Contacts of the helix formed by residues 398 - 412 (chain C) in PDB entry 5MKE
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 THR 398 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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396C SER* 2.9 37.9 + - - +
397C ARG* 1.3 77.0 - - - +
399C ARG* 1.3 59.9 + - - +
400C GLU* 2.2 36.3 + - - +
401C GLU* 4.0 19.5 - - + +
402C THR* 3.1 6.5 - - - +
543C ASN* 5.8 1.0 - - - +
1001C NAG 3.8 27.3 + - - -
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Residues in contact with ARG 399 (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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288C LEU* 3.5 38.0 + - + +
289C ASP* 4.4 2.5 - - - +
291C LEU* 2.7 33.1 + - - +
292C TYR* 4.3 4.9 + - - +
293C TRP* 3.2 63.2 - - + +
315C LEU* 5.7 5.1 - - - +
395C LEU* 5.1 7.1 - - - +
396C SER 4.1 6.4 + - - -
397C ARG* 3.3 21.5 + - - +
398C THR* 1.3 70.6 - - - +
400C GLU* 1.3 74.0 + - - +
402C THR* 3.2 26.5 + - - +
403C ALA* 4.1 5.7 + - - +
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Residues in contact with GLU 400 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398C THR* 2.2 33.1 + - - +
399C ARG* 1.3 82.8 + - - +
401C GLU* 1.3 71.5 + - + +
403C ALA* 3.4 9.7 + - - +
404C ALA* 3.5 7.2 + - - +
1001C NAG 5.0 2.6 + - - -
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Residues in contact with GLU 401 (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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396C SER* 5.0 1.3 - - - +
398C THR* 4.0 12.7 - - + +
400C GLU* 1.3 80.8 - - + +
402C THR* 1.3 57.3 + - - +
403C ALA 3.0 2.7 - - - -
404C ALA* 2.6 20.3 + - + -
405C GLN* 2.3 46.5 + - + +
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Residues in contact with THR 402 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288C LEU* 3.3 31.3 - - + +
395C LEU* 3.1 24.8 - - - +
396C SER* 3.1 26.9 + - - -
398C THR 3.1 15.3 - - - +
399C ARG* 3.2 26.7 + - - +
401C GLU* 1.3 75.9 - - - +
403C ALA* 1.3 59.5 + - - +
405C GLN* 3.5 16.5 - - - +
406C VAL* 3.7 17.5 - - - +
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Residues in contact with ALA 403 (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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284C GLU* 6.5 0.2 - - + -
288C LEU* 4.3 20.0 - - + -
399C ARG 4.4 4.5 - - - +
400C GLU 3.4 9.3 + - - +
401C GLU 3.0 0.4 - - - -
402C THR* 1.3 83.3 - - - +
404C ALA* 1.3 52.3 + - - +
405C GLN 3.2 0.2 - - - -
406C VAL* 3.1 11.2 + - + +
407C ALA* 2.6 32.6 + - - +
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Residues in contact with ALA 404 (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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400C GLU 3.5 3.7 + - - +
401C GLU* 2.6 34.9 + - + +
403C ALA* 1.3 72.3 - - - +
405C GLN* 1.3 55.1 + - - +
407C ALA* 3.3 11.3 - - + +
408C SER* 2.2 39.0 + - - -
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Residues in contact with GLN 405 (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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321C ILE* 5.4 0.2 - - - +
393C LEU* 3.9 23.0 - - + +
394C ASP 3.9 18.4 + - - -
395C LEU* 3.2 28.2 - - - +
396C SER* 4.2 15.9 - - - -
401C GLU* 2.3 35.2 + - + +
402C THR* 3.5 16.2 - - - +
404C ALA* 1.3 64.6 - - - +
406C VAL* 1.3 51.8 - - + +
408C SER* 2.8 10.4 + - - -
409C LEU* 2.2 45.0 + - + +
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Residues in contact with VAL 406 (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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280C TRP* 4.4 0.4 - - + -
283C THR* 4.3 30.5 - - + +
284C GLU* 5.6 4.0 - - + +
288C LEU* 5.9 2.7 - - + -
402C THR 3.7 14.4 - - - +
403C ALA* 3.1 12.5 + - - +
405C GLN* 1.3 75.8 - - + +
407C ALA* 1.3 50.9 + - - +
409C LEU* 3.1 21.3 - - + +
410C LYS 2.5 30.1 + - - -
414C TRP* 3.2 28.9 - - + +
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Residues in contact with ALA 407 (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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403C ALA 2.6 12.6 + - - +
404C ALA* 3.3 20.9 - - + +
406C VAL* 1.3 72.0 - - - +
408C SER* 1.3 60.8 + - - +
410C LYS* 3.0 11.2 + - - +
411C LYS* 2.8 23.4 + - - +
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Residues in contact with SER 408 (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 ASN* 4.0 7.4 + - - +
404C ALA 2.2 31.1 + - - -
405C GLN* 3.3 9.4 - - - -
407C ALA* 1.3 68.9 - - - +
409C LEU* 1.3 50.7 + - - +
411C LYS* 3.1 12.2 - - - +
412C ASN* 2.7 38.3 + - - -
1002C NAG 3.5 31.8 + - - -
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Residues in contact with LEU 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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321C ILE* 5.9 6.3 - - + -
365C ALA* 6.0 2.7 - - + -
393C LEU* 5.8 7.2 - - + -
405C GLN* 2.2 31.5 + - + +
406C VAL* 3.1 30.1 - - + +
408C SER* 1.3 67.6 - - - +
410C LYS* 1.3 54.2 + - - +
412C ASN* 3.8 15.0 - - + +
413C VAL 2.5 8.7 + - - -
414C TRP* 2.2 79.8 + - + +
415C LEU* 4.4 21.1 - - + -
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Residues in contact with LYS 410 (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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406C VAL 2.5 13.2 + - - +
407C ALA* 3.0 14.1 + - - +
409C LEU* 1.3 69.6 - - - +
411C LYS* 1.3 59.0 + - - +
412C ASN 3.0 1.8 - - - -
413C VAL* 2.6 34.1 + - + +
414C TRP* 3.4 33.6 - - + -
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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
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360C PRO* 4.0 12.6 - - - +
407C ALA 2.8 11.1 + - - +
408C SER* 3.1 23.8 + - - +
410C LYS* 1.3 72.4 - - - +
412C ASN* 1.3 61.0 + - - +
413C VAL* 4.8 2.6 - - - +
1002C NAG 2.9 58.1 + - - +
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Residues in contact with ASN 412 (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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360C PRO* 3.4 36.2 + - + +
362C ASN* 4.9 4.7 + - - +
365C ALA* 3.8 25.0 - - - +
366C TRP* 4.8 5.4 - - + -
408C SER* 2.7 28.3 + - - +
409C LEU* 3.3 17.1 + - + +
410C LYS 3.0 0.2 - - - -
411C LYS* 1.3 76.7 - - - +
413C VAL* 1.3 70.3 + - - +
414C TRP* 2.9 18.5 - - - +
1002C NAG 3.3 22.6 + - - +
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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