Contacts of the helix formed by residues 456 - 463 (chain C) in PDB entry 1T5A
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 ASN 456 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264C ASN* 6.0 1.6 - - - +
433C LYS* 3.5 15.3 + - + +
454C THR* 3.2 7.6 + - - +
455C ARG* 1.3 77.4 - - - +
457C PRO* 1.3 68.1 - - - +
458C GLN* 2.7 25.6 + - - +
459C THR* 2.9 50.2 + - - +
460C ALA 3.2 5.2 + - - -
473C LEU* 3.9 0.7 - - - -
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Residues in contact with PRO 457 (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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455C ARG 3.3 10.0 - - - +
456C ASN* 1.3 85.6 - - - +
458C GLN* 1.3 65.5 + - + +
460C ALA* 3.3 2.8 + - + +
461C ARG* 3.0 45.0 + - - +
473C LEU* 3.5 32.3 - - + -
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Residues in contact with GLN 458 (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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236C ASP* 4.0 18.6 + - - -
237C VAL 4.4 11.9 + - - -
238C ASP* 4.2 2.4 + - - +
264C ASN* 3.3 38.8 + - - +
265C ILE* 4.9 3.4 - - - +
456C ASN* 2.7 15.4 + - - +
457C PRO* 1.3 78.8 - - + +
459C THR* 1.3 60.9 - - + +
461C ARG* 3.2 23.2 + - - +
462C GLN* 2.9 59.2 + - + +
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Residues in contact with THR 459 (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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264C ASN* 5.9 5.2 - - - +
432C THR* 5.9 0.2 - - - +
433C LYS 3.0 29.3 + - - +
434C SER* 3.5 27.8 - - - +
435C GLY* 4.5 4.5 + - - -
439C HIS* 5.8 0.9 - - - -
454C THR* 3.3 10.3 + - - +
456C ASN* 2.9 35.3 + - - +
458C GLN* 1.3 81.7 - - + +
460C ALA* 1.3 55.0 + - - +
462C GLN* 3.8 12.2 - - - +
463C ALA* 3.0 30.7 + - - +
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Residues in contact with ALA 460 (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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107C PRO* 4.0 15.7 - - + +
454C THR* 3.5 25.4 - - + -
456C ASN 3.2 4.1 + - - +
457C PRO* 3.7 11.4 - - + +
458C GLN 3.2 0.4 - - - -
459C THR* 1.3 81.2 + - - +
461C ARG* 1.3 60.9 + - - +
463C ALA* 3.7 2.1 - - - +
464C HIS* 4.0 0.2 - - - -
471C PRO* 2.9 44.2 - - + +
472C VAL 4.8 1.6 - - - +
473C LEU* 4.3 9.9 - - + -
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Residues in contact with ARG 461 (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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92C ARG* 5.4 5.6 - - - +
105C TYR* 5.8 3.6 - - - -
107C PRO* 4.5 5.4 - - + -
108C VAL 3.0 39.5 - - - +
109C ALA* 3.6 9.9 - - + +
236C ASP* 3.9 24.5 + - - -
238C ASP* 2.7 38.3 + - - +
239C MET* 4.8 0.3 - - - +
457C PRO* 3.0 36.7 + - - +
458C GLN* 3.6 31.4 - - - +
460C ALA* 1.3 75.1 - - - +
462C GLN* 1.3 65.3 + - - +
463C ALA 3.1 3.0 + - - -
464C HIS* 3.1 27.5 + - - +
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Residues in contact with GLN 462 (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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238C ASP* 2.8 37.4 + - + +
239C MET* 4.7 10.1 - - + -
264C ASN* 2.7 29.3 + - - +
266C LYS* 3.6 33.2 - - + +
434C SER 5.6 1.0 - - - +
439C HIS* 5.7 2.2 - - + -
458C GLN* 2.9 38.0 + - + +
459C THR* 4.1 11.2 - - - +
461C ARG* 1.3 75.2 - - - +
463C ALA* 1.3 61.4 + - - +
464C HIS 3.1 1.0 + - - -
465C LEU* 3.3 25.0 + - + +
466C TYR* 4.4 4.4 - - - -
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Residues in contact with ALA 463 (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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435C GLY* 6.2 1.8 - - - -
439C HIS* 4.8 7.8 - - + -
452C ALA* 5.5 2.7 - - + -
459C THR 3.0 19.2 + - - +
460C ALA* 4.2 1.3 - - - -
461C ARG 3.1 1.0 - - - -
462C GLN* 1.3 77.8 - - - +
464C HIS* 1.3 63.4 + - - +
466C TYR* 3.0 28.0 + - - +
469C ILE* 3.8 25.2 - - + +
471C PRO* 3.6 24.9 - - + -
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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