Contacts of the helix formed by residues 422 - 428 (chain C) in PDB entry 6T8O
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 ARG 422 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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322C ASP* 3.0 44.5 + - - +
323C PRO 3.1 10.3 + - - -
324C ALA* 4.9 0.7 - - - -
325C GLU* 3.3 52.9 + - + +
419C GLN* 5.2 3.8 - - - +
420C MET* 3.2 34.0 + - - +
421C VAL* 1.3 72.1 + - - +
423C PHE* 1.3 66.5 + - - +
424C SER* 4.3 4.3 - - - +
425C GLU* 3.1 49.4 + - + +
426C VAL* 3.2 15.9 + - - +
695C PHE* 5.5 5.3 + - - +
700C GLU* 4.6 2.7 + - - -
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Residues in contact with PHE 423 (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 LEU* 3.7 21.3 - - + -
421C VAL 3.4 3.6 + - - -
422C ARG* 1.3 71.6 - - - +
424C SER* 1.3 59.6 + - - +
426C VAL* 3.1 6.1 + - + +
427C LEU* 3.0 58.0 + - + +
442C ALA* 4.1 26.5 - - + -
478C ALA* 4.0 20.0 - - + -
481C LEU* 4.4 21.8 - - + -
482C SER* 4.0 13.5 - - - -
485C PHE* 4.5 4.5 - + - -
694C ALA* 3.6 22.9 - - + -
695C PHE 3.7 19.6 + - - +
696C VAL* 4.9 9.6 - - + -
700C GLU* 4.7 7.4 - - - +
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Residues in contact with SER 424 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318C LEU 5.2 6.1 - - - -
321C LEU* 4.0 22.9 - - - +
322C ASP 3.7 13.5 + - - -
323C PRO* 3.4 10.0 + - - -
324C ALA* 3.3 27.7 + - - +
422C ARG* 4.3 3.5 - - - +
423C PHE* 1.3 79.0 - - - +
425C GLU* 1.3 61.6 + - - +
427C LEU* 3.5 3.8 + - - +
428C SER* 3.2 25.6 + - - -
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Residues in contact with GLU 425 (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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324C ALA* 3.8 22.3 - - + +
325C GLU 3.8 18.5 - - - +
327C LYS* 5.9 1.6 - - - +
419C GLN* 4.2 16.4 + - - -
421C VAL* 5.7 0.2 - - - -
422C ARG* 3.1 35.2 + - + +
424C SER* 1.3 81.0 + - - +
426C VAL* 1.3 62.5 + - - +
428C SER* 3.0 22.1 + - - +
429C SER* 4.4 0.7 + - - -
445C HIS* 3.7 25.4 + - + +
451C PRO* 5.0 1.6 - - - +
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Residues in contact with VAL 426 (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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421C VAL* 3.8 2.2 - - + -
422C ARG 3.3 14.6 - - - +
423C PHE* 3.1 12.5 + - + +
425C GLU* 1.3 79.5 - - - +
427C LEU* 1.3 61.6 + - - +
428C SER 3.3 0.7 + - - -
429C SER* 3.8 17.3 + - - -
432C TYR* 4.6 0.7 - - - +
442C ALA* 3.7 27.6 - - + +
443C LEU 4.7 0.2 - - - -
444C GLY* 3.9 20.9 - - - +
445C HIS* 3.6 26.9 - - + -
451C PRO* 4.3 11.0 - - + +
453C ILE* 4.2 8.3 - - + +
694C ALA* 3.8 19.5 - - + -
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Residues in contact with LEU 427 (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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318C LEU* 3.8 34.9 - - + +
321C LEU* 3.8 18.4 - - + -
423C PHE* 3.0 43.9 + - + +
424C SER* 3.5 5.1 + - - +
425C GLU 3.4 0.2 - - - -
426C VAL* 1.3 76.5 - - - +
428C SER* 1.3 55.4 + - - +
429C SER 3.2 8.2 + - - +
432C TYR* 3.4 49.2 - - + +
433C ASP* 4.9 2.8 + - - +
442C ALA* 3.8 22.9 - - + -
482C SER* 5.0 2.7 - - - +
485C PHE* 4.0 12.8 - - + -
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Residues in contact with SER 428 (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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318C LEU* 5.4 5.4 - - - -
424C SER 3.2 14.6 + - - -
425C GLU* 3.0 21.2 + - - +
426C VAL 3.2 0.8 - - - -
427C LEU* 1.3 76.0 - - - +
429C SER* 1.3 60.6 + - - +
430C PRO* 4.1 2.6 - - - +
433C ASP* 5.9 0.4 - - - -
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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