Contacts of the helix formed by residues 282 - 293 (chain D) in PDB entry 4K71
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 PRO 282 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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280D GLU 4.4 2.2 - - - +
281D LYS* 1.4 88.2 - - + +
283D LEU* 1.3 55.1 + - - +
284D LEU 3.2 2.2 + - - +
285D GLU* 3.2 26.2 + - + +
286D LYS* 2.7 32.7 + - - +
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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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13D ASP 5.9 3.1 - - - +
18D ASN* 6.1 3.1 - - - +
258D ALA* 3.9 41.5 - - + +
261D ALA* 4.6 1.1 - - + -
262D LYS* 4.4 21.3 - - + +
282D PRO* 1.3 74.2 - - - +
284D LEU* 1.3 60.9 + - - +
286D LYS* 3.9 27.6 - - - +
287D SER* 3.0 36.8 + - - +
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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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18D ASN* 4.3 20.6 - - - +
152D PRO 4.9 3.1 - - - +
155D LEU* 3.9 45.3 - - + +
156D PHE* 4.2 19.6 - - + +
159D LYS* 4.5 14.8 - - + -
257D ARG* 5.4 1.0 + - - -
282D PRO* 3.3 0.6 - - - +
283D LEU* 1.3 78.4 - - - +
285D GLU* 1.3 78.8 + - - +
287D SER* 3.4 4.2 + - - -
288D HIS* 3.4 20.3 + - - +
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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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156D PHE* 4.1 18.4 - - + -
159D LYS* 2.8 43.2 + - - +
281D LYS* 3.9 24.9 - - + +
282D PRO* 3.5 33.0 - - + +
284D LEU* 1.3 86.7 - - - +
286D LYS* 1.3 57.0 + - - +
288D HIS* 3.4 3.6 + - - +
289D CYS* 2.9 31.7 + - - +
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Residues in contact with LYS 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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261D ALA* 4.4 7.9 - - + -
262D LYS* 4.9 14.5 - - - +
265D CYS* 3.7 23.5 - - - +
278D CYS 3.7 18.8 - - - +
279D CYS* 4.0 13.8 + - - +
281D LYS* 3.7 17.2 + - - +
282D PRO* 2.7 21.3 + - - +
283D LEU* 3.6 30.9 - - - +
284D LEU 3.3 0.2 - - - -
285D GLU* 1.3 72.9 - - - +
287D SER* 1.3 62.1 + - - +
289D CYS* 3.4 2.1 + - - +
290D ILE* 3.0 44.0 + - + +
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Residues in contact with SER 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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257D ARG* 3.5 33.8 + - - -
258D ALA* 4.6 6.2 - - - -
261D ALA* 3.6 24.4 - - - +
283D LEU* 3.0 21.2 + - - +
284D LEU* 3.4 4.4 + - - -
286D LYS* 1.3 78.4 - - - +
288D HIS* 1.3 61.6 + - - +
290D ILE* 3.6 4.3 + - - +
291D ALA* 3.1 23.6 + - - +
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Residues in contact with HIS 288 (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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172A ALA* 2.7 32.3 + - + -
153D GLU* 4.9 13.9 + - + +
156D PHE* 3.3 54.4 - + + +
160D ARG* 5.1 0.9 - - - -
257D ARG* 4.4 7.5 + - - +
284D LEU 3.4 4.0 + - - +
285D GLU 3.4 7.4 + - - +
286D LYS 3.3 0.6 - - - -
287D SER* 1.3 76.6 - - - +
289D CYS* 1.3 69.9 + - + +
291D ALA* 3.1 17.7 + - - +
292D GLU* 3.1 48.1 + - - +
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Residues in contact with CYS 289 (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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277D GLU* 6.0 0.2 - - - -
278D CYS* 2.1 59.9 - - + -
281D LYS* 4.1 19.7 - - + +
285D GLU 2.9 18.6 + - - +
286D LYS 3.8 1.8 - - - +
288D HIS* 1.3 81.0 - - + +
290D ILE* 1.3 62.1 + - - +
292D GLU* 3.1 5.8 + - - -
293D VAL* 3.0 21.6 + - - +
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Residues in contact with ILE 290 (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 ARG* 4.3 9.0 + - - +
223D PHE* 4.8 6.7 - - + -
261D ALA* 4.0 22.9 - - + +
264D ILE* 3.9 32.3 - - + -
265D CYS* 3.8 26.9 - - - -
275D LEU* 3.9 22.2 - - + -
278D CYS* 3.5 12.8 - - + -
286D LYS* 3.0 28.5 + - + +
287D SER* 3.7 5.4 - - - +
289D CYS* 1.3 76.4 - - - +
291D ALA* 1.3 62.6 + - - +
292D GLU 3.3 0.9 + - - -
293D VAL* 3.5 16.1 - - - +
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Residues in contact with ALA 291 (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 ARG* 3.4 34.2 + - - +
257D ARG* 3.7 18.2 - - - +
287D SER 3.1 14.2 + - - +
288D HIS* 3.1 12.0 + - - +
290D ILE* 1.3 77.1 - - - +
292D GLU* 1.3 63.2 + - + +
293D VAL 3.6 0.2 - - - -
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Residues in contact with GLU 292 (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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172A ALA* 4.7 1.0 - - - +
173A ASP* 3.1 45.0 + - - +
153D GLU* 4.4 9.6 - - - +
222D ARG* 5.4 0.2 - - - +
288D HIS* 3.1 48.4 + - + +
289D CYS* 3.1 5.8 + - - +
291D ALA* 1.3 83.3 - - + +
293D VAL* 1.3 67.2 + - - +
294D GLU* 3.6 1.4 + - - -
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Residues in contact with VAL 293 (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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218D ARG* 5.7 1.2 + - - -
222D ARG* 4.0 16.5 - - - +
223D PHE* 4.3 16.6 - - + -
274D LYS* 3.4 37.9 - - + +
275D LEU* 4.2 15.5 - - + -
278D CYS* 4.2 14.6 - - - -
289D CYS* 3.0 13.6 + - - +
290D ILE 3.5 14.2 + - - +
291D ALA 3.6 0.4 - - - -
292D GLU* 1.3 81.4 - - - +
294D GLU* 1.3 75.6 + - + +
295D ASN* 3.7 1.2 + - - +
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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