Contacts of the helix formed by residues 275 - 289 (chain A) in PDB entry 1LAN
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 GLY 275 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A MET* 3.8 28.9 - - - -
272A ALA 2.9 14.6 + - - -
273A ASP 3.4 2.0 - - - -
274A MET* 1.3 77.9 - - - +
276A GLY* 1.3 61.2 + - - +
279A THR* 2.9 31.0 + - - +
359A THR* 4.1 5.9 - - - +
450A ILE* 3.7 7.6 - - - -
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Residues in contact with GLY 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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249A GLY* 3.8 7.2 - - - -
250A LYS 3.8 5.8 + - - -
274A MET 3.2 1.2 - - - -
275A GLY* 1.3 75.0 - - - +
277A ALA* 1.3 63.0 + - - +
279A THR* 3.1 17.3 + - - -
280A ILE* 3.2 18.0 + - - +
357A ALA* 3.4 28.3 - - - -
358A ALA* 4.1 4.7 - - - -
359A THR* 4.4 5.7 - - - +
450A ILE* 3.9 4.8 - - - +
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Residues in contact with ALA 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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183A PHE* 3.7 18.2 - - + -
249A GLY* 3.8 10.7 - - - +
250A LYS 3.2 14.2 + - - +
251A GLY* 3.9 11.2 - - - -
274A MET 3.1 8.6 + - - +
276A GLY* 1.3 76.7 - - - +
278A ALA* 1.3 62.0 - - - +
280A ILE* 3.7 2.4 - - - +
281A CYS* 3.1 30.0 + - - +
300A ALA* 3.9 22.4 - - + -
302A LEU* 4.5 1.6 - - + -
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Residues in contact with ALA 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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167A ALA* 3.9 23.8 - - + +
170A LEU* 4.1 9.6 - - + +
171A MET* 4.0 6.3 - - + -
183A PHE* 3.7 10.0 - - - -
274A MET* 2.9 32.9 + - + +
275A GLY 3.7 4.5 - - - +
277A ALA* 1.3 77.3 - - - +
279A THR* 1.3 56.3 + - - +
281A CYS* 3.9 0.9 - - - +
282A SER* 2.9 36.1 + - - -
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Residues in contact with THR 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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167A ALA* 4.4 3.8 - - + -
171A MET* 4.9 3.6 - - - -
275A GLY 2.9 20.6 + - - +
276A GLY* 3.1 12.5 + - - -
278A ALA* 1.3 75.2 - - - +
280A ILE* 1.3 63.4 + - - +
282A SER* 3.5 1.9 + - - -
283A ALA* 3.0 24.1 + - - +
357A ALA* 4.0 10.9 - - - +
450A ILE* 4.2 4.9 - - + +
469A GLY* 3.8 8.1 - - - +
470A ARG 3.5 27.6 - - - +
471A PRO* 4.1 3.8 - - - +
472A THR* 3.5 25.3 + - - +
475A LEU* 4.0 12.7 - - - +
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Residues in contact with ILE 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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247A PHE* 3.8 46.9 - - + +
248A VAL 4.1 7.9 - - - +
249A GLY* 3.9 22.4 - - - +
276A GLY 3.2 17.2 + - - +
277A ALA* 3.7 4.3 - - - +
279A THR* 1.3 76.8 + - - +
281A CYS* 1.3 78.0 + - - +
283A ALA* 3.5 3.5 + - - +
284A ILE* 3.1 28.3 + - + +
298A GLY* 4.4 4.5 - - - -
299A LEU 4.0 11.9 - - - +
300A ALA* 5.0 0.4 - - + -
355A ILE* 4.8 3.1 - - + +
356A ASN 5.1 0.4 - - - -
357A ALA* 3.7 22.9 - - + +
475A LEU* 4.1 11.7 - - + -
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Residues in contact with CYS 281 (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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166A LEU* 5.8 0.2 - - - -
170A LEU* 5.7 0.2 - - + -
183A PHE* 4.2 7.6 - - + -
187A VAL* 4.0 25.1 - - + -
230A LEU* 4.0 27.4 - - - -
232A ILE* 4.3 15.8 - - - +
277A ALA 3.1 24.7 + - - +
278A ALA 4.0 1.8 - - - +
280A ILE* 1.3 89.6 - - - +
282A SER* 1.3 64.1 + - - +
284A ILE* 3.2 4.2 + - - +
285A VAL* 3.1 27.2 + - - +
298A GLY 6.0 1.1 - - - -
300A ALA* 4.6 6.7 - - - -
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Residues in contact with SER 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A GLY* 3.3 22.3 - - - -
