Contacts of the helix formed by residues 322 - 329 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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309B PHE* 3.4 43.7 - - + +
314B ILE* 3.7 7.3 - - + -
238C LEU* 3.9 9.0 - - + -
264C TRP* 3.6 26.0 - - + -
321C LEU* 1.3 87.5 - - + +
323C SER* 1.3 61.9 + - - +
324C PHE* 3.5 28.9 - - + -
325C ALA* 3.2 8.5 + - + -
326C LYS* 2.8 24.3 + - - -
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Residues in contact with SER 323 (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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307B LEU 3.9 9.7 + - - -
308B LYS* 3.9 8.3 - - - -
309B PHE 2.7 30.7 + - - -
310B TYR 3.2 12.0 + - - -
311B ASN* 3.0 21.2 + - - +
322C PRO* 1.3 69.7 - - - +
324C PHE* 1.3 66.4 + - - +
326C LYS* 2.8 18.3 + - - +
327C LYS* 3.1 20.1 + - - +
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Residues in contact with PHE 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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104B CYS* 5.6 2.0 - - - -
308B LYS* 3.0 39.2 + - + +
309B PHE* 4.1 11.2 - + - -
238C LEU* 3.3 34.8 - - + -
239C TRP* 4.2 31.2 - + - -
242C MSE 3.7 10.8 - - + +
322C PRO* 3.5 29.2 - - + -
323C SER* 1.3 73.3 - - - +
325C ALA* 1.3 82.5 + - + +
327C LYS* 3.3 26.3 - - - +
328C VAL* 3.4 10.9 - - - +
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Residues in contact with ALA 325 (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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238C LEU* 3.9 15.9 - - + -
242C MSE 3.4 29.6 - - + -
321C LEU* 4.7 2.9 - - + -
322C PRO* 3.2 13.4 + - + +
323C SER 3.1 0.4 - - - -
324C PHE* 1.3 93.9 - - + +
326C LYS* 1.3 68.6 + - - +
327C LYS 3.3 0.4 - - - -
328C VAL* 3.1 2.8 + - - +
329C ILE* 2.8 30.0 + - + +
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Residues in contact with LYS 326 (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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311B ASN* 3.6 21.5 - - + +
313B GLU* 3.4 31.5 - - - -
321C LEU* 3.9 18.6 - - + +
322C PRO 2.8 14.3 + - - +
323C SER* 2.8 12.5 + - - +
325C ALA* 1.3 75.7 - - - +
327C LYS* 1.3 57.9 + - - +
329C ILE* 5.2 1.1 - - - -
330C GLU 2.6 47.6 + - - +
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Residues in contact with LYS 327 (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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306B PRO* 5.5 9.9 - - - +
323C SER* 3.1 11.0 + - - +
324C PHE* 3.3 24.0 - - - +
326C LYS* 1.3 78.2 - - - +
328C VAL* 1.3 83.9 + - + +
330C GLU* 3.0 16.7 + - - +
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Residues in contact with VAL 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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242C MSE 4.2 22.4 - - + +
246C GLU* 3.1 39.9 - - + +
324C PHE 3.4 19.1 - - - +
325C ALA 3.1 5.3 + - - +
327C LYS* 1.3 79.2 - - + +
329C ILE* 1.3 52.6 + - + +
330C GLU* 2.6 39.4 + - - +
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Residues in contact with ILE 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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238C LEU* 3.6 32.1 - - + -
242C MSE 3.8 13.5 - - + -
245C ILE* 3.6 20.9 - - + -
246C GLU* 5.5 8.3 - - - -
249C VAL* 4.3 24.9 - - + -
253C ARG* 3.1 11.5 + - - +
262C TYR* 4.1 15.0 - - + -
321C LEU* 3.9 19.1 - - + -
325C ALA 2.8 18.1 + - - +
328C VAL* 1.3 71.2 - - + +
330C GLU* 1.3 77.4 + - - +
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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