Contacts of the helix formed by residues 268 - 280 (chain D) in PDB entry 6CET
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 THR 268 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201D ALA* 4.9 9.9 - - + -
204D PHE* 3.6 24.5 - - + +
205D THR* 6.1 0.5 - - - +
267D TRP* 1.3 78.8 + - - +
269D SER* 1.3 61.6 + - - +
270D LEU* 3.1 5.8 - - - +
271D LEU* 3.2 51.6 + - + +
272D VAL* 3.9 6.2 + - - +
115N GLU* 5.6 1.5 - - - +
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Residues in contact with SER 269 (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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264D ARG* 5.0 9.8 - - - +
266D GLU* 5.7 3.1 - - - -
267D TRP 3.2 8.0 + - - -
268D THR* 1.3 74.7 - - - +
270D LEU* 1.3 59.8 + - - +
271D LEU 3.1 0.2 - - - -
272D VAL* 3.0 28.4 + - - +
273D THR* 3.1 20.6 + - - +
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Residues in contact with LEU 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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204D PHE* 5.0 14.4 - - + -
216D VAL* 5.0 5.8 - - + -
218D VAL* 4.4 20.4 - - + -
258D VAL* 5.0 6.1 - - + -
259D VAL* 3.8 27.8 - - + +
264D ARG* 3.5 24.8 - - - +
267D TRP* 3.6 31.2 - - + -
268D THR 3.1 3.3 - - - +
269D SER* 1.3 75.7 - - - +
271D LEU* 1.3 63.6 + - + +
273D THR* 2.7 29.3 + - + +
274D ILE* 2.9 29.1 + - + +
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Residues in contact with LEU 271 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196D VAL* 4.0 22.4 - - + +
197D ASN* 4.0 40.2 - - - +
200D LEU* 3.8 12.6 - - + -
201D ALA* 4.2 5.8 - - + +
204D PHE* 3.7 28.9 - - + -
268D THR* 3.2 37.6 + - + +
269D SER 3.1 0.2 - - - -
270D LEU* 1.3 79.2 - - + +
272D VAL* 1.3 57.8 + - + +
274D ILE* 3.3 3.3 + - - +
275D LYS* 2.9 41.9 + - - +
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Residues in contact with VAL 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268D THR 4.2 8.7 - - - +
269D SER* 3.0 17.6 + - - +
271D LEU* 1.3 76.4 - - + +
273D THR* 1.3 65.1 + - + +
275D LYS* 3.3 14.9 + - + +
276D LYS* 3.0 46.9 + - + +
115N GLU* 3.7 37.2 - - + +
152N SER* 5.2 7.6 - - - +
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Residues in contact with THR 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258D VAL* 5.0 9.7 - - - +
264D ARG* 6.1 1.1 - - - +
269D SER* 3.1 20.9 + - - +
270D LEU* 2.7 35.5 + - + +
272D VAL* 1.3 77.1 - - + +
274D ILE* 1.3 59.9 + - - +
276D LYS* 3.3 10.8 + - + +
277D LEU* 2.9 42.2 + - - +
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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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175D ILE* 4.3 12.8 - - + -
192D PHE* 3.7 23.8 - - + -
196D VAL* 4.0 14.1 - - + -
200D LEU* 4.6 13.7 - - + -
218D VAL* 4.1 24.2 - - + -
220D LEU* 4.7 19.4 - - + +
258D VAL* 4.4 14.8 - - + -
270D LEU* 2.9 29.3 + - + +
271D LEU* 3.8 4.5 - - - +
273D THR* 1.3 77.4 + - - +
275D LYS* 1.3 60.0 + - - +
277D LEU* 3.4 6.5 + - - +
278D PHE* 2.8 28.2 + - - +
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Residues in contact with LYS 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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192D PHE* 3.9 23.6 - - + -
193D GLU* 5.9 4.5 - - - -
196D VAL* 5.4 4.0 - - + -
197D ASN* 4.4 23.1 + - - +
271D LEU* 2.9 26.5 + - - +
272D VAL* 3.3 16.7 + - + +
274D ILE* 1.3 76.6 - - - +
276D LYS* 1.3 62.8 + - - +
278D PHE* 3.2 3.5 + - - +
279D ILE* 3.0 29.2 + - + +
111N THR* 4.3 24.4 + - - +
115N GLU* 5.6 3.8 + - - -
152N SER* 4.2 25.1 - - - +
153N ASN* 4.6 8.4 + - - +
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Residues in contact with LYS 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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272D VAL* 3.0 35.9 + - + +
273D THR* 3.3 10.5 + - + +
275D LYS* 1.3 75.0 - - - +
277D LEU* 1.3 64.5 + - + +
279D ILE* 3.2 4.5 + - - +
280D GLN* 3.0 33.6 + - - +
151N GLU* 3.4 48.0 + - - +
152N SER* 4.0 11.9 - - - -
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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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220D LEU* 4.0 25.6 - - + -
256D LYS* 3.9 26.2 - - + +
258D VAL* 3.8 29.4 - - + -
273D THR* 2.9 31.2 + - - +
274D ILE* 3.9 4.3 - - - +
276D LYS* 1.3 76.7 - - + +
278D PHE* 1.3 60.2 + - - +
280D GLN* 3.5 25.3 - - + +
281D TYR* 2.8 35.4 + - + +
284D LEU* 5.3 6.1 - - + +
829D PRO* 5.5 5.2 - - + -
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Residues in contact with PHE 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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177D MET* 4.5 14.4 - - - -
181D MET* 4.5 12.8 - - + -
182D TRP* 3.3 57.5 + + - -
190D LEU* 4.5 9.9 - - + -
192D PHE* 3.5 61.2 - + + -
220D LEU* 5.8 0.6 - - - +
274D ILE 2.8 18.7 + - - +
275D LYS 3.2 3.8 + - - +
277D LEU* 1.3 75.4 - - - +
279D ILE* 1.3 73.7 + - + +
281D TYR* 3.6 12.0 + - + +
282D PRO* 3.9 6.1 - - - +
154N THR* 5.7 1.3 - - - -
156N HIS* 5.1 7.0 - - - -
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Residues in contact with ILE 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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275D LYS* 3.0 12.0 + - + +
276D LYS 3.2 6.7 + - - +
278D PHE* 1.3 86.5 - - + +
280D GLN* 1.3 58.0 + - - +
281D TYR 3.2 3.7 + - - -
282D PRO* 3.6 10.4 - - - +
283D VAL* 5.3 1.4 - - - +
148N PRO* 6.2 0.7 - - + -
150N ASP 4.6 1.8 - - - +
151N GLU* 3.3 28.0 - - - +
152N SER* 3.5 24.9 - - - +
153N ASN 3.6 4.0 - - - +
154N THR* 3.8 35.9 - - + +
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Residues in contact with GLN 280 (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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276D LYS* 3.0 21.7 + - - +
277D LEU* 3.6 35.4 - - + +
279D ILE* 1.3 77.2 - - + +
281D TYR* 1.3 61.4 + - - +
282D PRO* 3.8 1.3 - - - -
283D VAL* 3.6 18.3 - - + +
284D LEU* 3.3 22.7 - - + +
829D PRO* 4.8 16.2 - - - +
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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