Contacts of the helix formed by residues 323 - 329 (chain A) in PDB entry 5AVL
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 ARG 323 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311A GLU* 2.7 34.2 + - - +
322A ASN* 1.3 75.9 - - + +
324A GLU* 1.3 56.6 + - - +
326A PHE* 3.4 4.2 + - - +
327A ALA* 3.1 26.5 + - - +
336A ILE* 3.8 21.6 - - + +
337A ASN* 3.9 24.2 + - - +
340A PHE* 3.4 51.7 - - + +
341A GLU* 4.5 2.8 - - - +
344A ARG* 3.1 29.5 - - - +
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Residues in contact with GLU 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 ASN* 3.1 13.0 + - - +
323A ARG* 1.3 77.3 - - - +
325A ASP* 1.3 64.9 + - - +
327A ALA* 3.3 10.0 + - + +
328A LYS* 3.0 60.8 + - + +
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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
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238A TRP* 3.8 31.6 + - + -
320A SER 3.8 6.8 - - - +
321A TYR* 3.5 17.5 - - + -
322A ASN* 2.7 47.1 + - - +
324A GLU* 1.3 74.0 - - - +
326A PHE* 1.3 59.3 - - - +
328A LYS* 3.4 13.8 + - - +
329A ALA* 2.9 27.4 + - - +
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Residues in contact with PHE 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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257A PHE* 3.9 13.9 - + - -
302A THR* 4.7 3.6 - - + -
313A ILE* 4.1 13.7 - - + -
315A PHE* 4.3 3.4 - + - -
321A TYR* 3.6 27.6 - + + -
322A ASN 2.9 19.9 + - - +
323A ARG 3.4 10.1 - - - +
325A ASP* 1.3 76.3 - - - +
327A ALA* 1.3 66.5 + - - +
329A ALA* 3.1 17.5 + - - +
330A GLY 3.4 0.5 + - - -
331A LEU* 3.4 36.7 + - + +
336A ILE* 3.6 18.8 - - + -
339A ILE* 4.2 8.7 - - + -
340A PHE* 3.8 28.3 - + - -
501A 4KQ 3.9 38.4 - - + -
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Residues in contact with ALA 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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250A ARG* 3.5 13.8 + - - -
323A ARG 3.1 10.7 + - - +
324A GLU* 3.3 14.1 + - + +
326A PHE* 1.3 77.3 - - - +
328A LYS* 1.3 58.5 + - + +
330A GLY* 2.9 18.5 + - - -
331A LEU 3.6 15.6 - - - +
333A VAL* 5.7 8.5 - - + -
336A ILE* 4.3 6.2 - - + +
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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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238A TRP* 5.5 1.1 - - + -
250A ARG* 3.9 18.2 + - - +
253A ARG* 3.0 55.4 + - - +
324A GLU* 3.0 50.4 + - + +
325A ASP* 3.4 12.5 + - - +
326A PHE 3.3 0.2 - - - -
327A ALA* 1.3 76.3 - - + +
329A ALA* 1.3 57.6 + - - +
330A GLY 3.2 1.6 + - - -
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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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238A TRP* 4.5 7.4 - - + -
253A ARG* 4.2 13.0 - - - +
254A PHE* 3.4 27.7 - - - -
257A PHE* 3.6 41.8 - - + -
321A TYR* 5.5 0.4 - - + -
325A ASP 2.9 14.3 + - - +
326A PHE* 3.1 11.6 + - - +
328A LYS* 1.3 76.8 - - - +
330A GLY* 1.3 56.1 + - - +
331A LEU* 3.5 3.6 + - - +
433A LYS* 5.1 0.2 - - - -
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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