Contacts of the helix formed by residues 288 - 301 (chain D) in PDB entry 3QEL
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 288 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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284D GLU* 4.3 13.4 + - - -
286D ASP 4.0 1.0 - - - -
287D TYR* 1.3 77.9 - - - +
289D LEU* 1.3 68.8 + - - -
290D PRO* 3.3 7.0 - - - -
291D ALA* 3.1 9.8 + - - +
292D ARG* 2.9 21.9 + - - +
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Residues in contact with LEU 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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41D LEU* 4.5 10.1 - - + -
44D THR 5.3 2.2 - - - +
45D SER* 4.7 14.8 - - - -
46D ASP 5.5 1.8 - - - +
50D ILE* 4.3 17.5 - - + -
100D ALA* 3.6 28.0 - - + -
126D ILE* 4.2 3.8 - - + -
127D HIS* 3.9 32.5 + - + +
284D GLU* 6.1 0.4 - - - +
288D GLY* 1.3 70.2 - - - -
290D PRO* 1.3 67.4 - - + +
292D ARG* 3.0 8.9 + - + +
293D VAL* 2.7 45.6 + - + +
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Residues in contact with PRO 290 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D ASP* 5.6 2.0 - - + +
49D ALA* 4.0 30.5 - - + +
50D ILE* 4.3 29.4 - - + +
288D GLY* 3.5 5.6 - - - -
289D LEU* 1.3 94.3 - - + +
291D ALA* 1.3 60.0 + - - +
293D VAL* 4.0 2.7 - - + +
294D ARG* 3.0 24.8 + - - +
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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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287D TYR* 3.5 23.1 - - + -
288D GLY 3.1 16.0 + - - +
290D PRO* 1.3 79.4 - - - +
292D ARG* 1.3 64.1 + - - +
294D ARG* 3.3 5.0 + - - +
295D ASP* 3.0 29.0 + - - +
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Residues in contact with ARG 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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126D ILE* 2.7 44.3 + - + +
127D HIS* 4.6 17.7 + - - +
131D SER* 5.2 1.8 + - - -
146D PHE* 3.7 27.9 + - + +
282D TYR* 2.9 52.1 + - - -
283D ASP 3.1 26.9 + - - -
284D GLU* 4.2 4.0 - - - +
287D TYR* 3.0 35.6 + - + +
288D GLY 2.9 15.4 + - - +
289D LEU* 3.4 10.1 - - - +
291D ALA* 1.3 77.5 - - - +
293D VAL* 1.3 58.8 + - - +
295D ASP* 2.9 4.3 + - - +
296D GLY* 2.8 27.0 + - - -
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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
----------------------------------------------------------
39D VAL* 3.8 35.9 - - + -
41D LEU* 4.9 2.9 - - + -
50D ILE* 3.8 30.5 - - + -
70D LEU* 5.7 0.2 - - + -
98D VAL* 4.5 3.6 - - + +
126D ILE* 3.5 23.6 - - + -
289D LEU* 2.7 39.5 + - + +
290D PRO* 4.0 3.4 - - + +
292D ARG* 1.3 71.0 - - - +
294D ARG* 1.3 60.9 + - - +
296D GLY* 3.6 1.3 + - - +
297D ILE* 3.0 36.5 + - + +
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Residues in contact with ARG 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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50D ILE 6.0 1.8 - - - +
290D PRO 3.0 19.1 + - - +
291D ALA* 3.6 5.8 - - - +
292D ARG 3.2 0.2 - - - -
293D VAL* 1.3 75.7 - - - +
295D ASP* 1.3 63.3 + - - +
297D ILE* 3.2 11.7 + - - +
298D ALA* 3.1 25.5 + - - +
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Residues in contact with ASP 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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146D PHE* 4.5 6.6 - - + -
287D TYR* 2.8 32.1 + - - +
291D ALA* 3.0 14.9 + - - +
292D ARG 2.9 5.9 + - - +
294D ARG* 1.3 82.4 - - - +
296D GLY* 1.3 57.5 + - - +
298D ALA* 3.2 10.4 + - - +
299D ILE* 2.9 27.2 + - - +
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Residues in contact with GLY 296 (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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98D VAL* 3.5 25.8 - - - +
124D LEU* 3.7 20.4 - - - +
126D ILE* 5.0 1.1 - - - -
146D PHE* 4.2 6.7 - - - -
292D ARG 2.8 18.5 + - - -
293D VAL 3.6 2.4 + - - -
295D ASP* 1.3 73.6 - - - +
297D ILE* 1.3 60.0 + - - +
299D ILE* 3.8 0.4 - - - -
300D ILE* 3.4 21.5 + - - +
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Residues in contact with ILE 297 (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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37D ILE* 3.7 26.9 - - + -
39D VAL* 4.2 15.5 - - + -
66D PRO* 3.9 21.1 - - + -
68D VAL* 3.4 31.0 - - + -
98D VAL* 4.7 4.0 - - + -
293D VAL* 3.0 23.3 - - + +
294D ARG* 3.2 9.3 + - - +
295D ASP 3.2 0.4 - - - -
296D GLY* 1.3 76.3 - - - +
298D ALA* 1.3 60.2 + - - +
299D ILE 3.3 0.7 - - - -
300D ILE 4.6 0.2 - - - +
301D THR* 2.9 34.9 + - - +
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Residues in contact with ALA 298 (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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294D ARG 3.1 13.9 + - - +
295D ASP* 3.2 14.3 + - - +
297D ILE* 1.3 75.8 - - - +
299D ILE* 1.3 65.4 + - - +
301D THR* 4.0 12.9 + - - +
303D ALA 4.6 1.4 + - - -
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Residues in contact with ILE 299 (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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124D LEU* 3.6 27.4 - - + -
146D PHE* 6.1 1.3 - - + -
295D ASP 2.9 14.2 + - - +
296D GLY 3.8 0.4 - - - +
297D ILE 3.3 0.2 - - - -
298D ALA* 1.3 76.5 - - - +
300D ILE* 1.3 58.3 + - + +
303D ALA* 2.9 32.4 + - - +
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Residues in contact with ILE 300 (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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35D ILE* 4.4 6.3 - - + -
37D ILE* 3.7 28.3 - - + -
95D GLN* 4.4 7.2 - - + +
96D GLY* 3.5 33.4 - - - +
97D VAL 3.6 21.8 - - - +
98D VAL* 4.2 5.6 - - + -
122D PRO* 4.7 13.0 - - + +
124D LEU* 4.4 13.5 - - + -
296D GLY 3.4 18.8 + - - +
297D ILE 4.3 0.2 - - - +
298D ALA 3.5 0.2 - - - -
299D ILE* 1.3 78.8 - - + +
301D THR* 1.3 62.6 + - - +
303D ALA* 3.5 5.4 + - - +
304D ALA* 3.1 23.3 + - + +
335D LEU* 5.7 3.1 - - + +
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Residues in contact with THR 301 (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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35D ILE* 3.9 10.4 - - - +
37D ILE* 3.6 5.7 - - - +
60D HIS* 5.8 2.0 - - + -
62D LEU* 4.9 11.0 - - + -
64D VAL* 3.7 25.9 - - + +
66D PRO* 3.3 36.6 - - + +
297D ILE* 2.9 20.2 + - - -
298D ALA* 4.2 9.6 - - - +
299D ILE 3.4 1.1 - - - -
300D ILE* 1.3 80.3 - - - +
303D ALA 3.2 14.0 + - - -
304D ALA 3.4 1.2 + - - -
305D SER* 3.0 36.1 + - - -
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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