Contacts of the helix formed by residues 648 - 654 (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 ILE 648 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372C LYS* 4.1 25.1 - - + -
373C ASP* 4.7 11.2 - - + +
376C ILE* 4.6 8.1 - - + -
410C VAL 3.8 18.6 - - - +
411C ASP* 4.2 8.3 - - + +
644C VAL* 3.3 24.7 - - + +
645C ILE* 3.7 22.9 - - + +
646C ALA 3.5 3.0 - - - +
647C ASN* 1.3 79.0 - - - +
649C ASP* 1.3 65.8 + - - +
650C GLN* 3.0 37.0 + - - +
653C PHE* 4.4 6.7 - - + -
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Residues in contact with ASP 649 (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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376C ILE* 4.5 6.6 - - + +
647C ASN 3.7 3.4 + - - -
648C ILE* 1.3 73.7 - - - +
650C GLN* 1.3 60.0 + - - +
651C SER* 2.7 29.5 + - - -
652C ASP* 3.3 34.1 + - - +
653C PHE* 4.3 2.1 - - - -
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Residues in contact with GLN 650 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372C LYS* 2.7 29.7 + - - +
408C GLN* 4.0 4.0 + - - +
410C VAL* 2.7 41.0 + - - +
645C ILE 4.5 4.2 + - - +
648C ILE* 3.0 29.0 + - - +
649C ASP* 1.3 69.5 + - - +
651C SER* 1.3 59.9 + - - +
652C ASP 3.1 2.0 - - - -
653C PHE* 3.2 21.6 + - - +
654C GLU* 3.9 3.1 + - - -
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Residues in contact with SER 651 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649C ASP* 2.7 24.5 + - - -
650C GLN* 1.3 72.8 - - - +
652C ASP* 1.3 62.3 + - - +
653C PHE 3.0 6.4 + - - -
654C GLU* 3.4 27.6 + - - +
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Residues in contact with ASP 652 (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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376C ILE* 3.3 26.3 - - - +
381C VAL* 3.6 29.4 - - + +
385C MET* 3.7 19.9 - - - +
649C ASP* 3.5 30.2 - - - +
650C GLN 3.1 0.6 - - - -
651C SER* 1.3 79.2 + - - +
653C PHE* 1.3 78.6 + - + +
654C GLU 3.4 1.0 + - - +
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Residues in contact with PHE 653 (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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372C LYS* 3.4 49.4 - - + -
375C VAL* 4.4 5.6 - - + -
376C ILE* 4.0 23.8 - - + -
381C VAL* 4.0 13.5 - - + -
384C THR* 5.5 1.1 - - + -
385C MET* 4.2 11.9 - - - -
408C GLN* 3.1 30.3 + - - +
413C LEU* 4.0 29.8 - - + -
648C ILE* 4.4 2.5 - - + -
649C ASP 4.3 4.3 - - - -
650C GLN* 3.2 17.2 + - - +
651C SER 3.0 0.6 - - - -
652C ASP* 1.3 103.7 - - + +
654C GLU* 1.3 63.7 - - - +
656C PHE* 2.9 18.1 + - + +
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Residues in contact with GLU 654 (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 MET* 3.4 10.7 - - - +
408C GLN* 5.2 0.4 - - - +
650C GLN 3.9 2.3 + - - -
651C SER* 3.4 24.2 + - - +
652C ASP 3.4 0.6 - - - +
653C PHE* 1.3 77.5 - - - +
655C GLY* 1.3 65.3 + - - +
656C PHE 3.4 0.2 + - - -
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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