Contacts of the helix formed by residues 325 - 335 (chain A) in PDB entry 1QCO
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 THR 325 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276A ASN* 3.8 27.8 - - + +
277A PRO* 5.2 1.3 - - + -
279A GLN* 5.6 1.1 - - - +
289A HIS* 2.8 34.5 + - + +
293A TYR* 4.0 13.7 - - - +
294A THR* 4.1 9.4 - - - +
322A MET* 5.9 1.1 - - - +
323A TYR 4.9 4.0 - - - +
324A TRP* 1.3 75.0 - - - +
326A MET* 1.3 64.8 + - - +
327A LEU 3.4 3.7 + - - -
328A GLN* 3.0 25.9 + - - +
329A GLN* 3.0 25.1 + - - +
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Residues in contact with MET 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A PHE* 3.5 41.2 - - + -
225A ILE* 3.9 16.2 - - + -
228A MET* 3.8 32.8 - - - +
266A MET* 4.0 6.5 - - + -
293A TYR* 4.0 13.1 + - + +
295A PHE* 3.5 37.9 - - + -
319A PHE* 3.8 18.4 - - + -
325A THR* 1.3 75.4 - - - +
327A LEU* 1.3 58.0 + - - +
329A GLN* 3.6 13.1 - - - +
330A LEU* 2.9 31.0 + - - +
348A SER* 6.4 0.7 - - - -
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Residues in contact with LEU 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A ILE* 4.2 11.2 - - + +
221A ALA* 3.8 10.3 - - + +
222A HIS* 3.5 37.0 - - + +
225A ILE* 3.8 15.9 - - + -
289A HIS* 3.8 34.8 - - + +
291A GLN* 4.3 15.5 - - + +
293A TYR* 3.7 35.7 - - + -
325A THR* 3.2 5.8 - - - +
326A MET* 1.3 77.3 - - - +
328A GLN* 1.3 56.3 + - - +
330A LEU* 3.6 0.4 + - - -
331A THR* 2.8 35.5 + - - -
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Residues in contact with GLN 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A PRO* 4.1 2.6 - - + +
218A ILE* 4.1 5.8 - - + -
279A GLN* 3.0 38.9 + - - +
283A PRO* 4.1 3.0 - - - +
287A LEU* 2.9 40.5 + - + +
288A CYS* 5.0 0.6 - - - +
289A HIS* 3.7 13.7 + - + +
324A TRP* 3.3 25.4 - - + -
325A THR* 3.0 37.9 + - - +
327A LEU* 1.3 73.6 - - - +
329A GLN* 1.3 59.9 + - - +
332A HIS* 2.9 32.6 + - - +
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Residues in contact with GLN 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A PHE* 3.6 48.2 - - + +
129A SER* 2.9 34.7 + - - +
156A PRO* 4.3 11.2 - - + -
204A PHE* 3.8 15.3 - - + -
322A MET* 4.9 1.2 - - - +
324A TRP* 4.1 5.8 + - + -
325A THR 3.0 18.4 + - - +
326A MET* 3.6 21.5 - - - +
327A LEU 3.3 0.2 - - - -
328A GLN* 1.3 76.9 - - - +
330A LEU* 1.3 57.3 + - - +
332A HIS* 3.4 1.4 + - - +
333A HIS* 2.9 31.1 + - - +
346A LEU* 4.7 0.7 - - - -
347A ALA 4.8 0.3 - - - +
348A SER* 3.7 16.1 + - - +
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Residues in contact with LEU 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A PHE* 4.0 23.1 - - + -
206A VAL* 4.1 13.2 - - + -
216A ILE* 4.1 12.8 - - + -
221A ALA* 3.6 41.7 - - + +
224A HIS* 3.9 20.2 - - + +
225A ILE* 4.8 3.6 - - + -
326A MET 2.9 18.2 + - - +
327A LEU* 3.9 3.1 - - - +
329A GLN* 1.3 77.0 - - - +
331A THR* 1.3 61.7 + - - +
333A HIS* 3.3 4.7 + - - +
334A SER* 3.2 23.0 + - - -
340A LEU* 3.4 25.4 - - + +
346A LEU* 4.3 10.0 - - + +
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Residues in contact with THR 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A ILE 3.4 18.7 + - - +
217A PRO* 4.7 0.9 - - + -
218A ILE* 3.3 30.8 + - + +
221A ALA* 3.6 7.6 - - - +
286A TYR* 3.5 34.1 - - + +
287A LEU* 4.6 0.9 - - + -
327A LEU 2.8 22.5 + - - -
328A GLN* 3.9 2.9 - - - -
330A LEU* 1.3 75.7 - - - +
332A HIS* 1.3 64.1 + - - +
334A SER* 3.1 9.0 + - - -
335A VAL* 3.0 23.0 + - + +
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Residues in contact with HIS 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A PHE* 4.9 1.3 - + - -
155A LEU* 3.8 30.8 - - + +
156A PRO* 3.5 40.3 + - + +
286A TYR* 2.9 32.4 + - - -
287A LEU* 4.1 8.7 - - + +
328A GLN 2.9 18.3 + - - +
329A GLN 3.8 2.0 - - - +
331A THR* 1.3 76.6 - - - +
333A HIS* 1.3 64.1 + - - +
334A SER 3.1 1.0 + - - -
335A VAL* 3.2 21.5 - - + +
679B GLN* 4.8 4.7 - - + -
743B GLU* 5.1 3.0 + - + +
750B PHE* 4.5 13.5 - + - -
751B LEU* 3.3 33.2 - - + +
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Residues in contact with HIS 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A THR* 2.7 44.7 + - + +
127A PHE* 4.1 3.8 - + + -
160A HIS* 4.7 2.5 - + - -
329A GLN 2.9 18.4 + - - +
330A LEU* 3.5 8.3 - - - +
331A THR 3.2 0.2 - - - -
332A HIS* 1.3 79.1 - - - +
334A SER* 1.3 58.0 + - - +
335A VAL 3.6 0.2 - - - -
338A CYS* 3.5 29.6 - - - +
340A LEU* 3.9 15.2 - - + +
346A LEU* 4.0 17.9 - - + +
662B ARG* 3.5 26.9 + - - -
750B PHE* 3.9 18.2 - + - -
751B LEU* 3.7 15.3 - - + +
754B SER* 5.3 0.4 - - - -
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Residues in contact with SER 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A ASN* 3.9 8.5 - - - -
215A PRO* 3.3 13.1 - - - +
216A ILE* 3.2 35.1 + - - +
330A LEU 3.2 15.6 + - - -
331A THR 3.1 5.2 + - - -
332A HIS 3.1 0.6 - - - -
333A HIS* 1.3 76.4 - - - +
335A VAL* 1.3 59.2 + - - +
336A ASN* 3.2 3.8 - - - -
337A GLY* 2.8 21.3 + - - -
338A CYS 3.8 17.0 - - - -
340A LEU* 4.3 8.5 - - - -
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Residues in contact with VAL 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A PRO* 3.9 18.3 - - + +
216A ILE 6.1 0.2 - - - -
286A TYR* 3.7 28.5 - - + +
331A THR* 3.0 14.8 + - + +
332A HIS* 3.2 17.7 - - + +
334A SER* 1.3 77.3 - - - +
336A ASN* 1.3 60.7 + - - +
337A GLY 3.5 0.9 + - - -
677B MET* 3.5 24.4 + - - +
678B GLY* 4.5 7.2 - - - -
690B TYR* 3.6 34.3 + - + +
751B LEU* 3.7 16.2 - - + -
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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