Contacts of the helix formed by residues 403 - 418 (chain C) in PDB entry 2HYE
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 ASN 403 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401C ARG* 3.8 1.2 - - - +
402C PRO* 1.3 91.5 - - - +
404C LYS* 1.3 67.9 + - - +
405C PRO* 3.4 4.3 - - - -
406C ALA* 3.7 4.9 + - - +
407C GLU* 3.4 17.7 + - - +
444C HIS 4.9 2.5 - - - +
448C VAL* 3.9 20.4 - - + +
685C THR* 5.8 3.6 - - + -
689C PHE* 3.4 33.3 - - + -
692C ARG* 3.1 27.2 + - - +
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Residues in contact with LYS 404 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358C ASP* 3.7 13.2 - - - +
361C MET* 4.2 8.7 - - + -
401C ARG* 3.2 37.3 + - - +
403C ASN* 1.3 72.5 - - - +
405C PRO* 1.3 79.4 - - + +
407C GLU* 2.8 49.6 + - - +
408C LEU* 2.8 29.3 + - + +
411C LYS* 5.2 2.4 - - - +
681C GLN* 3.5 10.6 + - - -
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Residues in contact with PRO 405 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352C VAL* 6.1 0.4 - - + -
361C MET* 4.0 17.8 - - + -
398C ILE* 3.8 30.3 - - + +
399C ASN* 5.1 2.9 - - - +
401C ARG* 3.0 32.5 - - + +
402C PRO 3.9 9.0 - - - +
404C LYS* 1.3 97.5 - - + +
406C ALA* 1.3 67.4 + - + +
408C LEU* 3.2 3.3 + - + +
409C ILE* 2.8 30.9 + - + +
443C ILE* 4.2 14.6 - - + -
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Residues in contact with ALA 406 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403C ASN* 4.0 8.5 - - - +
404C LYS 3.3 0.4 - - - -
405C PRO* 1.3 81.6 - - + +
407C GLU* 1.3 68.0 + - - +
409C ILE* 3.3 4.4 + - - +
410C ALA* 3.2 12.0 + - - +
443C ILE* 3.5 28.6 - - + +
444C HIS 5.2 0.9 - - - +
445C GLY* 3.4 26.5 - - - +
446C LYS 4.8 0.2 - - - +
448C VAL* 4.1 6.3 - - + -
449C PHE* 3.7 21.7 - - + +
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Residues in contact with GLU 407 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403C ASN* 3.4 10.2 + - - +
404C LYS* 2.8 41.0 + - - +
406C ALA* 1.3 72.0 - - - +
408C LEU* 1.3 56.3 + - - +
410C ALA* 2.7 35.3 + - - +
411C LYS* 3.1 33.9 + - + +
448C VAL* 4.1 8.2 - - + +
452C PHE* 3.6 42.4 - - + -
681C GLN* 2.9 30.0 - - - +
685C THR* 5.7 1.6 - - - +
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Residues in contact with LEU 408 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358C ASP* 3.7 28.0 - - + +
361C MET* 3.4 48.0 - - + -
362C VAL* 3.8 15.3 - - + +
404C LYS* 2.8 34.8 + - + +
405C PRO 3.7 2.7 - - - +
407C GLU* 1.3 75.0 - - - +
409C ILE* 1.3 64.3 + - - +
411C LYS* 3.0 26.9 + - + +
412C HIS* 2.8 24.4 + - - +
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Residues in contact with ILE 409 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362C VAL* 4.0 18.6 - - + +
365C LEU* 5.4 5.8 - - + -
405C PRO* 2.8 33.4 + - + +
406C ALA 3.4 5.4 - - - +
407C GLU 3.0 0.2 + - - -
408C LEU* 1.3 72.2 - - - +
410C ALA* 1.3 58.3 + - - +
412C HIS* 3.1 4.7 - - - +
413C VAL* 2.9 31.4 + - + +
436C ILE* 3.6 26.5 - - + -
439C LEU* 4.3 30.5 - - + -
440C PHE* 4.9 10.3 - - + +
443C ILE* 3.1 29.2 - - + -
449C PHE* 4.4 13.7 - - + -
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Residues in contact with ALA 410 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406C ALA 3.2 2.1 + - - +
407C GLU 2.7 16.2 + - - +
409C ILE* 1.3 71.0 - - - +
411C LYS* 1.3 57.0 + - - +
412C HIS 2.8 10.7 + - - -
413C VAL* 2.8 16.6 + - - +
414C ASP* 2.8 15.2 + - - +
449C PHE* 3.6 41.3 - - + +
452C PHE* 4.2 8.5 - - + -
453C TYR* 4.0 16.8 - - - +
456C ASP* 4.8 2.0 - - - +
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Residues in contact with LYS 411 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359C LYS* 6.1 1.0 - - - +
