Contacts of the helix formed by residues 424 - 433 (chain C) in PDB entry 4QG0
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 ASP 424 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146C TYR 3.1 17.2 + - - +
147C ILE* 3.5 5.7 - - - -
148C LYS* 2.7 52.6 + - - +
212C PRO* 3.5 2.8 - - - +
213C PHE* 2.9 46.6 + - + -
423C THR* 1.3 71.7 - - - +
425C ASN* 1.3 64.1 + - - +
426C ILE 3.0 3.6 - - - -
427C PHE* 2.9 24.7 + - - +
428C LEU* 4.0 2.9 + - - +
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Residues in contact with ASN 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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425B ASN* 2.5 39.0 + - - +
428B LEU* 3.5 30.3 - - + +
429B GLU* 4.8 2.0 - - - +
432B TYR* 3.6 25.2 - - + -
146C TYR 4.5 0.8 + - - -
421C LYS 5.0 1.2 - - - +
423C THR* 3.3 17.2 + - - +
424C ASP* 1.3 76.4 - - - +
426C ILE* 1.3 61.5 + - - +
428C LEU* 2.9 23.9 + - - +
429C GLU* 3.0 27.5 + - - +
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Residues in contact with ILE 426 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212C PRO* 5.1 1.6 - - + -
390C PHE* 3.7 28.3 - - + -
397C ILE* 4.9 8.1 - - + -
399C ILE* 4.6 10.5 - - + -
409C ILE* 4.4 21.3 - - + -
421C LYS 4.9 2.7 - - - +
422C LEU* 3.5 41.5 - - + -
423C THR 3.4 12.9 + - - +
424C ASP 2.9 1.0 + - - -
425C ASN* 1.3 79.3 - - - +
427C PHE* 1.3 66.6 + - - +
429C GLU* 2.9 29.5 + - + +
430C ILE* 3.0 24.8 + - + +
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Residues in contact with PHE 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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146B TYR* 3.5 25.1 - + - -
155C TYR* 3.8 17.7 - + - -
213C PHE* 3.6 29.8 - + + -
386C ILE* 3.9 24.9 - - + -
390C PHE* 4.3 10.4 - - + -
424C ASP 2.9 14.3 + - - +
426C ILE* 1.3 78.1 - - - +
428C LEU* 1.3 73.5 + - + +
431C LEU* 3.0 32.2 + - + +
445C LEU* 3.2 56.6 - - + +
448C ILE* 4.6 8.7 - - + -
449C GLU* 5.8 3.8 - - + -
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Residues in contact with LEU 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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146B TYR* 4.0 48.0 - - + -
423B THR* 4.6 0.2 - - - +
425B ASN* 3.4 44.9 - - + +
424C ASP 5.1 1.6 - - - +
425C ASN* 2.9 9.3 + - - +
427C PHE* 1.3 88.4 - - + +
429C GLU* 1.3 55.9 + - - +
431C LEU* 4.0 6.3 - - + -
432C TYR* 2.7 68.1 + - + +
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Residues in contact with GLU 429 (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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425B ASN* 4.8 4.9 + - - +
397C ILE* 4.3 28.6 - - + +
398C GLU 5.3 3.5 + - - +
425C ASN* 3.0 22.9 + - - +
426C ILE* 2.9 23.5 + - + +
428C LEU* 1.3 75.4 - - - +
430C ILE* 1.3 66.6 + - - +
432C TYR* 3.0 3.4 + - - +
433C SER* 2.8 26.7 + - - -
438C LEU* 6.2 0.2 - - + -
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Residues in contact with ILE 430 (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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389C ALA 4.2 4.9 - - - +
390C PHE* 3.8 33.4 - - + -
393C ALA* 3.6 28.9 - - + -
397C ILE* 4.5 12.1 - - + -
409C ILE* 5.0 1.8 - - + -
426C ILE* 3.0 17.5 + - + +
429C GLU* 1.3 77.9 - - - +
431C LEU* 1.3 62.8 + - - +
433C SER* 2.8 26.4 + - - +
438C LEU* 5.0 6.7 - - + +
441C ALA* 3.8 8.3 - - + -
442C ARG* 3.7 31.2 - - + +
445C LEU* 3.6 21.8 - - + -
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Residues in contact with LEU 431 (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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146B TYR* 5.3 2.0 - - + -
421B LYS* 5.8 1.2 - - - -
427C PHE* 3.0 29.6 + - + +
428C LEU* 3.0 19.0 + - + +
430C ILE* 1.3 76.7 - - - +
432C TYR* 1.3 83.5 + - + +
433C SER 3.6 0.3 + - - +
442C ARG* 4.0 13.9 - - - +
445C LEU* 3.9 24.7 - - + -
446C LYS* 3.8 36.8 - - + +
449C GLU* 3.6 33.2 - - + +
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Residues in contact with TYR 432 (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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143B ARG* 5.8 0.5 - - - -
146B TYR* 4.5 3.1 - - - -
420B THR* 4.3 4.3 + - + -
421B LYS* 3.4 63.4 + - + +
423B THR* 3.0 35.9 + - - +
425B ASN* 3.9 24.5 - - + -
429B GLU* 5.8 1.3 - - - -
428C LEU* 2.7 41.1 + - + +
429C GLU* 3.6 2.9 - - - +
431C LEU* 1.3 95.0 - - + +
433C SER* 1.3 68.7 + - - +
434C THR* 4.2 7.8 - - - +
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Residues in contact with SER 433 (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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429C GLU* 2.8 16.2 + - - -
430C ILE 2.8 17.4 + - - -
431C LEU 4.3 0.2 - - - +
432C TYR* 1.3 83.0 - - - +
434C THR* 1.3 61.9 + - - +
435C ASP* 4.4 2.7 - - - -
438C LEU* 3.6 31.1 - - - +
442C ARG* 2.9 35.2 + - - -
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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