166A LEU* 3.6 17.7 - - - +
167A ALA* 3.3 21.5 + - - -
170A LEU* 4.3 3.1 - - - +
278A ALA 2.9 22.2 + - - -
279A THR 4.0 0.2 - - - -
281A CYS* 1.3 73.8 - - - +
283A ALA* 1.3 66.2 + - - +
285A VAL* 3.2 8.8 + - - +
286A SER* 3.0 28.4 + - - -
472A THR* 4.0 9.9 - - - -
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Residues in contact with ALA 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A PHE* 4.9 3.1 - - + -
279A THR 3.0 19.1 + - - +
280A ILE* 3.6 6.7 - - - +
282A SER* 1.3 78.8 - - - +
284A ILE* 1.3 57.2 + - - +
286A SER* 3.4 2.1 + - - -
287A ALA* 3.0 28.6 + - - +
472A THR* 4.1 3.5 - - - +
475A LEU* 3.8 29.4 - - + -
476A ILE* 4.0 19.8 - - + +
479A LEU* 4.1 11.0 - - + +
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Residues in contact with ILE 284 (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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191A LEU* 4.2 12.8 - - + -
232A ILE* 3.7 22.7 - - + -
234A TYR* 4.2 19.4 - - + +
247A PHE* 4.3 12.8 - - + -
280A ILE* 3.1 18.2 + - + +
281A CYS 3.2 6.7 + - - +
283A ALA* 1.3 75.5 - - + +
285A VAL* 1.3 59.5 + - - +
287A ALA* 3.8 6.0 - - - +
288A ALA* 3.0 27.2 + - - +
296A ILE* 4.0 26.0 - - + +
297A VAL 4.2 1.3 - - - +
298A GLY* 3.5 35.7 - - - +
479A LEU* 5.1 2.9 - - + -
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Residues in contact with VAL 285 (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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163A GLY* 6.5 0.4 - - - -
166A LEU* 4.6 10.1 - - + -
187A VAL* 4.6 8.7 - - + +
190A ASN* 3.8 33.7 - - + +
191A LEU* 3.9 33.7 - - + +
194A ALA* 3.6 5.2 - - + +
281A CYS 3.1 19.7 + - - +
282A SER* 3.2 11.4 + - - +
284A ILE* 1.3 76.8 - - - +
286A SER* 1.3 58.3 + - - +
288A ALA* 3.3 4.0 + - - +
289A LYS* 2.9 35.7 + - + +
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Residues in contact with SER 286 (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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159A LEU* 3.7 20.8 + - - +
163A GLY* 3.4 24.4 - - - -
282A SER 3.0 14.2 + - - -
283A ALA 3.8 1.6 - - - -
285A VAL* 1.3 77.0 - - - +
287A ALA* 1.3 60.8 + - - +
289A LYS* 3.0 10.6 + - - +
290A LEU* 2.9 32.4 + - - +
476A ILE* 3.5 27.4 - - - +
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Residues in contact with ALA 287 (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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234A TYR* 4.0 3.2 + - - -
283A ALA 3.0 17.1 + - - +
284A ILE 3.8 5.4 - - - +
286A SER* 1.3 75.9 - - - +
288A ALA* 1.3 57.6 + - - +
290A LEU* 3.4 6.2 + - - +
291A ASP 3.1 19.9 + - - -
292A LEU* 3.1 39.8 + - + -
296A ILE* 3.9 15.3 - - + -
476A ILE* 5.0 3.0 - - + +
479A LEU* 3.9 16.6 - - + -
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Residues in contact with ALA 288 (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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191A LEU* 3.7 20.2 - - + -
194A ALA* 3.6 17.8 - - + +
195A SER* 3.9 11.1 - - - -
234A TYR* 3.8 27.3 + - + -
284A ILE 3.0 19.7 + - - +
285A VAL 3.4 6.1 - - - +
287A ALA* 1.3 74.5 - - - +
289A LYS* 1.3 64.7 + - - +
291A ASP* 3.0 15.4 + - - +
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Residues in contact with LYS 289 (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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159A LEU* 3.6 29.2 - - + +
162A SER* 6.3 2.5 - - - -
194A ALA* 3.4 28.1 - - + +
285A VAL* 2.9 28.1 + - + +
286A SER* 3.0 10.3 + - - +
288A ALA* 1.3 75.9 - - - +
290A LEU* 1.3 60.8 + - - +
291A ASP* 3.1 3.5 + - - +
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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