Contacts of the helix formed by residues 343 - 350 (chain C) in PDB entry 5T0H
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 343 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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341C GLY 3.5 3.4 + - - +
342C ILE* 1.3 72.9 - - - +
344C LEU* 1.3 62.5 + - - +
345C ARG* 2.8 43.3 + - - +
346C LYS* 3.5 30.4 - - + +
347C ILE* 3.3 9.4 + - - +
380C GLN* 2.6 45.1 + - - +
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Residues in contact with LEU 344 (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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326C LEU* 3.9 42.6 - - + +
329C LEU* 5.3 4.9 - - + -
330C LYS* 3.8 33.0 - - + +
342C ILE* 3.6 17.3 + - + +
343C ASN* 1.3 74.9 + - - +
345C ARG* 1.3 68.8 + - + +
347C ILE* 3.3 14.4 - - + +
348C ALA* 3.0 27.7 + - - +
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Residues in contact with ARG 345 (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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326C LEU* 5.8 9.4 - - - +
343C ASN* 2.8 25.3 + - - +
344C LEU* 1.3 75.2 - - + +
346C LYS* 1.3 58.2 + - - +
348C ALA* 3.7 1.5 - - - +
349C GLU* 2.9 51.7 + - - +
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Residues in contact with LYS 346 (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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343C ASN* 3.5 28.4 - - + +
345C ARG* 1.3 78.5 - - - +
347C ILE* 1.3 55.7 + - - +
349C GLU* 4.5 2.9 - - - +
350C LEU* 2.9 57.1 + - + +
380C GLN* 3.3 32.3 - - + +
384C GLU* 6.5 0.9 - - + -
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Residues in contact with ILE 347 (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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325C ARG 5.6 1.1 - - - +
326C LEU* 5.9 1.1 - - - -
329C LEU* 3.7 33.2 - - + -
342C ILE* 4.5 8.5 - - + -
343C ASN 3.3 17.6 + - - +
344C LEU* 3.3 23.1 - - + +
346C LYS* 1.3 82.8 - - - +
348C ALA* 1.3 68.1 + - + +
350C LEU* 4.5 2.5 - - + +
351C MET* 3.3 26.5 - - - +
362C VAL* 4.8 7.4 - - + -
363C CYS* 6.3 0.2 - - - -
380C GLN* 3.5 16.2 - - + +
383C PHE* 3.9 28.9 - - + -
384C GLU* 4.6 1.6 - - + +
387C VAL* 3.9 22.1 - - + +
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Residues in contact with ALA 348 (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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322C GLU* 3.1 18.0 - - - +
325C ARG* 3.7 15.2 - - + -
326C LEU* 3.6 29.4 - - + +
344C LEU 3.0 19.2 + - - +
345C ARG* 3.7 2.7 - - - +
347C ILE* 1.3 79.4 - - - +
349C GLU* 1.3 61.1 + - + +
351C MET* 3.0 33.4 + - - +
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Residues in contact with GLU 349 (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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322C GLU* 3.2 29.2 - - + +
345C ARG* 2.9 41.3 + - - +
346C LYS* 4.6 2.8 - - - +
348C ALA* 1.3 75.2 - - + +
350C LEU* 1.3 62.7 + - + +
351C MET 3.1 2.3 + - - -
352C PRO* 3.6 12.8 - - - +
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Residues in contact with LEU 350 (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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346C LYS* 2.9 46.4 + - + +
347C ILE* 4.5 4.7 - - + +
348C ALA 3.1 0.4 + - - -
349C GLU* 1.3 79.6 - - + +
351C MET* 1.3 56.1 + - - +
352C PRO* 3.3 10.0 - - - +
384C GLU* 4.6 17.0 - - + -
387C VAL* 3.5 35.4 - - + +
391C MET* 3.3 14.9 - - - +
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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