Contacts of the helix formed by residues 335 - 341 (chain C) in PDB entry 5Z58
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 335 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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378A PHE* 2.9 44.5 - - + -
380A LEU* 3.5 8.9 - - + +
381A PRO* 5.6 0.2 - - - +
333C ASP 3.4 3.9 + - - -
334C ILE* 1.3 75.4 - - - +
336C TYR* 1.3 84.8 + - - +
337C GLN* 3.3 13.2 + - - +
338C GLU* 3.1 25.1 + - + +
339C PHE* 3.3 23.0 + - - +
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Residues in contact with TYR 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193C THR* 4.1 15.4 + - - -
194C LYS* 5.7 7.0 + - - -
321C GLY* 3.9 25.0 - - - -
322C SER* 4.0 4.3 + - - -
324C ALA* 3.5 24.7 - - - +
325C LYS* 3.6 49.1 - - + -
328C ALA* 5.2 9.2 - - + -
334C ILE* 3.6 3.9 + - - +
335C ASN* 1.3 84.5 + - - +
337C GLN* 1.3 86.2 + - + +
339C PHE 4.3 0.2 - - - -
340C ALA* 3.6 7.6 + - + +
432C ASP* 4.1 7.6 + - - -
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Residues in contact with GLN 337 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194C LYS* 5.9 5.3 - - - +
335C ASN* 3.3 8.5 + - - +
336C TYR* 1.3 98.9 - - + +
338C GLU* 1.3 72.9 + - + +
339C PHE 3.2 2.0 - - - -
340C ALA* 3.6 4.3 - - - +
341C LYS* 3.1 45.1 + - + +
436C GLN* 6.1 0.8 - - - +
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Residues in contact with GLU 338 (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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372A PRO* 4.9 10.6 - - - +
378A PHE* 3.8 33.6 - - + +
335C ASN* 3.1 28.8 + - + +
336C TYR 3.7 0.2 - - - -
337C GLN* 1.3 81.8 - - + +
339C PHE* 1.3 60.6 + - - +
341C LYS* 3.8 8.6 + - - +
342C ARG* 3.4 56.4 + - - +
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Residues in contact with PHE 339 (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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380A LEU* 5.6 12.1 - - + +
384A VAL* 6.4 1.6 - - + -
323C PHE* 6.2 1.3 - + - -
324C ALA* 3.6 24.5 - - + -
327C TYR* 3.4 44.0 - + + -
334C ILE* 4.5 14.8 - - + -
335C ASN 3.3 20.5 + - - +
336C TYR 4.1 3.6 - - - +
338C GLU* 1.3 76.5 - - - +
340C ALA* 1.3 65.1 + - - +
342C ARG* 3.0 16.2 + - - +
343C LEU* 3.5 41.7 + - + +
356C PHE* 3.8 28.3 - + - -
372C PHE* 4.2 11.4 - + + -
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Residues in contact with ALA 340 (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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320C LEU* 3.5 21.6 - - + +
321C GLY* 3.4 33.4 - - - +
324C ALA* 4.1 3.1 - - + -
336C TYR* 3.6 14.3 + - + +
337C GLN* 3.3 8.9 + - - +
339C PHE* 1.3 79.1 - - - +
341C LYS* 1.3 64.2 + - + +
342C ARG 3.1 1.6 + - - -
343C LEU* 3.3 21.3 + - - +
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Residues in contact with LYS 341 (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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370A PRO* 5.0 17.9 + - + +
371A LEU* 5.8 3.8 - - - +
372A PRO* 4.0 37.8 - - + +
303C LEU* 3.3 40.5 - - + +
337C GLN* 3.1 31.6 + - + +
338C GLU* 4.1 9.3 - - - +
339C PHE 3.2 0.6 - - - -
340C ALA* 1.3 80.3 - - + +
342C ARG* 1.3 61.6 + - + +
343C LEU 3.5 0.9 - - - -
347C ILE* 4.4 4.7 - - - +
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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