Contacts of the helix formed by residues 292 - 301 (chain A) in PDB entry 3L73
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 292 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276A ILE 4.1 10.8 - - - -
277A ILE* 2.5 30.8 + - - -
278A GLY* 4.9 4.3 - - - -
279A ARG 5.2 2.7 - - - -
290A LEU* 3.3 3.9 - - - +
291A SER* 1.3 75.3 - - - +
293A ARG* 1.3 65.4 + - - +
294A LEU 3.7 2.4 + - - -
295A ALA* 2.9 27.5 + - - +
296A ALA* 2.9 20.8 + - - +
307A PHE* 4.0 2.1 - - - -
356A ARG* 4.5 1.0 - - - +
90B GLU* 5.5 0.4 + - - -
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Residues in contact with ARG 293 (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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276A ILE* 5.0 2.9 + - - -
277A ILE* 6.0 0.4 - - - +
291A SER 3.1 8.4 + - - +
292A SER* 1.3 70.5 + - - +
294A LEU* 1.3 57.9 + - - +
296A ALA* 3.0 9.9 + - - +
297A LEU* 2.9 39.0 + - + +
341A GLU* 3.0 28.5 + - - +
344A ARG* 3.1 51.0 - - - +
353A GLU* 3.8 9.4 - - - +
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Residues in contact with LEU 294 (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 ILE* 4.1 15.9 - - + +
292A SER* 3.3 3.0 + - - +
293A ARG* 1.3 78.3 - - - +
295A ALA* 1.3 52.5 + - - +
297A LEU* 3.5 5.1 + - + +
298A ALA* 2.7 35.2 + - - +
303A LEU* 5.0 0.7 - - + -
307A PHE* 3.5 36.1 - - + -
322A PHE* 6.1 3.6 - - + -
334A MET* 3.4 32.5 - - + -
337A CYS* 3.9 15.7 - - + +
338A ALA* 3.9 33.7 - - + +
341A GLU* 4.0 16.5 - - + +
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Residues in contact with ALA 295 (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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279A ARG 4.7 2.9 - - - +
280A TYR* 4.0 16.3 - - + -
290A LEU* 3.9 24.0 - - + -
292A SER* 2.9 28.6 + - - +
294A LEU* 1.3 76.9 - - - +
296A ALA* 1.3 60.0 + - - +
298A ALA* 3.2 4.6 + - - +
299A VAL* 2.8 36.2 + - - +
307A PHE* 3.8 9.5 - - + -
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Residues in contact with ALA 296 (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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287A GLY 5.0 1.6 - - - -
288A LYS* 4.4 21.0 - - - +
290A LEU* 4.5 10.2 - - - +
292A SER 2.9 10.7 + - - +
293A ARG* 3.4 12.6 - - - +
295A ALA* 1.3 76.0 - - - +
297A LEU* 1.3 53.7 + - + +
299A VAL* 2.9 9.9 + - - +
300A GLU* 2.7 38.9 + - - +
87B ARG* 6.3 0.4 - - - +
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Residues in contact with LEU 297 (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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293A ARG* 2.9 25.0 + - + +
294A LEU* 3.7 6.3 - - - +
296A ALA* 1.3 72.0 - - + +
298A ALA* 1.3 69.1 + - - +
300A GLU* 3.5 22.4 - - - +
301A HIS* 2.8 42.5 + - + +
303A LEU* 3.7 13.9 - - + +
337A CYS* 4.1 26.7 - - + -
341A GLU* 4.5 15.9 - - - +
3C PRO* 5.9 2.0 - - + -
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Residues in contact with ALA 298 (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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280A TYR* 4.2 13.3 - - + -
294A LEU 2.7 23.4 + - - +
295A ALA* 3.3 10.8 - - - +
297A LEU* 1.3 71.7 - - - +
299A VAL* 1.3 57.2 + - - +
302A LYS* 3.0 9.4 + - - -
303A LEU* 2.8 39.5 + - + +
304A CYS* 3.9 28.4 + - - +
307A PHE* 4.7 3.8 - - + -
334A MET* 4.9 1.6 - - - -
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Residues in contact with VAL 299 (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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280A TYR* 3.5 35.2 - - + +
287A GLY* 3.9 19.7 - - - +
288A LYS* 3.5 28.7 - - + +
295A ALA 2.8 29.3 + - - +
296A ALA* 2.9 6.7 + - - +
298A ALA* 1.3 73.8 - - - +
300A GLU* 1.3 66.8 + - - +
302A LYS* 3.0 34.1 + - - +
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Residues in contact with GLU 300 (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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288A LYS* 5.4 5.8 - - + +
296A ALA* 2.7 19.6 + - - +
297A LEU* 3.5 19.1 + - - +
299A VAL* 1.3 74.7 - - - +
301A HIS* 1.3 90.7 + - + +
302A LYS* 3.7 8.6 + - - +
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Residues in contact with HIS 301 (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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297A LEU* 2.8 38.2 + - + +
300A GLU* 1.3 108.7 + - + +
302A LYS* 1.3 72.7 + - - +
303A LEU* 3.1 21.2 + - + +
330A SER* 5.6 0.3 - - - -
1C MET 3.6 29.3 + - - -
2C ALA 4.4 0.4 - - - -
3C PRO* 4.2 35.1 - - + +
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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