404C LYS* 5.2 2.4 - - - +
407C GLU* 3.1 39.5 + - + +
408C LEU* 3.0 24.1 + - + +
410C ALA* 1.3 78.0 - - - +
412C HIS* 1.3 60.4 + - - +
414C ASP* 3.7 13.5 - - - +
415C SER* 3.5 17.5 + - - -
452C PHE* 4.9 3.8 - - + -
456C ASP* 4.2 14.8 - - - +
676C GLU* 3.1 36.7 + - - +
681C GLN* 5.3 0.6 - - - +
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Residues in contact with HIS 412 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362C VAL* 3.2 34.1 - - + +
363C GLN* 3.7 23.9 + - + +
366C LEU* 4.0 9.1 - - + +
408C LEU 2.8 11.4 + - - +
409C ILE* 3.1 15.5 - - + +
411C LYS* 1.3 75.7 - - - +
413C VAL* 1.3 67.1 + - + +
414C ASP 3.1 1.3 - - - -
415C SER* 3.0 17.3 + - - -
416C LYS* 3.1 41.9 + - - +
436C ILE* 3.9 19.6 - - + +
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Residues in contact with VAL 413 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409C ILE* 2.9 27.1 + - + +
410C ALA* 2.8 10.0 + - - +
412C HIS* 1.3 77.1 + - - +
414C ASP* 1.3 57.8 + - - +
416C LYS* 2.9 27.6 + - - +
417C LEU* 3.3 19.8 + - + +
433C LEU* 4.3 12.6 - - + -
436C ILE* 4.4 16.6 - - + -
449C PHE* 4.3 12.3 - - + -
453C TYR* 4.5 10.5 - - + -
460C ARG* 5.5 0.2 - - - -
475C MET* 4.0 32.5 - - + -
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Residues in contact with ASP 414 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410C ALA 2.8 14.4 + - - +
411C LYS* 3.7 13.0 - - - +
412C HIS 3.1 0.2 - - - -
413C VAL* 1.3 77.9 - - - +
415C SER* 1.3 61.6 + - - +
416C LYS 3.0 0.7 + - - -
417C LEU* 3.4 6.6 + - - +
418C ARG* 2.6 58.1 + - - +
456C ASP* 3.5 43.0 - - + +
460C ARG* 3.8 19.9 + - - +
674C MET* 5.2 0.5 - - - +
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Residues in contact with SER 415 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411C LYS 3.5 9.2 + - - -
412C HIS* 3.0 12.5 + - - -
414C ASP* 1.3 83.1 + - - +
416C LYS* 1.3 66.2 + - - +
417C LEU 3.4 0.2 - - - -
418C ARG* 4.3 14.8 + - - +
423C GLU* 4.7 3.1 - - - +
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Residues in contact with LYS 416 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363C GLN* 5.1 4.8 + - - -
412C HIS* 3.1 44.9 + - + +
413C VAL* 2.9 14.4 + - + +
415C SER* 1.3 87.0 - - - +
417C LEU* 1.3 65.0 + - + +
422C LYS* 6.1 1.6 - - - +
423C GLU* 1.4 39.6 - - + +
429C LEU* 4.3 11.1 - - + +
432C THR* 5.1 18.0 - - - +
433C LEU* 5.4 2.7 - - + -
436C ILE* 4.8 7.9 - - + -
467C ALA* 4.0 0.5 - - - +
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Residues in contact with LEU 417 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413C VAL* 3.3 23.4 + - + +
414C ASP 3.4 1.5 + - - +
416C LYS* 1.3 93.8 - - + +
418C ARG* 1.3 59.2 + - - +
423C GLU* 3.6 1.1 - - - -
429C LEU* 4.7 6.3 - - + -
433C LEU* 4.3 18.6 - - + -
453C TYR* 4.1 11.4 - - - +
460C ARG* 2.9 36.5 - - - +
466C SER* 3.0 9.5 - - - -
467C ALA* 2.6 33.6 + - + +
471C ALA* 5.6 4.3 - - + +
472C GLU* 3.5 28.9 - - + +
475C MET* 4.6 6.5 - - + -
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Residues in contact with ARG 418 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414C ASP* 2.6 48.5 + - - +
415C SER* 4.3 13.7 - - - +
416C LYS 3.6 1.2 - - - -
417C LEU* 1.3 77.8 - - - +
419C ALA* 1.3 67.3 + - - +
420C GLY 3.4 0.2 + - - -
423C GLU* 2.8 24.4 - - - +
456C ASP* 4.9 5.7 + - - -
459C LYS* 5.7 2.8 - - - +
460C ARG* 4.7 7.0 - - + +
465C LYS 4.3 7.2 - - - +
466C SER* 4.5 0.2 - - - +
467C ALA* 3.7 5.1 + - - -
674C MET* 3.0 70.4 + - + +
675C LYS* 4.8 10.8 - - - +
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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
------------------------------------------------------------
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