Contacts of the helix formed by residues 278 - 295 (chain D) in PDB entry 3O9Z
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 GLY 278 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D LEU* 4.7 2.2 - - - -
123D ARG* 4.3 10.5 - - - -
124D VAL 3.4 15.3 - - - -
125D TYR* 4.0 6.3 - - - -
276D GLY 3.5 3.2 + - - -
277D PHE* 1.3 73.0 - - - +
279D LEU* 1.3 60.9 + - - -
280D ASP 3.2 3.1 - - - -
281D GLU* 2.7 17.9 + - - -
282D ALA* 2.9 31.7 + - - +
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Residues in contact with LEU 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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103D LEU* 3.8 25.1 - - + -
110D ILE* 3.9 19.6 - - + +
113D LEU* 3.8 29.4 - - + -
114D LYS* 3.6 45.1 - - + +
117D GLU* 3.5 34.1 - - + +
123D ARG* 5.0 3.6 - - - +
124D VAL* 3.8 13.9 + - + -
278D GLY* 1.3 73.4 - - - -
280D ASP* 1.3 62.8 + - - +
282D ALA* 4.0 0.3 - - - +
283D ALA* 3.0 28.8 + - - +
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Residues in contact with ASP 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114D LYS* 2.8 36.2 + - - +
278D GLY 3.2 0.6 - - - -
279D LEU* 1.3 79.5 - - - +
281D GLU* 1.3 74.9 + - - +
283D ALA* 3.9 10.4 + - - +
284D GLU* 4.9 2.3 + - - +
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Residues in contact with GLU 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123D ARG* 5.4 1.4 + - - -
128D LEU* 4.8 0.9 - - + -
131D ARG* 3.1 45.6 + - - +
188D ASP* 3.9 1.2 - - - +
191D ALA* 6.1 0.7 - - - +
276D GLY 4.1 5.0 - - - +
277D PHE* 4.0 17.4 - - + -
278D GLY* 2.7 39.2 + - - +
280D ASP* 1.3 88.0 + - - +
282D ALA* 1.3 61.2 + - - +
283D ALA 3.5 0.2 + - - -
284D GLU* 4.5 5.4 + - - +
285D ALA 5.4 0.7 + - - -
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Residues in contact with ALA 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D LEU* 3.7 32.5 - - + -
110D ILE* 5.0 0.4 - - + -
126D THR* 4.0 14.4 - - + -
128D LEU* 4.8 4.0 - - + -
188D ASP* 4.6 6.2 - - - +
278D GLY 2.9 16.9 + - - +
279D LEU 3.3 2.0 + - - +
281D GLU* 1.3 79.4 - - - +
283D ALA* 1.3 63.8 + - - +
284D GLU 3.3 1.8 + - - -
285D ALA* 3.6 7.4 + - - +
286D ILE* 3.4 23.8 + - + +
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Residues in contact with ALA 283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107D PRO* 5.7 0.7 - - - +
110D ILE* 4.2 29.1 - - + +
279D LEU 3.0 16.9 + - - +
280D ASP* 3.9 6.7 + - - +
281D GLU 3.4 1.4 - - - -
282D ALA* 1.3 79.2 - - - +
284D GLU* 1.3 64.3 + - - +
286D ILE* 3.2 4.8 + - - +
287D ARG* 2.9 23.3 + - - +
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Residues in contact with GLU 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191D ALA* 3.6 25.8 - - + -
195D GLY 4.3 6.5 - - - +
196D ARG* 3.8 20.0 + - - +
197D ALA 2.9 25.6 + - - -
280D ASP 4.9 2.2 + - - +
281D GLU 4.5 3.8 + - - +
282D ALA 3.3 1.0 + - - -
283D ALA* 1.3 79.6 - - - +
285D ALA* 1.3 63.9 + - - +
287D ARG* 2.9 38.2 + - - +
288D VAL* 3.0 32.5 + - + +
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Residues in contact with ALA 285 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184D ILE* 3.6 15.5 - - + +
187D PHE* 3.8 8.6 - - + +
188D ASP* 3.4 49.3 + - + +
191D ALA* 4.5 2.2 - - + +
281D GLU 5.4 0.2 + - - -
282D ALA 3.6 5.6 + - - +
283D ALA 3.4 0.2 - - - -
284D GLU* 1.3 79.0 - - - +
286D ILE* 1.3 56.2 + - - +
288D VAL* 3.3 7.7 + - - +
289D ALA* 2.9 31.5 + - - +
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Residues in contact with ILE 286 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D PRO* 4.7 0.4 - - + -
103D LEU* 3.8 16.6 - - + +
104D VAL* 3.6 37.7 - - + +
105D LEU 4.0 6.0 - - - +
106D TRP 3.9 30.1 - - - +
107D PRO* 4.0 2.7 - - + -
110D ILE* 3.7 26.7 - - + -
184D ILE* 4.3 15.3 - - + -
282D ALA* 3.4 16.7 + - + +
283D ALA* 3.2 7.7 + - - +
284D GLU 3.2 0.8 - - - -
285D ALA* 1.3 79.3 - - + +
287D ARG* 1.3 56.6 + - - +
289D ALA* 3.8 2.1 - - - +
290D ALA* 2.9 28.8 + - - +
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Residues in contact with ARG 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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107D PRO* 3.8 24.0 - - + +
