Contacts of the helix formed by residues 346 - 353 (chain A) in PDB entry 6Q6Q
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 346 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145A GLY* 4.6 1.1 - - - -
146A GLY* 3.9 25.1 - - - -
345A ALA* 1.3 81.6 - - - +
347A SER* 1.3 66.2 + - - -
348A GLN* 3.2 4.9 + - - -
349A ILE* 3.4 6.0 + - - +
350A ARG* 3.0 33.3 + - - +
436A ASN* 4.3 3.0 + - - -
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Residues in contact with SER 347 (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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70A PRO* 3.8 11.7 - - - +
128A LEU* 6.1 0.3 - - - +
142A ASP 3.9 13.6 + - - -
143A ALA* 3.9 28.5 - - - +
146A GLY 4.5 1.6 - - - +
346A GLY* 1.3 73.4 - - - -
348A GLN* 1.3 65.8 + - - +
350A ARG* 3.6 18.0 + - - +
351A ASN* 2.7 43.4 + - - +
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Residues in contact with GLN 348 (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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47A GLY 5.0 2.6 - - - +
53A THR* 3.7 12.6 - - + +
70A PRO* 4.0 24.3 - - + +
71A ALA* 4.0 2.7 - - - +
72A ASN* 3.2 40.4 + - - +
124A SER* 3.6 6.9 + - - -
143A ALA 3.5 21.2 + - - -
146A GLY* 3.5 25.5 - - - +
147A ASN* 3.1 25.5 + - - -
346A GLY* 4.3 1.6 - - - -
347A SER* 1.3 77.9 + - - +
349A ILE* 1.3 64.5 + - - +
351A ASN* 3.2 4.2 + - - +
352A MET* 3.2 27.9 + - - +
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Residues in contact with ILE 349 (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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47A GLY 3.4 22.4 - - - +
72A ASN* 3.3 15.9 - - - +
75A LEU* 4.1 10.5 - - + -
269A THR* 3.9 20.2 - - + -
344A LEU* 5.2 3.1 - - + -
345A ALA* 4.0 24.9 - - + -
346A GLY* 3.4 5.3 + - - +
348A GLN* 1.3 77.3 + - - +
350A ARG* 1.3 57.7 + - - +
352A MET* 3.9 5.8 - - - +
353A ALA* 2.8 35.0 + - + +
3003A FAD 3.8 45.5 - - + -
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Residues in contact with ARG 350 (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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142A ASP* 3.9 20.8 + - - +
311A SER* 3.5 0.5 - - - -
312A LEU* 3.3 19.5 + - + +
313A ALA* 3.1 36.1 + - + +
316A LYS* 4.3 17.8 - - - +
341A LEU* 3.3 23.6 + - - -
342A GLY 3.7 17.4 + - - -
344A LEU* 2.6 59.8 + - + +
345A ALA 3.4 14.6 + - - -
346A GLY* 3.0 15.1 + - - +
347A SER* 3.6 24.9 - - - +
349A ILE* 1.3 78.3 - - - +
351A ASN* 1.3 60.1 + - - +
352A MET 3.4 0.7 + - - -
353A ALA* 3.5 5.2 - - - +
435A GLU* 5.6 0.6 + - - -
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Residues in contact with ASN 351 (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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67A ARG* 4.4 12.6 + - - -
69A HIS* 3.5 39.3 + - - +
70A PRO* 3.5 28.6 - - - +
311A SER* 3.8 14.0 + - - -
313A ALA* 3.6 22.6 - - - +
314A GLN* 5.8 0.3 - - - +
347A SER* 2.7 40.2 + - - +
348A GLN 3.2 1.1 + - - +
350A ARG* 1.3 75.1 - - - +
352A MET* 1.3 59.3 + - - +
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Residues in contact with MET 352 (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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69A HIS* 4.7 3.1 - - + -
71A ALA* 3.7 16.8 - - + -
72A ASN* 3.5 39.0 - - - +
75A LEU* 4.0 15.5 - - + +
76A ILE* 3.7 25.6 - - + -
266A MET 4.5 1.0 - - - -
267A GLY* 3.2 42.0 + - - +
269A THR* 3.9 8.7 - - + -
311A SER* 4.8 1.9 - - - -
348A GLN 3.3 14.1 - - - +
349A ILE* 3.2 9.3 + - - +
351A ASN* 1.3 80.8 - - - +
353A ALA* 1.3 66.8 + - - +
354A SER* 3.5 1.9 + - - -
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Residues in contact with ALA 353 (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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269A THR* 3.5 11.3 - - - +
311A SER* 3.1 8.0 - - - -
312A LEU* 3.0 36.1 + - + -
349A ILE* 2.8 23.0 + - + +
350A ARG 3.5 0.5 - - - +
352A MET* 1.3 74.3 - - - +
354A SER* 1.3 58.8 + - - +
3003A FAD 3.5 41.1 - - - +
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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