Contacts of the helix formed by residues 412 - 418 (chain C) in PDB entry 5W5T
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 THR 412 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C GLU* 3.6 34.8 - - + +
33C ARG* 5.1 7.0 - - - +
379C ASP* 4.1 20.9 - - + +
382C VAL* 3.8 8.3 - - - -
410C LEU* 4.3 7.2 - - + -
411C ILE* 1.3 78.3 - - - +
413C GLN* 1.3 64.7 + - - +
414C SER* 3.6 10.1 + - - -
415C MET* 3.1 42.9 + - + +
416C ILE* 3.1 14.3 + - - +
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Residues in contact with GLN 413 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C ARG* 5.7 3.2 - - - +
379C ASP* 5.2 1.2 + - - +
380C HIS 6.0 0.4 - - - +
381C GLY 4.2 3.8 - - - +
382C VAL* 3.4 18.9 - - + +
383C VAL* 2.9 38.9 + - - +
412C THR* 1.3 74.7 - - - +
414C SER* 1.3 57.4 + - - +
416C ILE* 3.1 23.2 + - - +
417C ASP* 2.8 64.0 + - - +
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Residues in contact with SER 414 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C GLU* 5.9 1.9 - - - +
412C THR* 3.2 10.5 + - - -
413C GLN* 1.3 78.5 - - - +
415C MET* 1.3 65.1 + - - +
417C ASP* 3.7 11.0 - - - +
418C LYS* 3.3 44.8 + - - +
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Residues in contact with MET 415 (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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29C GLU* 3.7 37.7 - - + +
400C ARG 3.8 17.1 - - - +
401C PHE* 3.7 24.0 - - + -
402C ARG* 3.5 15.9 - - + +
410C LEU* 3.2 29.2 - - + +
412C THR* 3.1 30.8 + - + +
414C SER* 1.3 83.1 + - - +
416C ILE* 1.3 64.4 + - - +
417C ASP 3.5 0.2 + - - -
418C LYS* 3.5 18.0 + - - +
419C LEU* 3.4 19.3 + - - +
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Residues in contact with ILE 416 (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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382C VAL* 4.3 14.8 - - + -
383C VAL 3.8 3.8 - - - +
384C ILE* 4.2 2.5 - - + -
385C PRO* 3.7 31.2 - - + -
388C LEU* 4.1 18.8 - - + -
401C PHE* 3.9 13.7 - - + -
411C ILE* 3.7 23.6 - - + -
412C THR 3.1 12.1 + - - +
413C GLN* 3.1 24.8 + - - +
415C MET* 1.3 76.5 - - - +
417C ASP* 1.3 64.1 + - - +
419C LEU* 3.0 26.8 + - + +
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Residues in contact with ASP 417 (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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413C GLN* 2.8 50.3 + - - +
414C SER* 3.7 10.8 - - - +
415C MET 3.2 0.2 - - - -
416C ILE* 1.3 79.1 - - - +
418C LYS* 1.3 59.7 + - + +
419C LEU 3.2 4.5 + - - +
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Residues in contact with LYS 418 (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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414C SER* 3.3 37.5 + - - +
415C MET* 4.0 12.2 - - - +
416C ILE 3.3 0.8 - - - -
417C ASP* 1.3 76.0 - - + +
419C LEU* 1.3 63.8 + - + +
420C ASP 4.0 0.2 + - - -
421C LEU 5.3 0.7 - - - +
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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