Contacts of the helix formed by residues 323 - 330 (chain A) in PDB entry 2A72
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 323 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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321A GLU 3.3 5.3 + - - -
322A PRO* 1.3 76.6 - - - +
324A GLN* 1.3 64.3 + - - +
325A GLN* 3.4 11.6 + - - +
326A ARG* 3.1 26.2 + - - +
327A VAL* 3.1 19.3 + - - +
447B LEU 5.7 0.2 - - - -
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Residues in contact with GLN 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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322A PRO 3.9 0.2 + - - -
323A SER* 1.3 72.9 - - - +
325A GLN* 1.3 57.2 + - - +
327A VAL* 3.3 7.1 + - - +
328A LYS* 2.9 57.9 + - + +
447B LEU 5.2 1.3 - - - -
448B LEU* 3.3 34.0 + - + +
449B GLN* 3.9 10.9 + - - +
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Residues in contact with GLN 325 (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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323A SER* 3.4 9.8 + - - +
324A GLN* 1.3 79.4 - - - +
326A ARG* 1.3 62.5 + - - +
328A LYS* 3.6 11.2 + - - +
329A ARG* 3.1 38.7 + - - +
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Residues in contact with ARG 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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320A LYS 5.4 3.8 + - - -
322A PRO* 4.2 27.9 - - + +
323A SER* 3.1 23.7 + - - +
325A GLN* 1.3 78.9 - - - +
327A VAL* 1.3 61.9 + - - +
329A ARG* 3.2 34.6 + - - +
330A TRP* 3.3 22.7 + - - +
340A ASP* 2.9 41.7 + - - +
341A PRO* 4.8 5.5 - - - +
342A VAL* 3.2 28.2 - - - +
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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
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322A PRO* 3.8 22.7 - - + +
323A SER 3.1 13.5 + - - +
324A GLN 3.8 6.1 - - - +
326A ARG* 1.3 72.7 - - - +
328A LYS* 1.3 60.4 + - - +
330A TRP* 3.2 24.0 + - + +
444B TYR* 2.6 48.8 + - + -
447B LEU* 3.7 31.2 - - + +
448B LEU* 3.8 28.7 - - + +
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Residues in contact with LYS 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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324A GLN* 2.9 48.7 + - + +
325A GLN* 3.7 10.3 - - - +
327A VAL* 1.3 75.6 - - - +
329A ARG* 1.3 58.9 + - - +
331A GLY* 2.9 24.1 + - - -
332A PHE* 3.5 18.4 - - + -
444B TYR* 3.5 7.4 + - - -
448B LEU* 3.4 18.6 - - + -
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Residues in contact with ARG 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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325A GLN* 3.1 36.9 + - - +
326A ARG* 3.2 41.2 + - - +
328A LYS* 1.3 75.3 - - - +
330A TRP* 1.3 65.7 + - + +
332A PHE* 3.0 28.4 + - + +
336A GLU* 3.3 36.0 + - + +
340A ASP* 4.9 3.0 + - - -
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Residues in contact with TRP 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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322A PRO* 4.7 4.7 - - + -
326A ARG* 3.3 18.7 + - + -
327A VAL* 3.5 30.1 - - + +
328A LYS 3.1 1.0 + - - -
329A ARG* 1.3 79.0 - - + +
331A GLY* 1.3 49.2 + - - +
332A PHE 3.3 0.9 - - - -
333A GLY 3.4 6.5 - - - +
336A GLU 4.1 14.6 - - - -
337A ALA* 3.9 21.3 - - + +
340A ASP* 2.9 30.2 + - + +
342A VAL* 3.9 21.8 - - + -
343A GLY* 3.4 29.8 - - - -
346A GLN* 4.1 14.4 - - + -
435B TYR* 2.6 33.8 + - - -
438B PHE* 4.3 7.9 - + + -
439B ILE* 4.3 3.8 - - + -
444B TYR* 3.7 24.7 - + + -
447B LEU* 4.0 23.6 - - + -
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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