Contacts of the helix formed by residues 280 - 287 (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 GLN 280 (chain D).
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Specific contacts
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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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Residues in contact with TYR 281 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177D MET* 3.5 38.1 - - + +
182D TRP* 4.2 23.8 - + - -
220D LEU* 5.4 9.9 - - + -
221D PHE* 4.2 1.0 - - - -
222D SER* 2.6 36.6 + - - -
254D PHE* 4.6 7.0 - - + +
256D LYS* 5.6 8.3 - - + -
277D LEU* 2.8 19.3 + - + +
278D PHE* 3.7 11.2 - - - +
279D ILE 3.2 3.4 - - - -
280D GLN* 1.3 77.9 - - - +
282D PRO* 1.3 68.0 - - + +
284D LEU* 3.1 22.0 + - + +
285D VAL* 3.0 47.0 + - + +
297D ASP* 5.9 2.9 - - + -
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Residues in contact with PRO 282 (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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182D TRP* 4.8 20.0 - - + +
278D PHE 3.9 6.3 - - - +
279D ILE 3.6 13.7 - - - +
281D TYR* 1.3 96.0 - - + +
283D VAL* 1.3 62.8 + - + +
285D VAL* 3.3 9.0 + - + +
286D ARG* 2.8 33.5 + - + +
297D ASP* 6.1 0.9 - - - +
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Residues in contact with VAL 283 (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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279D ILE 5.3 0.9 - - - +
280D GLN* 3.6 22.0 - - + +
282D PRO* 1.3 79.1 - - + +
284D LEU* 1.3 52.6 + - + +
285D VAL 3.1 4.5 - - - -
286D ARG* 3.2 29.1 + - - +
287D LEU* 3.1 25.7 + - + +
288D GLU* 2.8 24.5 - - - +
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Residues in contact with LEU 284 (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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254D PHE* 4.3 6.4 - - - -
256D LYS* 5.2 19.1 - - + -
277D LEU* 5.3 6.3 - - + +
280D GLN* 3.3 24.9 - - + +
281D TYR* 3.2 29.4 - - + +
283D VAL* 1.3 75.8 - - - +
285D VAL* 1.3 56.8 + - + +
288D GLU* 2.9 31.3 - - + +
826D VAL* 4.8 8.3 - - + -
828D PRO* 3.7 37.7 - - + -
829D PRO* 5.6 2.9 - - + -
833D SER* 5.2 3.6 - - - +
835D LEU* 6.0 3.2 - - + +
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Residues in contact with VAL 285 (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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222D SER* 4.6 2.2 - - - +
224D THR* 3.6 28.1 - - + +
254D PHE* 3.5 31.7 - - + -
281D TYR* 3.0 49.1 + - + +
282D PRO* 3.6 10.3 - - + +
283D VAL 3.1 0.2 - - - -
284D LEU* 1.3 78.9 - - + +
286D ARG* 1.3 63.6 + - + +
288D GLU* 3.4 4.7 - - - +
289D GLN* 4.1 8.5 + - - +
296D GLY* 4.6 11.4 - - - -
297D ASP* 5.3 2.9 - - + +
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Residues in contact with ARG 286 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282D PRO* 2.8 22.3 + - - +
283D VAL* 3.2 19.3 + - - +
285D VAL* 1.3 75.4 - - + +
287D LEU* 1.3 100.6 + - + +
288D GLU* 3.2 13.7 + - - +
289D GLN* 6.1 0.2 - - - -
290D ALA 5.1 4.5 - - - +
291D GLU* 5.5 3.8 - - - +
294D PRO* 4.7 27.8 - - + +
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Residues in contact with LEU 287 (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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283D VAL* 3.1 21.6 + - + +
286D ARG* 1.3 116.4 - - + +
288D GLU* 1.3 64.5 + - - +
291D GLU* 5.0 20.6 - - + +
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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