196D ARG* 3.5 37.2 - - - +
197D ALA* 2.9 32.7 + - - +
283D ALA 2.9 12.7 + - - +
284D GLU* 2.9 44.6 + - - +
286D ILE* 1.3 76.0 - - - +
288D VAL* 1.3 65.6 + - - +
290D ALA* 3.3 3.3 + - - +
291D LEU* 3.1 47.2 + - + +
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Residues in contact with VAL 288 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187D PHE* 4.5 16.4 - - + +
191D ALA* 6.1 0.9 - - + -
197D ALA* 3.8 16.2 - - + -
200D VAL* 4.8 4.9 - - + -
214D LEU* 4.3 22.9 - - + -
284D GLU* 3.0 41.1 + - + +
285D ALA* 3.8 9.2 - - - +
287D ARG* 1.3 78.6 - - - +
289D ALA* 1.3 51.9 + - - +
291D LEU* 3.0 12.7 + - - +
292D LEU* 2.7 54.5 + - + +
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Residues in contact with ALA 289 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179D ALA* 5.8 0.2 - - - +
180D THR* 3.5 25.9 + - - +
184D ILE* 3.7 20.0 - - + -
187D PHE* 5.3 4.5 - - + -
285D ALA 2.9 17.3 + - - +
286D ILE* 3.9 3.6 - - - +
288D VAL* 1.3 76.6 - - - +
290D ALA* 1.3 63.0 + - - +
292D LEU* 3.1 15.2 + - + +
293D ARG* 3.0 32.3 + - - +
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Residues in contact with ALA 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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105D LEU 4.1 0.7 - - - +
106D TRP* 3.8 10.3 - - + -
107D PRO* 3.8 24.0 - - + -
286D ILE 2.9 18.1 + - - +
287D ARG 3.6 4.5 - - - +
289D ALA* 1.3 77.0 - - - +
291D LEU* 1.3 60.1 + - + +
293D ARG* 3.4 24.9 + - - +
294D THR* 2.9 31.4 + - - +
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Residues in contact with LEU 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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200D VAL* 4.2 25.1 - - + -
287D ARG* 3.1 43.5 + - + +
288D VAL* 3.0 11.0 + - - +
290D ALA* 1.3 77.8 - - + +
292D LEU* 1.3 62.5 + - - +
294D THR* 3.6 7.9 - - - +
295D LEU* 3.0 56.5 + - + +
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Residues in contact with LEU 292 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179D ALA* 3.9 20.4 - - + -
187D PHE* 3.4 47.3 - - + -
200D VAL* 3.6 29.2 - - + -
201D GLU 4.9 0.2 - - - +
202D VAL* 4.0 13.7 - - + +
205D ARG* 3.0 26.4 + - - -
210D ASN* 5.1 2.6 - - - +
214D LEU* 4.5 2.7 - - + -
223D TRP* 3.6 24.0 - - + -
288D VAL* 2.7 29.6 + - + +
289D ALA* 3.1 10.7 + - - +
291D LEU* 1.3 72.7 - - - +
293D ARG* 1.3 57.4 + - - +
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Residues in contact with ARG 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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102D PRO* 6.1 0.2 - - - +
105D LEU* 2.9 36.7 + - - +
106D TRP* 3.5 36.7 - - + -
172D GLU* 3.8 31.6 - - - +
176D GLY* 2.8 39.3 + - - +
177D GLY* 5.5 0.9 - - - -
179D ALA* 6.5 0.4 - - + -
180D THR* 2.7 33.5 + - - +
205D ARG* 3.9 17.3 + - - +
286D ILE 5.2 0.4 + - - -
289D ALA* 3.0 19.2 + - - +
290D ALA* 3.6 16.9 - - - +
291D LEU 3.1 0.2 - - - -
292D LEU* 1.3 76.9 - - - +
294D THR* 1.3 68.9 + - + +
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Residues in contact with THR 294 (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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106D TRP* 3.9 21.3 - - + -
172D GLU* 5.6 0.9 - - - +
205D ARG* 4.3 2.1 + - - -
290D ALA 2.9 22.6 + - - +
291D LEU* 3.1 12.9 + - - +
293D ARG* 1.3 93.9 - - + +
295D LEU* 1.3 68.3 + - - +
296D PRO* 3.7 1.7 - - - +
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Residues in contact with LEU 295 (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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200D VAL* 3.6 46.4 - - + +
201D GLU* 5.1 0.9 - - - -
202D VAL* 4.4 11.4 - - + +
205D ARG* 2.8 32.9 + - - +
291D LEU* 3.0 40.0 + - + +
294D THR* 1.3 77.3 + - - +
296D PRO* 1.3 82.7 - - + +
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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
------------------------------------------------------------
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