Contacts of the helix formed by residues 420 - 427 (chain C) in PDB entry 5W5G
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 GLY 420 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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446A LEU* 5.2 6.0 - - - +
447A GLU* 5.2 16.8 - - - -
416C GLN* 6.2 1.8 - - - -
417C ARG* 3.4 25.2 + - - +
418C SER 3.6 0.4 + - - -
419C GLY* 1.3 75.8 - - - +
421C PHE* 1.3 59.5 + - - -
422C ARG 3.2 9.7 + - - -
423C ASP* 3.4 18.9 + - - +
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Residues in contact with PHE 421 (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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447A GLU* 3.5 27.8 - - + +
449A ASN* 3.5 25.4 - - - -
393C LEU* 3.8 13.0 - - + +
397C PHE* 3.6 66.4 - + + -
398C ASP 4.7 4.5 - - - -
399C ALA 5.6 0.4 - - - -
401C GLY* 3.7 17.3 - - - -
420C GLY* 1.3 68.3 - - - -
422C ARG* 1.3 90.0 + - - +
423C ASP 3.2 3.1 - - - -
424C TYR* 3.3 31.6 + - + +
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Residues in contact with ARG 422 (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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449A ASN* 3.9 32.1 - - - +
393C LEU* 4.1 22.5 - - - +
394C SER* 5.6 1.0 - - - +
419C GLY 5.2 4.7 - - - +
420C GLY 3.2 2.8 - - - +
421C PHE* 1.3 104.7 - - + +
423C ASP* 1.3 66.2 + - - +
424C TYR 3.1 0.2 - - - -
425C GLU* 3.2 25.2 + - + +
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Residues in contact with ASP 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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417C ARG* 3.8 27.7 + - - +
418C SER* 4.8 0.9 + - - -
419C GLY* 3.4 28.4 + - - +
420C GLY 3.4 14.7 - - - +
421C PHE 3.2 0.6 - - - -
422C ARG* 1.3 78.0 - - - +
424C TYR* 1.3 61.1 + - - +
425C GLU 3.1 2.0 + - - -
426C LYS* 3.6 11.8 + - - +
427C ASP* 3.6 15.4 - - - +
502C ALA* 3.8 28.2 + - + +
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Residues in contact with TYR 424 (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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392C TRP* 3.6 23.5 + + + -
393C LEU* 3.9 2.9 - - + -
397C PHE* 4.4 12.8 - + - -
414C LEU* 4.1 16.4 - - + -
415C PRO* 2.6 50.2 + - - +
417C ARG* 3.3 29.6 - - + +
421C PHE* 3.3 33.1 + - + +
422C ARG 3.1 0.8 - - - -
423C ASP* 1.3 75.0 - - - +
425C GLU* 1.3 63.6 + - - +
426C LYS 3.2 0.7 - - - -
427C ASP 3.3 17.2 + - - -
428C ALA* 3.3 14.9 + - - +
429C PRO* 3.9 20.0 - - + -
461C LEU* 3.5 24.2 - - + +
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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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385C ASP* 5.0 7.8 - - - +
390C LYS 5.6 4.3 - - - +
392C TRP* 5.0 5.8 + - - +
393C LEU* 4.0 19.9 - - + +
422C ARG* 3.2 18.9 + - + +
423C ASP 3.1 0.8 - - - -
424C TYR* 1.3 79.0 - - - +
426C LYS* 1.3 66.4 + - + +
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Residues in contact with LYS 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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383C ARG* 5.9 2.0 + - - -
385C ASP* 5.9 1.6 - - - -
422C ARG 4.8 0.2 + - - -
423C ASP* 3.6 6.2 + - - +
424C TYR 3.2 0.4 - - - -
425C GLU* 1.3 84.5 - - + +
427C ASP* 1.3 61.5 + - - +
428C ALA 3.9 1.1 - - - -
462C ARG* 4.9 5.1 + - - -
495C VAL* 4.5 5.6 - - - -
496C ALA* 3.5 28.9 + - + +
499C THR* 3.2 38.6 + - - +
500C LEU 3.7 14.5 + - - -
501C PRO* 3.6 31.1 - - + +
502C ALA 5.3 1.3 - - - +
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Residues in contact with ASP 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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417C ARG* 2.6 49.7 + - - +
423C ASP 3.6 4.7 + - - +
424C TYR* 3.3 8.9 + - - -
426C LYS* 1.3 80.0 - - - +
428C ALA* 1.3 66.7 + - - +
459C PRO 4.9 0.2 - - - +
460C SER* 3.5 12.1 - - - -
461C LEU* 3.0 33.9 + - - +
462C ARG* 4.6 5.4 + - - +
501C PRO* 4.4 7.9 - - + -
503C TRP* 3.7 22.8 + - - -
504C ILE* 4.2 2.1 + - - +
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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
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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