Contacts of the helix formed by residues 323 - 331 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A HIS* 3.1 26.0 - - - -
109A PHE* 3.2 14.3 - - - -
304A SER 4.7 6.1 - - - -
322A GLN* 1.3 70.2 - - - +
324A ILE* 1.3 62.7 + - - -
325A ASP* 3.2 12.1 + - - -
326A ILE* 3.1 28.4 - - - +
327A GLU 3.8 0.5 + - - -
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Residues in contact with ILE 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A HIS* 3.4 34.1 - - + +
109A PHE* 3.8 12.8 - - + -
320A TRP* 3.3 27.1 - - + +
321A SER 5.5 1.6 - - - +
322A GLN 2.8 13.8 + - - +
323A GLY* 1.3 71.7 - - - +
325A ASP* 1.3 61.9 + - - +
326A ILE 3.4 0.5 + - - -
327A GLU* 3.6 14.7 + - - +
328A ARG* 3.8 8.3 + - - +
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Residues in contact with ASP 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A LEU* 4.8 5.1 - - - +
301A VAL* 4.2 22.2 - - + +
302A ASP 4.6 0.5 - - - +
303A VAL* 4.4 3.7 - - - +
304A SER* 4.0 24.0 + - - -
321A SER 5.0 7.2 + - - +
322A GLN 5.0 0.4 - - - -
323A GLY* 3.7 15.7 + - - +
324A ILE* 1.3 77.0 - - - +
326A ILE* 1.3 88.8 + - - +
328A ARG* 3.8 12.0 + - - +
329A ALA* 3.9 11.1 + - - +
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Residues in contact with ILE 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A TYR* 3.2 29.8 - - + +
72A ALA* 5.2 0.4 - - + -
93A HIS 5.0 2.0 - - - +
94A THR* 5.0 1.1 - - + -
95A SER* 3.6 31.9 - - - +
292A ALA* 5.5 0.2 - - - +
293A PHE* 4.5 11.9 - - + -
296A LEU* 4.1 26.0 - - + +
303A VAL* 4.7 8.3 - - + -
304A SER 6.2 0.2 - - - +
323A GLY* 3.1 23.8 - - - +
325A ASP* 1.3 91.8 + - - +
327A GLU* 1.3 60.1 + - - +
329A ALA* 3.2 6.6 + - - +
330A LEU* 2.9 40.6 + - + +
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Residues in contact with GLU 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A SER* 3.5 20.2 - - - +
108A GLN* 3.2 11.0 - - - +
109A PHE* 2.9 62.7 + - + -
111A ILE* 5.8 0.9 - - + -
323A GLY 3.8 0.4 + - - -
324A ILE* 3.6 9.7 + - - +
325A ASP 3.5 0.4 - - - -
326A ILE* 1.3 82.1 - - - +
328A ARG* 1.3 61.8 + - - +
330A LEU* 4.5 3.4 - - - -
331A LYS* 3.0 59.9 + - + +
346A THR 5.1 0.2 - - - +
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Residues in contact with ARG 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295A TYR* 5.5 7.5 + - - -
324A ILE 3.8 8.3 + - - +
325A ASP* 3.8 9.4 + - - +
326A ILE 3.3 0.8 - - - -
327A GLU* 1.3 78.5 - - - +
329A ALA* 1.3 56.4 + - + +
331A LYS* 4.4 1.8 - - - -
332A MET* 3.2 42.5 + - + +
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Residues in contact with ALA 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292A ALA* 3.7 9.8 - - + +
295A TYR* 3.9 22.9 - - + +
296A LEU* 3.4 33.9 - - + -
325A ASP 4.3 4.5 - - - +
326A ILE 3.2 5.5 + - - +
328A ARG* 1.3 78.3 - - - +
330A LEU* 1.3 61.7 + - - +
331A LYS 3.3 2.0 - - - -
332A MET* 3.5 14.7 + - - +
333A VAL* 3.6 14.4 - - - +
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Residues in contact with LEU 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A ALA* 5.5 4.5 - - + -
95A SER* 3.5 34.1 - - - +
97A VAL* 5.2 1.6 - - + -
111A ILE* 3.8 22.0 - - + -
288A VAL* 3.7 17.3 - - + +
289A ILE* 4.2 27.4 - - + -
292A ALA* 3.7 23.3 - - + -
293A PHE* 5.2 8.3 - - + -
326A ILE* 2.9 32.8 + - + +
327A GLU* 3.5 4.0 + - - +
329A ALA* 1.3 77.5 - - - +
331A LYS* 1.3 57.5 + - + +
332A MET 3.2 1.8 - - - -
333A VAL* 3.3 24.9 - - - +
344A PHE* 3.9 3.2 - - - -
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Residues in contact with LYS 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A GLN* 3.8 3.6 + - - -
109A PHE 4.5 0.2 - - - +
110A VAL 3.8 6.7 + - - +
111A ILE* 3.8 26.2 - - + -
327A GLU* 3.0 48.7 + - + +
328A ARG* 4.4 2.0 - - - +
330A LEU* 1.3 77.0 - - + +
332A MET* 1.3 60.3 + - - +
333A VAL 3.4 2.2 - - - +
344A PHE* 4.0 34.7 + - + +
345A ASP 3.8 21.3 - - - +
346A THR* 3.4 12.6 + - - +
347A TYR 3.4 9.9 + - - -
348A GLY* 3.4 29.1 - - - +
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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