Contacts of the helix formed by residues 322 - 329 (chain D) in PDB entry 2Q41
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 PRO 322 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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309A PHE* 3.2 48.5 - - + -
311A ASN* 4.0 0.2 - - - -
314A ILE* 3.6 14.4 - - + -
238D LEU* 3.7 11.2 - - + -
264D TRP* 3.6 23.6 - - + -
321D LEU* 1.3 87.1 - - + +
323D SER* 1.3 55.6 + - - +
324D PHE* 4.2 7.9 - - + -
325D ALA* 3.1 14.9 + - + -
326D LYS* 2.5 36.7 + - - +
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Residues in contact with SER 323 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307A LEU* 3.7 13.5 + - - +
308A LYS 3.1 18.2 + - - -
310A TYR 2.7 31.6 + - - +
311A ASN* 3.5 12.5 + - - +
322D PRO* 1.3 67.0 - - - +
324D PHE* 1.3 56.8 + - - +
325D ALA 2.4 18.4 + - - -
326D LYS* 2.5 21.7 + - - -
327D LYS* 2.9 12.5 + - - +
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Residues in contact with PHE 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A CYS* 4.8 3.4 - - - -
307A LEU 4.7 1.1 + - - -
308A LYS* 2.7 55.2 + - + +
309A PHE* 3.4 27.6 - + + -
238D LEU* 3.7 24.0 - - + -
239D TRP* 4.0 35.4 - + - -
242D MSE 4.3 7.9 - - + +
264D TRP* 6.2 0.2 - + - -
322D PRO* 4.2 11.2 - - + -
323D SER* 1.3 71.1 - - - +
325D ALA* 1.3 69.3 + - + +
327D LYS* 3.9 17.8 - - - +
328D VAL* 4.0 12.8 - - - +
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Residues in contact with ALA 325 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238D LEU* 4.0 11.7 - - + -
242D MSE 3.3 35.1 - - + +
321D LEU* 4.5 2.2 - - + -
322D PRO* 3.1 28.9 + - + +
323D SER 2.4 12.5 + - - -
324D PHE* 1.3 77.3 - - + +
326D LYS* 1.3 65.4 + - - +
327D LYS 3.0 3.0 + - - -
328D VAL 3.5 2.1 + - - -
329D ILE* 3.3 22.8 + - - +
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Residues in contact with LYS 326 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311A ASN* 4.0 24.6 - - + +
313A GLU* 2.9 37.4 + - - +
321D LEU* 4.0 25.1 - - + +
322D PRO 2.5 22.6 + - - +
323D SER* 2.5 7.6 + - - +
325D ALA* 1.3 72.0 - - - +
327D LYS* 1.3 62.8 + - - +
329D ILE 3.7 2.4 - - - +
330D GLU* 3.5 18.4 + - - +
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Residues in contact with LYS 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323D SER 2.9 12.5 + - - +
324D PHE* 3.9 13.5 - - - +
325D ALA 3.0 1.0 - - - -
326D LYS* 1.3 74.3 - - - +
328D VAL* 1.3 64.2 + - + +
330D GLU* 2.8 33.1 + - - +
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Residues in contact with VAL 328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242D MSE 3.6 34.5 - - + +
246D GLU* 3.1 45.4 - - + +
324D PHE 4.0 10.3 - - - +
325D ALA 3.5 0.8 + - - -
327D LYS* 1.3 82.7 - - + +
329D ILE* 1.3 54.4 + - - +
330D GLU* 2.6 32.6 + - - +
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Residues in contact with ILE 329 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238D LEU* 3.7 15.3 - - + -
242D MSE 3.6 23.1 - - - -
245D ILE* 3.4 32.3 - - + +
246D GLU* 5.2 3.6 - - - +
249D VAL* 3.6 33.2 - - + -
253D ARG* 4.1 5.3 + - - +
262D TYR* 4.5 11.4 - - + -
321D LEU* 4.4 23.6 - - + +
325D ALA 3.3 10.9 + - - +
326D LYS 3.7 4.7 - - - +
328D VAL* 1.3 73.2 - - + +
330D GLU* 1.3 74.7 + - - +
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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