Contacts of the helix formed by residues 303 - 312 (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 ALA 303 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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298D ALA 4.6 1.6 + - - -
299D ILE 2.9 29.5 + - - +
300D ILE* 3.6 8.3 - - - +
301D THR 3.2 16.6 + - - -
304D ALA* 1.3 70.0 + - - +
305D SER* 3.2 1.7 - - - +
306D ASP* 3.0 25.9 + - - +
307D MET* 3.0 13.9 + - - +
335D LEU* 3.8 22.9 - - + +
338D TYR* 3.9 29.4 + - - +
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Residues in contact with ALA 304 (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* 3.8 25.1 - - + -
64D VAL* 4.1 6.3 - - + -
95D GLN* 5.8 3.8 - - + -
300D ILE* 3.1 14.1 + - + +
301D THR 3.7 3.8 - - - +
303D ALA* 1.3 78.8 - - - +
305D SER* 1.3 58.3 + - - +
307D MET* 3.3 0.9 + - - -
308D LEU* 2.9 31.9 + - - +
314D ILE* 3.6 22.9 - - + +
335D LEU* 4.2 12.0 - - + +
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Residues in contact with SER 305 (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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62D LEU* 3.8 14.5 - - - +
63D SER* 3.5 33.2 + - - -
64D VAL* 3.9 9.7 - - - +
301D THR 3.0 17.7 + - - -
303D ALA 5.3 0.7 - - - -
304D ALA* 1.3 75.9 - - - +
306D ASP* 1.3 63.4 + - - +
308D LEU* 3.2 5.8 + - - +
309D SER* 2.8 34.1 + - - -
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Residues in contact with ASP 306 (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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303D ALA* 3.0 20.5 + - - +
305D SER* 1.3 86.3 + - - +
307D MET* 1.3 63.1 + - - +
309D SER* 3.5 5.6 + - - -
310D GLU* 3.3 22.3 + - - +
338D TYR* 4.3 17.0 - - + +
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Residues in contact with MET 307 (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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303D ALA 3.0 13.7 + - - +
304D ALA 3.9 3.4 - - - +
306D ASP* 1.3 76.1 - - - +
308D LEU* 1.3 60.4 + - - +
310D GLU* 4.9 1.3 - - - -
311D HIS* 2.9 42.8 + - + +
313D PHE* 3.6 38.1 - - + +
314D ILE* 4.4 2.2 - - + -
315D PRO* 3.7 31.0 - - + -
334D MET* 3.5 35.4 - - + +
335D LEU* 4.0 28.3 - - + -
338D TYR* 4.9 6.3 - - + +
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Residues in contact with LEU 308 (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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329B ILE* 4.5 15.7 - - + +
33D PRO* 4.4 18.2 - - + -
63D SER* 4.2 24.0 - - - +
64D VAL* 4.9 8.7 - - + -
304D ALA 2.9 17.1 + - - +
305D SER* 3.7 4.0 - - - +
307D MET* 1.3 77.6 - - - +
309D SER* 1.3 57.8 + - - +
310D GLU 3.1 1.6 + - - -
312D SER* 2.7 40.0 + - - +
313D PHE* 3.3 32.7 + - - +
314D ILE* 4.2 11.4 - - + +
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Residues in contact with SER 309 (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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63D SER* 4.2 16.9 + - - -
305D SER* 2.8 19.9 + - - -
306D ASP* 3.9 6.5 - - - -
308D LEU* 1.3 76.7 - - - +
310D GLU* 1.3 59.1 + - - +
312D SER 4.8 0.2 - - - -
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Residues in contact with GLU 310 (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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306D ASP 3.3 14.9 + - - +
307D MET* 4.2 2.5 - - - +
308D LEU 3.1 0.4 - - - -
309D SER* 1.3 80.6 - - - +
311D HIS* 1.3 81.5 + - + +
312D SER 3.6 1.1 - - - -
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Residues in contact with HIS 311 (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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332B SER* 3.8 8.7 + - - -
334B MET* 4.0 18.3 - - + +
337B ARG* 5.4 7.8 + - - +
307D MET* 2.9 29.3 + - + +
310D GLU* 1.3 95.4 - - + +
312D SER* 1.3 72.9 + - - +
313D PHE* 2.8 32.6 + - + +
334D MET* 4.2 23.6 - - + -
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Residues in contact with SER 312 (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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328B ARG 4.6 3.3 - - - +
329B ILE 4.4 1.2 - - - +
331B GLN 3.2 12.1 - - - +
332B SER* 5.7 2.5 - - - -
333B ASN 6.2 0.7 - - - -
308D LEU* 2.7 30.7 + - - +
310D GLU 3.6 1.2 - - - -
311D HIS* 1.3 78.8 - - - +
313D PHE* 1.3 60.4 + - - +
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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