Contacts of the helix formed by residues 268 - 280 (chain A) in PDB entry 1LWW
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 ASP 268 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249A LYS* 3.5 26.9 - - + +
267A VAL* 1.3 75.8 - - - +
269A VAL* 1.3 63.6 + - - +
270A HIS* 2.9 26.8 + - - +
271A MET* 3.0 29.4 + - - +
272A TRP* 3.1 29.7 + - - -
319A PHE* 3.5 1.6 - - - -
328A BRG 3.4 13.5 + - - +
23E PED 2.6 24.5 + - - +
24E G 3.9 5.6 - - - -
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Residues in contact with VAL 269 (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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268A ASP* 1.3 83.0 - - - +
270A HIS* 1.3 77.2 + - + +
272A TRP* 3.4 7.6 + - + +
273A HIS* 3.0 24.7 + - + +
22E A 3.5 43.5 - - - +
23E PED 4.1 8.5 - - - -
24E G 3.1 21.4 + - - +
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Residues in contact with HIS 270 (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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268A ASP* 2.9 24.8 + - - +
269A VAL* 1.3 89.0 - - + +
271A MET* 1.3 57.7 + - - +
273A HIS* 3.3 5.2 + - - +
274A ILE* 2.9 34.8 + - - +
319A PHE* 3.6 26.0 - + + -
322A ASP* 3.0 35.8 + - + +
323A LEU* 3.6 16.2 - - + +
22E A 4.5 6.2 - - - -
23E PED 2.8 40.8 + - - -
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Residues in contact with MET 271 (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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265A VAL* 5.4 0.4 - - + -
266A PRO 3.4 20.2 - - - +
267A VAL* 4.4 4.9 - - + -
268A ASP* 3.0 30.0 + - - +
270A HIS* 1.3 76.0 - - - +
272A TRP* 1.3 57.3 + - - +
274A ILE* 3.7 25.9 - - + +
275A ALA* 2.9 29.8 + - - +
299A LEU* 3.9 5.7 - - + +
303A PHE* 3.8 39.7 - - + -
307A TRP* 4.6 4.9 - - + -
315A GLN* 3.8 38.6 - - + +
318A LEU* 4.9 0.9 - - + -
319A PHE* 4.3 10.8 - - - -
328A BRG 3.7 3.4 - - - +
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Residues in contact with TRP 272 (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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267A VAL* 3.6 16.8 - - + +
268A ASP* 3.1 26.2 + - - +
269A VAL* 3.6 7.9 - - + +
270A HIS 3.2 0.2 - - - -
271A MET* 1.3 77.7 - - - +
273A HIS* 1.3 61.0 + - - +
275A ALA* 3.3 1.8 + - - +
276A GLN* 3.0 61.7 + - + +
281A TRP* 3.6 31.6 - + - -
283A PRO* 3.9 6.7 - - + -
289A LYS 4.1 4.3 - - - -
290A GLY* 3.4 26.7 - - - -
291A PRO* 3.6 27.4 - - + +
295A THR* 3.2 32.1 - - - -
296A ASN* 2.7 22.2 + - - +
299A LEU* 3.9 13.5 - - + +
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Residues in contact with HIS 273 (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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269A VAL* 3.0 19.1 + - + +
270A HIS* 3.6 7.0 - - - +
272A TRP* 1.3 77.6 - - - +
274A ILE* 1.3 56.7 + - - +
276A GLN* 3.4 12.5 + - - +
277A ARG* 2.9 81.0 + - + +
322A ASP* 4.5 9.9 - - - +
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Residues in contact with ILE 274 (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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119A HIS* 5.0 0.2 - - + -
270A HIS 2.9 21.2 + - - +
271A MET* 3.7 19.5 - - + +
273A HIS* 1.3 76.4 - - - +
275A ALA* 1.3 57.1 + - - +
277A ARG* 4.7 3.6 - - - +
278A ASP* 2.9 49.5 + - - +
279A TYR* 3.5 11.0 - - + -
303A PHE* 4.7 5.6 - - + -
318A LEU* 3.6 59.5 - - + +
319A PHE* 4.1 1.1 - - - +
322A ASP* 3.9 22.7 - - + +
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Residues in contact with ALA 275 (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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271A MET 2.9 17.7 + - - +
272A TRP 3.5 4.5 - - - +
274A ILE* 1.3 77.3 - - - +
276A GLN* 1.3 62.1 + - - +
279A TYR* 3.2 21.0 + - - +
281A TRP* 3.1 33.0 + - + -
299A LEU* 3.6 32.1 - - + -
302A PHE* 5.4 0.4 - - + -
303A PHE* 3.9 10.5 - - + -
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Residues in contact with GLN 276 (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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272A TRP* 3.0 51.8 + - + +
273A HIS* 4.0 10.6 + - - +
275A ALA* 1.3 78.1 - - + +
277A ARG* 1.3 58.5 + - + +
280A SER* 3.2 22.5 + - - -
281A TRP* 3.9 20.9 - - + +
282A HIS* 5.6 6.7 + - + -
289A LYS 4.8 4.7 - - - +
290A GLY* 5.9 0.2 - - - -
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Residues in contact with ARG 277 (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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119A HIS* 5.4 0.6 + - - -
273A HIS* 2.9 71.4 + - + +
274A ILE* 4.7 4.4 - - - +
276A GLN* 1.3 77.1 - - + +
278A ASP* 1.3 93.2 + - - +
279A TYR 4.0 0.2 + - - -
280A SER* 4.6 3.0 + - - -
322A ASP* 3.7 20.2 + - - +
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Residues in contact with ASP 278 (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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119A HIS* 3.3 49.8 + - + +
274A ILE* 2.9 33.2 + - - +
277A ARG* 1.3 117.3 + - - +
279A TYR* 1.3 71.8 + - + +
280A SER* 3.8 0.7 - - - -
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Residues in contact with TYR 279 (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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117A ASP* 2.6 39.4 + - - -
119A HIS* 3.4 19.8 + - + -
120A PHE 4.4 0.3 + - - -
274A ILE* 3.5 27.4 - - + -
275A ALA* 3.2 16.3 + - - +
278A ASP* 1.3 92.3 - - + +
280A SER* 1.3 75.1 + - - +
281A TRP* 3.2 3.9 + - + +
302A PHE* 4.3 21.7 - + + -
303A PHE* 4.1 12.1 - + - -
306A LEU* 3.6 21.8 - - + -
307A TRP* 3.5 11.8 - + - -
318A LEU* 3.6 3.9 - - + +
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Residues in contact with SER 280 (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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275A ALA 3.2 3.0 + - - -
276A GLN 3.2 17.2 + - - -
277A ARG 5.1 2.8 + - - -
278A ASP 3.8 0.5 - - - -
279A TYR* 1.3 81.1 - - - +
281A TRP* 1.3 65.0 + - - +
282A HIS* 3.3 18.3 + - - -
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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