Contacts of the helix formed by residues 323 - 331 (chain C) in PDB entry 3P3W
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 GLY 323 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93C HIS 3.5 17.0 - - - -
109C PHE* 2.8 24.3 - - - -
304C SER 4.7 3.8 + - - -
322C GLN* 1.3 71.8 - - - +
324C ILE* 1.3 58.6 + - - +
325C ASP* 3.0 15.2 + - - -
326C ILE* 3.7 29.5 - - - +
327C GLU 3.9 1.9 + - - -
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Residues in contact with ILE 324 (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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295B TYR* 5.1 0.2 - - - +
328B ARG 5.8 1.8 - - - +
332B MET* 4.0 41.1 - - + -
93C HIS* 3.7 27.8 - - + +
109C PHE* 3.9 10.5 - - + -
322C GLN 3.2 28.6 - - - +
323C GLY* 1.3 75.2 - - - +
325C ASP* 1.3 65.7 + - - +
326C ILE 3.4 0.4 - - - -
327C GLU* 4.1 8.5 - - - +
328C ARG* 3.3 26.7 + - + +
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Residues in contact with ASP 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B ARG* 4.5 17.2 - - - +
296C LEU* 3.9 17.1 - - + +
301C VAL* 4.7 17.9 - - + +
302C ASP 5.0 8.8 - - - +
303C VAL* 5.3 7.8 - - + -
304C SER 4.4 9.2 + - - +
322C GLN* 3.6 10.9 + - - -
323C GLY 3.0 21.9 + - - -
324C ILE* 1.3 82.7 - - - +
326C ILE* 1.3 69.1 + - + +
328C ARG* 3.9 10.5 - - - +
329C ALA* 4.0 3.6 + - - +
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Residues in contact with ILE 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C TYR* 4.0 27.1 - - + +
72C ALA* 5.7 0.2 - - + -
93C HIS 5.6 0.4 - - - +
94C THR* 6.1 0.4 - - - -
95C SER* 3.5 16.6 - - - +
293C PHE* 3.5 34.1 - - + -
296C LEU* 3.7 20.4 - - + -
303C VAL* 5.1 6.5 - - + -
323C GLY* 3.7 26.7 - - - +
325C ASP* 1.3 81.8 - - + +
327C GLU* 1.3 63.3 + - - +
328C ARG 3.1 2.0 - - - -
329C ALA* 3.1 3.7 + - - +
330C LEU* 2.9 40.9 + - + +
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Residues in contact with GLU 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C SER* 3.3 18.0 + - - +
108C GLN* 3.1 13.5 + - - +
109C PHE* 2.8 71.6 + - + -
111C ILE* 4.9 2.7 - - + -
323C GLY 3.9 1.5 + - - +
324C ILE* 3.8 10.9 + - + +
325C ASP 3.7 0.2 - - - -
326C ILE* 1.3 77.8 - - - +
328C ARG* 1.3 61.7 + - - +
330C LEU* 4.5 3.6 - - - -
331C LYS* 2.8 53.6 + - - +
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Residues in contact with ARG 328 (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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346B THR* 5.2 13.6 - - - +
324C ILE* 3.3 22.1 + - + +
325C ASP* 3.9 6.5 - - - +
326C ILE 3.1 0.4 - - - -
327C GLU* 1.3 80.5 - - - +
329C ALA* 1.3 58.5 - - - +
331C LYS* 4.1 7.2 + - - +
332C MET* 3.6 20.1 + - - +
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Residues in contact with ALA 329 (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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292C ALA* 3.8 25.9 - - + +
295C TYR* 4.5 13.8 - - + +
296C LEU* 4.3 14.4 - - + -
325C ASP 4.3 9.0 - - - +
326C ILE* 3.1 7.5 + - - +
328C ARG* 1.3 76.8 - - + +
330C LEU* 1.3 62.9 + - - +
331C LYS 3.3 0.9 - - - -
332C MET* 3.4 24.5 - - + +
333C VAL* 3.5 14.4 - - - +
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Residues in contact with LEU 330 (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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72C ALA* 5.0 9.4 - - + -
95C SER* 3.6 30.1 - - - +
97C VAL* 5.1 6.5 - - + -
111C ILE* 3.8 22.0 - - + -
288C VAL* 3.7 32.0 - - + +
289C ILE* 4.2 17.5 - - + -
292C ALA* 3.8 19.5 - - + -
293C PHE* 5.4 4.7 - - + -
326C ILE* 2.9 29.5 + - + +
327C GLU 4.4 1.6 - - - +
328C ARG 3.5 0.2 - - - -
329C ALA* 1.3 77.5 - - - +
331C LYS* 1.3 57.7 + - - +
332C MET 3.3 1.3 - - - -
333C VAL* 3.4 21.3 - - - +
344C PHE* 4.2 8.5 - - - -
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Residues in contact with LYS 331 (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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108C GLN* 3.3 15.2 - - - +
109C PHE 4.0 4.6 - - - +
110C VAL 4.0 11.0 - - - -
111C ILE* 4.1 13.5 - - + -
327C GLU* 2.8 52.8 + - + +
328C ARG 4.1 3.3 + - - +
329C ALA 3.3 0.4 - - - -
330C LEU* 1.3 78.5 - - - +
332C MET* 1.3 58.0 + - - +
333C VAL 3.7 0.2 - - - -
344C PHE* 3.0 34.4 - - + +
345C ASP 4.2 9.6 - - - +
346C THR* 2.6 32.1 + - + +
347C TYR 3.7 18.5 + - - -
348C GLY* 4.1 3.6 - - - +
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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