO 4.3 0.7 - - - -
400K LYS* 1.3 74.7 - - - +
402K ASP* 1.3 65.2 + - - +
404K VAL* 3.0 21.4 + - - +
405K VAL* 3.0 20.0 + - - +
435K LEU* 3.8 28.3 - - + -
578K MET* 3.5 19.7 - - + -
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Residues in contact with ASP 402 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395K HIS* 2.9 24.1 + - + -
400K LYS* 3.9 4.9 - - - -
401K MET* 1.3 75.3 - - - +
403K SER* 1.3 72.0 + - - +
405K VAL* 3.3 12.5 + - - +
406K TYR* 3.3 12.8 + - - +
578K MET* 3.7 37.1 - - + +
579K LEU* 4.5 4.5 - - + +
582K TYR* 3.2 40.7 - - + +
583K ARG* 3.7 19.3 + - + +
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Residues in contact with SER 403 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400K LYS* 3.1 44.8 + - - +
402K ASP* 1.3 85.1 + - - +
404K VAL* 1.3 57.7 + - - +
406K TYR* 3.4 6.1 + - - +
407K ASP* 2.7 32.2 + - - +
583K ARG* 2.8 29.5 + - - +
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Residues in contact with VAL 404 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398K LEU* 5.7 5.6 - - + -
399K PRO 3.9 11.4 - - - +
400K LYS* 3.0 17.7 + - + +
401K MET* 3.0 14.8 + - - +
403K SER* 1.3 74.5 - - - +
405K VAL* 1.3 61.5 + - + +
407K ASP* 3.1 10.2 + - - +
408K PHE* 2.9 27.9 + - + +
422K TRP* 3.5 29.8 - - + -
543K LYS* 5.1 9.4 - - - -
545K ILE* 4.2 13.5 - - + -
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Residues in contact with VAL 405 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401K MET* 3.0 24.1 + - + +
402K ASP 3.4 7.0 - - - +
403K SER 3.3 0.2 - - - -
404K VAL* 1.3 77.5 - - + +
406K TYR* 1.3 56.2 + - - +
408K PHE* 3.3 6.2 + - - +
409K LEU* 2.9 37.7 + - + +
435K LEU* 5.5 0.7 - - + -
439K LEU* 4.5 13.7 - - + -
442K LEU* 3.7 26.9 - - + -
575K LEU* 4.7 6.5 - - + -
578K MET* 3.5 25.4 - - + -
579K LEU* 3.5 24.0 - - + -
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Residues in contact with TYR 406 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402K ASP 3.3 4.0 + - - +
403K SER 3.7 7.4 - - - +
404K VAL 3.3 0.6 - - - -
405K VAL* 1.3 79.0 - - - +
407K ASP* 1.3 70.3 + - - +
409K LEU* 3.5 18.1 + - + +
410K LYS* 3.2 62.8 + - + +
579K LEU* 4.6 2.4 - - + +
583K ARG* 3.9 33.0 - - + +
587K GLU* 3.1 59.3 + - + +
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Residues in contact with ASP 407 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403K SER* 2.7 24.8 + - - +
404K VAL* 3.1 10.8 + - - +
406K TYR* 1.3 83.4 - - - +
408K PHE* 1.3 60.6 + - - +
410K LYS* 3.8 3.9 - - - +
411K CYS* 2.8 31.6 + - - +
422K TRP* 4.2 14.4 - - + -
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Residues in contact with PHE 408 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404K VAL* 2.9 16.7 + - + +
405K VAL* 3.7 7.4 - - - +
407K ASP* 1.3 74.4 - - - +
409K LEU* 1.3 70.2 + - + +
411K CYS* 3.1 3.3 + - - +
412K MET* 2.9 61.2 + - + +
422K TRP* 3.9 38.8 - + + -
439K LEU* 4.4 26.7 - - + -
443K CYS* 4.0 15.5 - - - -
469K LEU* 3.7 21.5 - - + -
524K GLY 4.3 2.9 - - - -
525K ILE* 3.5 40.4 - - + -
