Contacts of the helix formed by residues 276 - 287 (chain D) in PDB entry 6APL
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 276 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89D PRO* 3.9 20.7 - - + +
90D VAL 2.9 23.1 + - - +
91D LEU 3.2 23.6 - - - +
92D LEU* 3.7 28.4 - - + +
96D LEU* 4.0 18.6 - - + +
101D LEU* 4.6 12.6 - - + +
105D LEU* 5.0 1.6 - - + -
274D LEU 3.6 2.0 + - - -
275D LEU* 1.3 70.5 - - - +
277D PRO* 1.3 76.2 - - + +
278D ASP* 3.0 49.2 + - + +
279D PHE* 3.0 15.5 + - + +
280D ILE* 3.1 14.5 + - - +
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Residues in contact with PRO 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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92D LEU* 3.9 17.9 - - + -
105D LEU* 4.1 17.5 - - + -
111D PRO 3.3 22.8 - - - +
112D TYR 3.9 16.2 - - - +
113D GLY* 4.1 3.4 - - - +
114D TRP* 4.6 2.0 - - + -
231D PRO* 4.0 15.5 - - + -
237D TYR* 4.4 11.7 - - - +
275D LEU 3.5 7.0 - - - +
276D HIS* 1.3 92.9 - - + +
278D ASP* 1.3 55.9 + - - +
280D ILE* 3.1 7.5 + - + +
281D SER* 2.8 33.0 + - - -
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Residues in contact with ASP 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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88D ILE* 3.6 14.4 - - + +
89D PRO* 6.0 1.3 - - + -
101D LEU* 3.7 17.8 - - - +
104D ARG* 4.2 15.9 + - - -
105D LEU* 3.8 16.4 - - - +
112D TYR 5.4 0.2 - - - +
276D HIS* 3.0 31.1 + - + +
277D PRO* 1.3 77.0 - - - +
279D PHE* 1.3 54.1 + - - +
281D SER* 3.2 9.7 + - - -
282D TYR* 2.7 36.0 + - - +
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Residues in contact with PHE 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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88D ILE* 4.0 14.7 - - + +
89D PRO 3.2 24.9 + - - +
90D VAL* 3.6 37.0 - - + +
275D LEU* 4.0 11.9 - - + -
276D HIS* 3.0 11.9 + - + +
278D ASP* 1.3 77.9 - - - +
280D ILE* 1.3 57.7 + - - +
282D TYR* 3.6 14.8 + + - +
283D LEU* 3.0 55.4 + - + +
312D THR* 3.4 34.3 - - - -
315D HIS* 4.0 32.3 - + - -
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Residues in contact with ILE 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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111D PRO* 3.9 37.0 - - + +
112D TYR* 4.1 11.7 - - + -
230D ILE* 4.3 7.2 - - + -
231D PRO* 4.0 19.5 - - + -
275D LEU* 3.7 28.9 - - + -
276D HIS 3.1 12.8 + - - +
277D PRO 3.1 6.5 + - - +
279D PHE* 1.3 74.8 - - + +
281D SER* 1.3 60.8 + - - +
283D LEU* 3.1 8.2 + - + +
284D THR* 2.8 41.2 + - - +
303D PRO* 4.8 10.1 - - + -
308D LEU* 4.7 13.0 - - + -
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Residues in contact with SER 281 (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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112D TYR* 3.3 41.8 + - - +
277D PRO 2.8 21.9 + - - -
278D ASP* 3.6 11.5 + - - -
280D ILE* 1.3 73.3 - - - +
282D TYR* 1.3 62.6 + - - +
284D THR* 3.3 2.3 + - - -
285D GLU* 3.0 26.7 + - - +
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Residues in contact with TYR 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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84D PHE* 3.5 1.2 - - - -
85D ASN* 2.9 33.5 + - + -
88D ILE* 3.5 32.3 - - + -
278D ASP 2.7 20.0 + - - +
279D PHE* 3.7 13.5 - + - +
281D SER* 1.3 74.7 - - - +
283D LEU* 1.3 71.2 - - + +
285D GLU* 3.3 2.9 + - - -
286D ARG* 2.9 70.5 + - + +
287D PHE* 3.2 16.8 - + - -
315D HIS* 2.9 34.7 + + - -
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Residues in contact with LEU 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 PHE* 3.0 47.7 + - + +
280D ILE* 3.1 7.2 + - + +
282D TYR* 1.3 97.3 - - + +
284D THR* 1.3 63.0 + - - +
287D PHE* 3.0 33.9 + - + +
288D LEU* 3.2 9.7 + - - +
303D PRO* 5.2 7.0 - - + -
308D LEU* 4.6 19.1 - - + +
311D LEU* 3.6 46.0 - - + -
315D HIS* 4.0 9.2 - - + -
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Residues in contact with THR 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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112D TYR* 3.2 35.1 - - + +
280D ILE 2.8 17.4 + - - -
281D SER 3.8 4.0 - - - -
283D LEU* 1.3 76.6 - - - +
285D GLU* 1.3 59.4 + - - +
288D LEU 2.9 17.7 + - - +
289D LYS* 2.9 31.9 + - - -
293D ILE* 4.2 13.2 - - + -
301D TYR* 3.9 13.5 - - + -
303D PRO* 3.6 19.7 - - + +
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Residues in contact with GLU 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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281D SER 3.0 16.6 + - - +
282D TYR* 4.1 2.5 - - - +
284D THR* 1.3 77.9 - - - +
286D ARG* 1.3 71.0 + - + +
289D LYS* 3.3 54.7 + - - +
293D ILE* 5.9 1.6 - - - +
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Residues in contact with ARG 286 (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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82D GLY 3.6 9.5 + - - -
83D LEU* 3.4 50.1 - - + +
84D PHE 3.3 28.7 - - - +
85D ASN* 3.7 24.2 - - - +
282D TYR* 2.9 44.8 + - + +
285D GLU* 1.3 84.1 - - + +
287D PHE* 1.3 72.5 - - + +
289D LYS* 5.7 0.2 - - - -
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Residues in contact with PHE 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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80D PHE* 4.5 12.6 - + - -
83D LEU* 3.4 21.5 - - + -
84D PHE* 3.4 35.4 - + - -
282D TYR* 3.2 36.1 - + - -
283D LEU* 3.0 31.1 + - + +
285D GLU 3.3 0.8 - - - -
286D ARG* 1.3 91.5 - - + +
288D LEU* 1.3 69.0 + - + +
289D LYS* 3.9 3.9 + - - -
311D LEU* 4.6 11.9 - - + -
315D HIS* 4.4 3.6 - + - -
355D LEU* 4.5 6.8 - - - +
359D LEU* 4.1 37.9 - - + +
363D LEU* 5.6 1.6 - - + -
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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