Contacts of the helix formed by residues 324 - 331 (chain A) in PDB entry 2W8I
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 SER 324 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322A ASP* 2.6 33.3 + - - -
323A ALA* 1.3 71.1 - - - +
325A ALA* 1.3 49.7 + - - -
326A MET 2.8 4.5 - - - -
327A VAL* 2.7 40.5 + - - +
46B LEU* 3.1 18.9 - - - +
47B ASP* 5.3 0.3 + - - -
50B VAL* 5.3 7.2 - - - -
301B VAL* 4.5 5.6 - - - +
315B ILE* 4.0 26.7 - - - -
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Residues in contact with ALA 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A LEU* 3.8 19.8 - - + +
319A ASN 3.8 19.7 - - - +
320A ALA* 4.2 4.5 - - - -
322A ASP 2.7 17.8 + - - +
324A SER* 1.3 71.2 + - - +
326A MET* 1.3 56.7 + - - +
327A VAL* 2.9 13.9 + - - -
328A LEU* 3.1 23.5 + - + +
44B TYR* 4.6 9.9 - - - +
46B LEU* 3.7 20.2 - - + +
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Residues in contact with MET 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A LEU* 4.9 1.1 - - + -
279A ALA* 5.1 3.7 - - + +
282A LEU* 3.7 31.9 - - + -
288A ILE* 4.8 4.5 - - - -
298A ILE* 4.6 3.8 - - + -
318A LEU* 3.6 23.6 - - + -
320A ALA* 4.3 14.6 - - + +
322A ASP 3.9 1.0 + - - -
323A ALA* 2.9 28.6 + - + +
324A SER 2.8 0.4 - - - -
325A ALA* 1.3 77.0 - - - +
327A VAL* 1.3 60.2 + - - +
328A LEU 3.2 0.7 - - - -
329A GLY* 3.3 22.5 + - - -
330A THR* 3.6 3.6 - - - +
260B MET* 3.8 26.7 - - + +
339B ILE* 3.2 30.1 - - + +
341B TYR* 6.5 0.4 - - + -
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Residues in contact with VAL 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A ALA 4.4 0.4 + - - -
324A SER 2.7 23.1 + - - +
325A ALA* 4.3 2.0 - - - -
326A MET* 1.3 77.0 - - - +
328A LEU* 1.3 73.2 + - + +
330A THR* 3.0 28.8 + - + +
331A GLU* 3.5 18.4 - - - +
46B LEU* 5.3 4.3 - - + -
50B VAL* 6.2 2.0 - - + -
301B VAL* 3.8 19.9 - - + +
303B GLN* 4.7 10.3 - - + +
312B ILE* 3.9 24.9 - - + +
313B ALA* 3.7 27.8 - - + -
339B ILE* 4.5 0.4 - - - +
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Residues in contact with LEU 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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55A MET* 3.0 46.2 - - + +
56A THR 4.4 0.2 - - - -
57A PRO* 4.2 27.4 - - + -
60A ILE* 4.1 19.6 - - + +
318A LEU* 4.2 8.7 - - + -
325A ALA* 3.1 12.0 + - - +
327A VAL* 1.3 92.4 - - + +
329A GLY* 1.3 53.8 + - - +
330A THR 3.0 5.4 - - - -
331A GLU* 2.7 34.0 + - - +
332A PHE* 3.1 13.9 + - - +
44B TYR* 4.0 15.0 - - + +
46B LEU* 6.4 1.1 - - + -
312B ILE* 4.4 9.2 - - + -
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Residues in contact with GLY 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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277A THR* 3.5 1.2 - - - -
278A LEU* 3.1 39.8 + - - +
279A ALA* 2.8 25.0 + - - -
318A LEU* 4.9 1.2 - - - +
325A ALA 4.1 1.2 + - - -
326A MET* 3.3 19.2 + - - +
327A VAL 3.3 1.0 - - - -
328A LEU* 1.3 78.7 - - - +
330A THR* 1.3 59.5 + - - +
331A GLU 3.6 0.2 + - - -
332A PHE* 3.7 2.2 + - - -
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Residues in contact with THR 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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277A THR* 3.4 20.3 - - - +
279A ALA* 3.8 14.8 - - + -
326A MET 3.6 4.3 - - - +
327A VAL* 3.0 16.3 + - + +
328A LEU 3.0 0.8 + - - -
329A GLY* 1.3 77.1 - - - +
331A GLU* 1.3 68.0 + - - +
332A PHE 3.5 0.4 - - - -
333A GLN* 4.7 1.4 + - - -
258B PHE* 4.3 8.1 - - + -
303B GLN* 4.3 9.5 + - - +
337B TYR* 4.2 28.1 + - - +
339B ILE* 3.4 39.5 - - + -
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Residues in contact with GLU 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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60A ILE* 3.3 27.8 - - + +
64A ARG* 2.9 34.4 + - - +
327A VAL* 3.5 21.0 - - - +
328A LEU* 2.7 16.3 + - - +
330A THR* 1.3 85.9 - - - +
332A PHE* 1.3 56.8 + - - +
333A GLN* 3.8 10.3 + - - +
303B GLN* 3.1 49.3 + - - +
312B ILE* 5.0 5.9 - - - +
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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