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Residues in contact with LEU 409 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361K LEU* 4.2 11.1 - - + +
365K PHE* 3.9 26.9 - - + -
405K VAL* 2.9 28.0 + - + +
406K TYR* 3.6 21.1 - - + +
408K PHE* 1.3 78.8 - - + +
410K LYS* 1.3 65.3 + - + +
412K MET* 3.0 17.6 + - - +
413K VAL* 3.0 18.2 + - + +
442K LEU* 4.3 7.9 - - + -
443K CYS* 3.5 29.6 - - - -
579K LEU* 3.9 28.9 - - + -
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Residues in contact with LYS 410 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358K GLU* 3.3 30.3 + - - +
406K TYR* 3.2 57.4 + - + +
407K ASP* 4.0 3.6 - - - +
409K LEU* 1.3 78.1 - - + +
411K CYS* 1.3 58.9 + - - +
413K VAL* 2.9 13.5 + - + +
414K TYR* 2.7 61.4 + - + +
587K GLU 4.0 11.9 + - - -
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Residues in contact with CYS 411 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407K ASP 2.8 20.1 + - - +
408K PHE 3.1 6.5 + - - +
410K LYS* 1.3 76.4 - - - +
412K MET* 1.3 63.5 + - + +
414K TYR* 4.3 4.6 - - - +
415K ASN* 3.4 16.6 + - - -
416K ILE* 4.7 5.1 + - - +
419K LYS 4.2 15.0 - - - +
420K ARG* 3.9 16.1 - - - +
422K TRP* 3.2 33.0 - - + +
523K PRO* 5.8 0.2 - - - +
542K VAL* 4.4 11.0 - - - -
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Residues in contact with MET 412 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357K ARG* 2.8 32.9 + - - +
408K PHE* 2.9 57.9 + - + +
409K LEU* 3.2 9.6 - - - +
411K CYS* 1.3 83.2 - - - +
413K VAL* 1.3 55.4 + - - +
415K ASN* 3.7 5.4 + - - +
420K ARG 3.2 27.6 - - - +
443K CYS* 5.2 0.4 - - - -
468K PHE* 3.7 26.0 - - + -
469K LEU* 4.0 11.2 - - - -
523K PRO* 3.6 32.7 - - + +
524K GLY 4.0 7.6 - - - +
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Residues in contact with VAL 413 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357K ARG* 3.7 23.4 - - + +
358K GLU* 3.5 43.3 - - + +
361K LEU* 3.5 25.4 - - + -
409K LEU 3.1 16.4 - - - +
410K LYS* 2.9 21.0 + - + +
412K MET* 1.3 78.0 - - - +
414K TYR* 1.3 73.6 + - + +
415K ASN* 3.2 1.0 + - - +
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Residues in contact with TYR 414 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410K LYS* 2.7 58.7 + - + +
411K CYS* 4.3 4.9 - - - +
413K VAL* 1.3 79.7 - - + +
415K ASN* 1.3 71.3 + - - +
416K ILE* 4.0 23.3 - - + +
561L GLU* 5.7 3.6 - - + -
565L GLU* 3.5 61.2 - - + +
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Residues in contact with ASN 415 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357K ARG* 3.6 36.5 + - - +
411K CYS 3.4 11.1 + - - -
412K MET* 3.7 4.0 + - - +
413K VAL 3.1 2.0 - - - +
414K TYR* 1.3 84.0 - - - +
416K ILE* 1.3 58.6 + - - +
417K PRO* 3.6 0.3 - - - +
420K ARG* 3.0 34.8 + - - +
520K ILE* 5.3 2.3 - - - +
523K PRO* 5.1 2.4 - - - +
564L LEU 4.0 3.1 - - - +
565L GLU 4.7 0.5 - - - +
567L ARG* 2.8 48.1 + - - +
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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
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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