Contacts of the helix formed by residues 327 - 337 (chain D) in PDB entry 1LFD
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 327 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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323D ARG* 3.4 20.0 - - - +
326D GLU* 1.3 74.4 - - - +
328D ARG* 1.3 61.7 + - - +
330D ALA* 3.4 4.4 + - - +
331D GLN* 3.1 32.6 + - - +
341D TYR* 3.8 9.5 - - - -
343D GLU* 3.1 27.9 + - - +
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Residues in contact with ARG 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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326D GLU* 3.1 25.5 + - + +
327D SER* 1.3 76.3 - - - +
329D GLN* 1.3 65.4 + - - +
331D GLN* 3.0 21.7 + - + +
332D ASP* 2.9 46.6 + - - +
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Residues in contact with GLN 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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290D PHE* 3.9 25.8 - - + -
324D THR 4.6 4.0 + - - -
325D VAL* 4.1 8.8 - - + +
326D GLU* 3.0 48.1 + - + +
328D ARG* 1.3 76.9 - - - +
330D ALA* 1.3 58.7 + - - +
332D ASP* 3.3 10.0 + - - +
333D LEU* 3.1 26.3 + - - +
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Residues in contact with ALA 330 (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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282D PHE* 3.6 17.7 - - + -
290D PHE* 3.6 15.5 - - + -
313D LEU* 3.3 11.3 - - + +
325D VAL* 4.9 0.9 - - + -
326D GLU 3.4 5.5 + - - +
327D SER 3.4 3.9 + - - +
328D ARG 3.3 0.4 - - - -
329D GLN* 1.3 79.5 - - - +
331D GLN* 1.3 59.8 + - - +
333D LEU* 3.2 1.2 + - - +
334D ALA* 3.0 23.6 + - - +
341D TYR* 3.3 37.9 - - + +
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Residues in contact with GLN 331 (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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327D SER* 3.1 27.7 + - - +
328D ARG* 3.0 36.1 + - - +
330D ALA* 1.3 76.0 - - - +
332D ASP* 1.3 63.3 + - - +
334D ALA* 3.4 1.7 + - - +
335D ARG* 3.0 40.4 + - - +
341D TYR* 3.9 24.5 - - + -
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Residues in contact with ASP 332 (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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328D ARG* 2.9 47.3 + - - +
329D GLN* 3.5 8.8 - - - +
330D ALA 3.2 0.2 - - - -
331D GLN* 1.3 82.9 + - - +
333D LEU* 1.3 61.2 - - - +
335D ARG* 3.6 15.5 + - - +
336D SER* 3.2 21.8 + - - -
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Residues in contact with LEU 333 (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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290D PHE* 3.7 18.6 - - + -
293D ILE* 4.1 10.5 - - + -
294D HIS* 3.4 43.7 - - + +
313D LEU* 4.2 7.2 - - + -
329D GLN 3.1 12.6 + - - +
330D ALA 3.4 9.0 - - - +
332D ASP* 1.3 76.3 - - - +
334D ALA* 1.3 64.6 + - - +
336D SER* 2.6 24.7 + - - +
337D TYR* 3.0 51.2 + - + +
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Residues in contact with ALA 334 (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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313D LEU* 3.9 12.3 - - + +
330D ALA 3.0 10.5 + - - +
331D GLN 3.4 3.1 + - - +
333D LEU* 1.3 75.2 - - - +
335D ARG* 1.3 52.6 + - + +
337D TYR* 3.1 2.9 + - - -
338D GLY 2.7 30.3 + - - -
339D ILE* 2.9 41.9 + - + +
341D TYR* 3.6 28.0 - - + -
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Residues in contact with ARG 335 (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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331D GLN* 3.0 33.2 + - + +
332D ASP* 3.7 16.2 - - - +
333D LEU 3.2 0.2 - - - -
334D ALA* 1.3 76.3 - - + +
336D SER* 1.3 56.5 + - - +
338D GLY* 2.9 20.1 + - - +
339D ILE 4.4 1.1 + - - -
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Residues in contact with SER 336 (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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297D ARG* 4.9 2.1 + - - -
332D ASP 3.2 10.6 + - - -
333D LEU* 2.6 30.5 + - - +
335D ARG* 1.3 78.8 - - - +
337D TYR* 1.3 68.5 + - - +
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Residues in contact with TYR 337 (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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293D ILE* 5.1 3.4 - - + -
294D HIS* 3.4 41.0 + + - +
297D ARG* 3.5 71.6 + - + +
298D GLU* 5.6 1.4 - - - +
311D MET* 6.0 0.2 - - - -
313D LEU* 5.5 4.0 - - + -
333D LEU* 3.0 45.5 + - + -
334D ALA* 3.4 7.9 - - - +
335D ARG 3.1 0.2 - - - -
336D SER* 1.3 83.9 + - - +
338D GLY* 1.3 61.6 + - - +
339D ILE* 3.4 31.4 - - + +
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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