Contacts of the helix formed by residues 269 - 279 (chain D) in PDB entry 3LEE
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 HIS 269 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169D ASP* 4.9 3.6 + - - -
206D SER* 4.0 32.3 - - - +
209D LEU* 3.7 18.8 - - + +
210D PHE* 3.9 22.2 - - + -
213D LYS* 3.1 44.5 + - + +
265D ASN* 4.1 8.9 + - - -
266D ALA 3.3 14.9 + - - +
267D LEU 3.0 1.0 + - - -
268D HIS* 1.3 82.2 - - + +
270D ILE* 1.3 66.5 + - - +
271D PRO 3.4 0.2 - - - -
272D ASP* 3.0 18.8 + - - +
273D VAL* 3.1 11.8 + - - +
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Residues in contact with ILE 270 (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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210D PHE* 4.0 13.5 - - + -
267D LEU* 3.6 34.8 - - + +
269D HIS* 1.3 76.2 - - - +
271D PRO* 1.3 66.3 - - + +
273D VAL* 2.5 36.1 + - + +
274D ILE* 2.9 31.9 + - + +
297D ILE* 3.5 33.2 - - + -
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Residues in contact with PRO 271 (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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267D LEU 3.6 6.5 - - - +
268D HIS* 3.4 19.3 - - - +
269D HIS 3.5 0.2 - - - -
270D ILE* 1.3 96.6 - - + +
272D ASP* 1.3 63.5 + - - +
274D ILE* 3.4 12.0 + - + +
275D THR* 3.0 27.4 + - - +
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Residues in contact with ASP 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202D GLU* 4.2 2.9 - - - +
203D ARG* 3.3 39.9 + - + +
206D SER* 3.1 31.6 + - - -
268D HIS 5.7 1.1 - - - -
269D HIS* 3.0 12.6 + - - +
270D ILE 2.8 3.6 + - - -
271D PRO* 1.3 76.3 - - - +
273D VAL* 1.3 55.0 + - - +
274D ILE 3.0 1.8 - - - -
275D THR* 3.0 10.1 + - - +
276D TYR* 2.7 36.9 + - - +
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Residues in contact with VAL 273 (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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206D SER* 4.5 7.4 - - - +
207D MET* 3.5 23.8 - - - -
210D PHE* 4.2 17.9 - - + -
269D HIS 3.1 16.8 + - - +
270D ILE* 2.5 22.7 + - + +
272D ASP* 1.3 72.6 - - - +
274D ILE* 1.3 56.7 + - + -
276D TYR* 3.9 0.2 - - - +
277D LEU* 3.1 43.0 + - + +
293D GLN* 3.4 33.4 - - + +
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Residues in contact with ILE 274 (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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270D ILE* 2.9 37.0 + - + +
271D PRO* 3.6 9.9 - - + +
273D VAL* 1.3 77.8 - - + +
275D THR* 1.3 62.4 + - + +
276D TYR 3.2 0.2 - - - -
277D LEU* 4.2 4.9 - - + +
278D SER* 2.7 30.0 + - - -
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Residues in contact with THR 275 (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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203D ARG* 3.3 43.6 + - - +
271D PRO 3.0 20.2 - - - +
272D ASP* 3.0 5.4 + - - +
274D ILE* 1.3 75.7 - - + +
276D TYR* 1.3 63.8 + - - +
278D SER* 2.7 19.2 + - - -
279D ARG* 3.2 25.0 + - - +
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Residues in contact with TYR 276 (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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180D GLY 4.7 0.7 + - - -
183D LEU* 5.6 0.3 - - - +
184D SER* 2.9 31.5 + - - -
187D PHE* 4.0 15.8 - - - -
197D VAL* 3.8 24.1 - - + +
200D ASP 5.6 0.4 - - - -
203D ARG* 3.7 27.1 - - + +
204D ALA* 4.0 11.7 - - + -
207D MET* 3.5 41.7 - - + -
272D ASP 2.7 20.3 + - - +
273D VAL 3.9 4.5 - - - +
275D THR* 1.3 75.8 + - - +
277D LEU* 1.3 66.1 + - + +
279D ARG* 3.2 26.2 + - - +
280D LEU* 3.5 15.0 - - + +
289D CYS* 3.9 16.4 - - - -
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Residues in contact with LEU 277 (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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207D MET* 4.0 9.0 - - + -
273D VAL* 3.1 39.0 + - + +
274D ILE* 4.5 5.2 - - + +
275D THR 3.5 0.2 - - - -
276D TYR* 1.3 79.5 - - - +
278D SER* 1.3 61.1 + - - +
280D LEU* 3.4 28.4 + - + +
286D PHE* 3.7 20.0 - - + -
289D CYS* 3.6 17.9 - - + -
290D ALA* 3.4 44.0 - - + +
293D GLN* 4.6 5.2 - - + -
294D VAL* 6.0 2.7 - - + -
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Residues in contact with SER 278 (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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274D ILE* 2.7 19.8 + - - -
275D THR* 2.7 26.5 + - - -
276D TYR 3.1 0.2 - - - -
277D LEU* 1.3 79.9 - - - +
279D ARG* 1.3 57.0 + - - +
280D LEU 3.4 0.2 - - - -
281D ARG* 2.8 23.1 + - - -
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Residues in contact with ARG 279 (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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196A LEU* 3.6 31.7 - - + +
199A GLU* 3.0 32.1 + - - +
193D GLU* 3.9 5.4 - - - +
194D ASP* 4.9 0.3 - - - +
196D LEU* 3.1 24.7 - - - +
197D VAL* 4.5 25.3 - - + +
200D ASP* 2.9 35.2 + - - +
203D ARG* 3.6 18.7 - - - +
275D THR* 3.2 26.1 + - - +
276D TYR* 3.2 20.6 - - + +
278D SER* 1.3 74.5 - - - +
280D LEU* 1.3 63.6 + - - +
281D ARG* 3.2 15.3 + - - +
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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