Contacts of the helix formed by residues 424 - 433 (chain C) in PDB entry 3IW4
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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423C GLY* 1.3 73.3 - - - -
425C LEU* 1.3 66.4 + - - +
426C MET* 3.1 26.4 + - - +
427C TYR* 3.1 21.4 + - - +
428C HIS* 3.2 13.2 + - - -
466C LEU 4.6 3.8 - - - +
467C ASP* 4.9 9.2 - - - +
469C VAL 3.4 14.4 - - - +
470C MET* 3.8 14.1 - - + +
901C LW4 4.0 22.5 - - - -
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Residues in contact with LEU 425 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423C GLY 4.3 0.2 + - - -
424C ASP* 1.3 69.8 - - - +
426C MET* 1.3 68.5 + - - +
428C HIS* 3.1 3.3 + - - +
429C ILE* 2.7 28.4 + - - +
435C PHE* 4.3 12.6 - - + -
443C TYR* 4.3 23.6 - - + -
447C ILE* 4.8 0.7 - - + -
466C LEU* 3.8 24.2 - - + +
469C VAL* 2.8 36.7 + - + +
470C MET 5.2 2.0 - - - -
471C LEU* 3.9 31.9 - - + +
477C ILE* 4.7 4.5 - - + -
527C LEU* 4.6 4.9 - - + -
531C MET* 4.2 21.3 - - - -
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Residues in contact with MET 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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424C ASP* 3.1 12.0 + - - +
425C LEU* 1.3 77.2 - - - +
427C TYR* 1.3 65.7 + - - +
429C ILE* 3.1 9.7 + - - +
430C GLN* 2.9 49.7 + - - +
466C LEU* 4.2 36.2 + - + +
467C ASP* 4.6 13.7 - - - +
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Residues in contact with TYR 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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423C GLY* 5.2 3.8 - - - -
424C ASP* 3.1 21.5 + - - +
426C MET* 1.3 78.2 - - - +
428C HIS* 1.3 92.5 + + - +
430C GLN* 2.6 39.5 + - - +
431C GLN* 3.0 53.9 + - + +
617C LYS* 6.1 0.7 - - - +
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Residues in contact with HIS 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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422C GLY 2.5 31.8 + - - -
423C GLY* 3.5 17.4 + - - -
424C ASP 3.2 13.5 + - - -
425C LEU* 3.1 8.8 + - + +
427C TYR* 1.3 101.9 - + - +
429C ILE* 1.3 63.4 + - - +
431C GLN* 3.5 14.0 + - + +
432C VAL* 3.6 15.4 - - - +
435C PHE* 3.6 13.9 - - + -
471C LEU* 3.4 24.5 - - + +
614C PHE* 3.6 23.5 - + + -
616C PRO* 3.9 12.3 - - - +
617C LYS 5.6 0.8 + - - -
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Residues in contact with ILE 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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425C LEU* 2.7 20.1 + - + +
426C MET* 3.3 10.8 - - - +
428C HIS* 1.3 69.2 - - - +
430C GLN* 1.3 71.3 + - + +
432C VAL* 2.9 15.0 + - - +
433C GLY 2.9 30.3 + - - +
434C LYS* 4.4 5.6 - - - -
435C PHE* 3.4 26.9 - - + -
466C LEU* 3.9 32.3 - - + -
530C GLU* 4.2 7.2 - - + +
531C MET* 3.8 32.5 - - + +
534C GLY* 4.9 4.3 - - - +
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Residues in contact with GLN 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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426C MET* 2.9 38.5 + - - +
427C TYR* 2.6 41.6 + - - +
429C ILE* 1.3 75.8 - - + +
431C GLN* 1.3 66.1 + - - +
432C VAL 3.2 1.4 + - - -
433C GLY* 3.5 9.6 + - - +
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Residues in contact with GLN 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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427C TYR* 3.0 62.6 + - + +
428C HIS* 3.7 11.4 - - + +
429C ILE 3.0 0.6 + - - -
430C GLN* 1.3 86.0 + - - +
432C VAL* 1.3 65.9 + - + +
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Residues in contact with VAL 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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428C HIS 3.6 12.1 - - - +
429C ILE 2.9 6.1 + - - +
431C GLN* 1.3 84.5 - - + +
433C GLY* 1.3 58.0 + - - +
434C LYS* 2.9 31.9 + - - +
435C PHE* 3.5 25.8 - - + -
439C GLN* 4.3 7.6 - - - +
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Residues in contact with GLY 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 ILE* 2.9 19.7 + - - +
430C GLN* 3.5 9.8 + - - -
431C GLN 3.7 0.2 - - - -
432C VAL* 1.3 73.3 - - - +
434C LYS* 1.3 60.4 + - - +
534C GLY* 3.5 18.5 - - - +
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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