Contacts of the helix formed by residues 394 - 406 (chain C) in PDB entry 6M04
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 GLU 394 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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391C PRO 5.3 0.7 - - - +
392C LEU* 2.9 10.2 + - + +
393C LYS* 1.3 75.6 - - - +
395C TYR* 1.3 61.9 + - - +
396C SER* 3.2 6.5 + - - -
397C PHE* 3.6 15.8 + - - +
398C GLU* 3.7 7.8 + - - +
416C PHE* 4.6 20.6 - - + +
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Residues in contact with TYR 395 (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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391C PRO* 3.8 18.8 + - + +
393C LYS 3.7 0.4 - - - -
394C GLU* 1.3 75.2 - - - +
396C SER* 1.3 59.2 + - - +
397C PHE 3.4 0.2 - - - -
398C GLU* 3.6 20.2 - - + +
399C LYS* 2.9 25.8 + - - +
421C HIS* 3.3 25.7 + - + +
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Residues in contact with SER 396 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393C LYS 5.3 2.2 - - - -
394C GLU 3.2 2.1 - - - +
395C TYR* 1.3 74.5 - - - +
397C PHE* 1.3 60.1 + - - +
399C LYS* 3.2 7.6 - - - +
400C VAL* 3.0 31.8 + - - +
415C ASP* 3.4 13.3 + - - +
417C ALA 3.3 23.2 + - - -
418C PHE* 5.0 2.5 - - - -
420C LEU* 3.5 29.8 - - - +
421C HIS* 3.3 23.5 + - - -
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Residues in contact with PHE 397 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394C GLU 3.6 9.0 + - - +
395C TYR 3.4 0.2 - - - -
396C SER* 1.3 78.3 - - - +
398C GLU* 1.3 57.4 + - - +
400C VAL* 3.4 3.0 + - - -
401C ARG* 2.9 24.7 + - - +
413C LYS* 3.3 38.2 - - - +
414C ASN* 3.7 11.7 - - - -
415C ASP 3.4 14.5 + - - +
416C PHE* 5.3 2.2 - - + -
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Residues in contact with GLU 398 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394C GLU 3.7 3.9 + - - +
395C TYR* 3.4 26.2 + - + +
396C SER 3.2 0.6 - - - -
397C PHE* 1.3 79.2 - - - +
399C LYS* 1.3 61.4 + - - +
401C ARG* 3.2 9.7 + - + +
402C GLU* 2.9 33.6 + - - +
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Residues in contact with LYS 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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395C TYR 2.9 18.4 + - - +
396C SER* 3.2 13.9 - - - +
398C GLU* 1.3 79.9 + - - +
400C VAL* 1.3 64.1 + - + +
402C GLU* 3.6 8.7 - - + +
403C GLU* 2.8 28.9 + - - +
420C LEU* 3.4 41.5 + - - +
421C HIS* 3.9 22.2 - - + +
424C ASP* 4.0 14.0 + - - +
431C SER* 2.5 34.5 + - - +
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Residues in contact with VAL 400 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396C SER* 3.0 22.5 + - - +
397C PHE* 3.7 5.4 - - - +
399C LYS* 1.3 79.7 - - - +
401C ARG* 1.3 58.1 + - - +
403C GLU* 3.3 22.5 - - - +
404C SER* 2.9 27.5 + - - -
411C ASP* 3.8 24.2 - - + +
413C LYS* 3.9 15.3 - - - -
415C ASP* 5.2 5.8 - - + +
420C LEU* 3.8 26.2 - - + -
434C PHE* 6.1 2.7 - - + -
435C GLY* 4.9 3.4 - - - -
438C LEU* 4.0 12.3 - - + -
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Residues in contact with ARG 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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397C PHE 2.9 14.5 + - - +
398C GLU* 3.2 13.4 + - + +
400C VAL* 1.3 76.8 - - - +
402C GLU* 1.3 56.8 + - - +
404C SER* 3.3 9.5 + - - -
405C SER* 2.9 29.5 + - - -
413C LYS* 3.7 17.4 - - + +
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Residues in contact with GLU 402 (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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398C GLU* 2.9 23.1 + - - +
399C LYS* 3.3 11.9 + - + +
401C ARG* 1.3 73.1 - - - +
403C GLU* 1.3 58.8 + - - +
405C SER* 2.8 31.7 + - - -
406C PHE* 3.0 46.6 + - + -
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Residues in contact with GLU 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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399C LYS* 2.8 14.2 + - + +
400C VAL* 3.3 26.6 - - - +
402C GLU* 1.3 76.3 - - - +
404C SER* 1.3 61.4 + - - +
406C PHE* 3.4 15.7 + - + -
407C SER* 3.1 31.6 + - - -
420C LEU* 5.9 0.2 - - - +
431C SER* 2.9 25.8 + - - +
432C LYS* 2.8 45.7 - - + +
435C GLY* 3.1 26.1 + - - -
436C VAL* 4.3 1.5 + - + +
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Residues in contact with SER 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 VAL 2.9 16.7 + - - -
401C ARG* 3.3 12.4 - - - -
402C GLU 3.2 0.2 - - - -
403C GLU* 1.3 74.7 - - - +
405C SER* 1.3 61.8 + - - +
406C PHE 3.3 1.0 + - - -
407C SER* 3.4 8.9 + - - +
408C ASP* 3.4 13.3 + - - -
409C ILE 3.5 12.2 + - - -
410C PRO* 3.8 8.7 - - - +
411C ASP* 2.7 40.2 + - - +
413C LYS* 5.3 0.2 - - - +
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Residues in contact with SER 405 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401C ARG 2.9 17.7 + - - -
402C GLU* 2.8 28.8 + - - -
404C SER* 1.3 76.5 - - - +
406C PHE* 1.3 59.1 + - - +
408C ASP 5.1 0.2 - - - -
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Residues in contact with PHE 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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402C GLU* 3.0 55.1 + - + -
403C GLU* 3.6 9.4 - - + -
405C SER* 1.3 80.5 - - - +
407C SER* 1.3 55.9 + - - +
408C ASP 3.9 0.9 - - - +
432C LYS* 3.5 39.5 - - + -
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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