Contacts of the helix formed by residues 293 - 303 (chain B) in PDB entry 1L0N
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 293 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A GLU* 4.7 0.2 + - - -
279B LEU 3.3 13.5 + - - -
280B GLY* 4.2 11.7 - - - -
281B ALA 6.0 0.4 - - - -
290B ASN* 3.3 20.6 + - - -
291B ALA 3.1 4.4 - - - -
292B THR* 1.3 76.1 + - - +
294B SER* 1.3 63.4 + - - +
295B LEU* 4.3 1.0 - - - +
296B TYR* 3.1 25.6 + - - +
297B GLN* 3.1 23.2 + - - +
309B VAL 5.2 2.8 + - - -
363B LYS* 5.0 2.5 - - - +
31I GLN* 5.6 3.3 + - - -
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Residues in contact with SER 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B VAL* 3.4 22.5 + - - +
279B LEU* 3.0 13.3 + - - -
292B THR 3.4 6.3 + - - -
293B SER* 1.3 71.7 - - - +
295B LEU* 1.3 64.0 + - - +
297B GLN* 4.3 3.7 - - - +
298B ALA* 3.2 23.0 + - - +
343B GLN* 2.6 31.5 + - - +
347B ILE* 4.8 4.3 - - - +
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Residues in contact with LEU 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B LEU* 3.1 40.7 + - + +
280B GLY* 5.6 0.4 - - - -
293B SER* 4.5 1.1 - - - +
294B SER* 1.3 76.1 - - - +
296B TYR* 1.3 59.8 + - - +
298B ALA* 2.9 4.0 + - - +
299B VAL* 2.8 31.5 + - - +
309B VAL* 4.3 17.3 - - + +
310B SER* 4.1 5.2 - - - +
311B ALA* 3.9 25.8 - - - +
324B PHE* 3.9 21.3 - - + -
340B ALA* 3.6 33.4 - - + +
343B GLN* 3.8 16.4 - - + -
344B VAL* 4.5 3.8 - - + -
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Residues in contact with TYR 296 (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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289B SER* 4.0 20.9 - - - -
290B ASN* 3.9 12.8 - - + +
293B SER* 3.1 23.9 + - - +
295B LEU* 1.3 77.9 - - - +
297B GLN* 1.3 60.9 + - - +
299B VAL* 3.2 1.4 + - - -
300B ALA* 2.8 39.3 + - + +
305B GLN* 5.8 0.9 - - - -
307B PHE* 3.5 29.1 + + - -
308B ASP* 3.5 19.1 - - - -
309B VAL* 3.8 19.3 - - + +
31I GLN* 2.9 42.3 + - + +
35I PRO* 3.1 23.8 - - + +
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Residues in contact with GLN 297 (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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289B SER* 2.8 21.4 + - - -
290B ASN* 2.6 27.7 + - - +
291B ALA* 3.6 20.5 - - - +
293B SER 3.1 15.1 + - - +
294B SER* 4.4 3.6 - - - +
296B TYR* 1.3 77.9 - - - +
298B ALA* 1.3 62.4 + - - +
300B ALA* 3.9 7.0 - - - +
301B LYS* 3.1 26.5 + - - +
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Residues in contact with ALA 298 (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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294B SER 3.2 19.2 + - - +
295B LEU 2.9 5.0 + - - +
297B GLN* 1.3 80.2 - - - +
299B VAL* 1.3 62.2 + - - +
301B LYS* 3.8 16.7 - - - +
302B GLY 4.2 2.1 + - - -
339B ALA* 4.0 16.4 - - - +
343B GLN* 3.8 28.7 - - + +
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Residues in contact with VAL 299 (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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295B LEU 2.8 21.3 + - - +
298B ALA* 1.3 70.2 - - - +
300B ALA* 1.3 66.8 + - - +
302B GLY 3.2 4.5 + - - -
303B VAL* 3.0 29.8 + - + +
307B PHE* 3.4 31.2 - - + -
309B VAL* 4.1 16.6 - - + -
336B VAL* 3.8 49.8 - - + +
339B ALA* 4.0 7.4 - - - +
340B ALA* 4.1 12.8 - - + +
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Residues in contact with ALA 300 (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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296B TYR* 2.8 31.0 + - + +
297B GLN* 3.9 9.9 - - - +
299B VAL* 1.3 73.1 - - - +
301B LYS* 1.3 63.2 + - - +
303B VAL 2.9 18.5 + - - +
304B HIS* 5.1 2.1 + - - -
305B GLN* 5.7 0.9 - - - +
307B PHE* 3.5 24.0 - - + -
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Residues in contact with LYS 301 (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 GLN 3.1 18.2 + - - +
298B ALA* 3.8 10.8 - - - +
299B VAL 3.2 0.2 + - - -
300B ALA* 1.3 77.0 - - - +
302B GLY* 1.3 59.8 + - - +
304B HIS* 4.5 9.4 - - - -
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Residues in contact with GLY 302 (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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298B ALA 4.2 2.0 + - - -
299B VAL 3.2 5.0 + - - -
301B LYS* 1.3 81.1 - - - +
303B VAL* 1.3 67.1 + - - +
304B HIS* 4.1 15.6 + - - -
335B ASP* 5.5 2.3 - - - +
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Residues in contact with VAL 303 (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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299B VAL* 3.0 28.2 + - + +
300B ALA* 2.9 21.4 + - - +
302B GLY* 1.3 82.6 - - - +
304B HIS* 1.3 65.4 + - - +
305B GLN* 3.5 9.3 + - - +
306B PRO 5.5 1.3 - - - +
307B PHE* 4.2 17.9 - - + -
332B SER* 4.5 15.9 - - - +
335B ASP* 4.3 20.6 - - + +
336B VAL* 4.1 25.8 - - + +
339B ALA* 5.7 1.3 - - + -
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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