Contacts of the helix formed by residues 327 - 337 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323B ARG* 3.3 13.4 + - - +
326B GLU* 1.3 73.1 - - - +
328B ARG* 1.3 57.8 + - - +
330B ALA* 3.2 2.8 + - - +
331B GLN* 2.9 50.4 + - - +
341B TYR* 4.4 6.7 - - - -
343B GLU* 2.7 33.7 + - - -
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Residues in contact with ARG 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326B GLU* 3.1 21.5 - - + +
327B SER* 1.3 78.7 - - - +
329B GLN* 1.3 58.8 + - - +
331B GLN* 2.9 32.8 + - - +
332B ASP* 3.0 57.3 + - - +
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Residues in contact with GLN 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290B PHE* 3.7 22.0 - - + -
324B THR 4.3 4.0 + - - -
325B VAL* 3.6 20.5 - - + +
326B GLU* 3.0 57.4 + - + +
328B ARG* 1.3 78.9 - - - +
330B ALA* 1.3 61.4 + - - +
332B ASP* 4.0 9.3 - - - +
333B LEU* 3.2 22.0 + - - +
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Residues in contact with ALA 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282B PHE* 3.8 15.7 - - + -
290B PHE* 3.8 13.5 - - + -
313B LEU* 3.3 12.0 - - + +
325B VAL* 4.8 0.2 - - + -
326B GLU 4.0 7.0 - - - +
327B SER 3.2 4.9 + - - +
328B ARG 3.2 0.6 - - - -
329B GLN* 1.3 79.6 - - - +
331B GLN* 1.3 59.7 + - - +
333B LEU 3.2 1.0 + - - -
334B ALA* 2.9 23.9 + - - +
341B TYR* 3.3 39.0 - - + +
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Residues in contact with GLN 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327B SER* 2.9 40.4 + - - +
328B ARG* 2.9 40.8 + - - +
330B ALA* 1.3 75.6 - - - +
332B ASP* 1.3 56.5 + - - +
334B ALA* 3.2 2.6 + - - +
335B ARG* 2.8 35.0 + - - +
341B TYR* 3.4 29.6 - - + -
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Residues in contact with ASP 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328B ARG* 3.0 50.7 + - - +
329B GLN* 4.0 8.1 - - - +
331B GLN* 1.3 76.6 - - - +
333B LEU* 1.3 57.3 + - - +
335B ARG* 3.4 34.1 + - - +
336B SER* 3.0 25.5 + - - -
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Residues in contact with LEU 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290B PHE* 3.8 20.2 - - + -
293B ILE* 3.9 9.9 - - + -
294B HIS* 3.6 37.0 - - + +
313B LEU* 4.2 7.2 - - + -
329B GLN 3.2 14.9 + - - +
330B ALA 3.4 8.1 - - - +
331B GLN 3.2 0.4 - - - -
332B ASP* 1.3 76.1 - - - +
334B ALA* 1.3 60.3 + - - +
336B SER* 2.7 24.1 + - - +
337B TYR* 3.0 56.4 + - + +
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Residues in contact with ALA 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313B LEU* 3.9 12.3 - - + +
330B ALA 2.9 16.1 + - - +
331B GLN 3.6 3.6 - - - +
333B LEU* 1.3 73.8 - - - +
335B ARG* 1.3 55.7 + - - +
337B TYR* 3.2 1.9 + - - -
338B GLY 2.7 27.4 + - - -
339B ILE* 2.8 36.2 + - + +
340B PRO 4.1 3.1 - - - +
341B TYR* 3.6 26.2 - - + +
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Residues in contact with ARG 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331B GLN 2.8 17.1 + - - +
332B ASP* 3.4 38.0 + - - +
333B LEU 3.2 0.2 - - - -
334B ALA* 1.3 78.6 - - - +
336B SER* 1.3 70.8 + - - +
338B GLY* 2.9 19.7 + - - +
339B ILE 4.7 1.3 - - - -
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Residues in contact with SER 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297B ARG* 5.4 1.6 + - - -
332B ASP 3.0 13.8 + - - -
333B LEU* 2.7 31.0 + - - +
335B ARG* 1.3 90.1 - - - +
337B TYR* 1.3 68.9 + - - +
338B GLY 3.5 0.3 + - - -
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Residues in contact with TYR 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293B ILE 4.9 4.7 - - - -
294B HIS* 3.4 36.6 + - - +
297B ARG* 3.3 68.6 + - + +
313B LEU* 5.1 8.3 - - + -
333B LEU* 3.0 51.8 + - + +
334B ALA* 3.6 5.6 - - - +
335B ARG 3.2 0.2 - - - -
336B SER* 1.3 82.4 + - - +
338B GLY* 1.3 63.1 + - - +
339B ILE* 3.5 32.7 + - + +
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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