Contacts of the helix formed by residues 342 - 350 (chain A) in PDB entry 1QQT
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 LYS 342 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A SER* 3.7 32.1 - - - -
20A ILE 3.6 8.7 - - - +
21A HIS* 3.9 2.2 - - + +
22A LEU* 4.8 0.4 - - - -
340A PHE* 4.0 23.5 + - + +
341A ILE* 1.3 81.4 - - - +
343A ALA* 1.3 66.7 + - - +
344A SER* 3.3 16.5 + - - +
345A THR* 3.1 23.5 + - - +
346A TRP* 3.0 18.4 + - - +
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Residues in contact with ALA 343 (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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20A ILE* 2.9 23.3 + - + +
21A HIS* 3.8 3.2 - - - +
22A LEU* 4.5 5.2 - - - -
25A MET* 4.1 14.8 - - + -
83A ASP* 4.0 21.3 - - + +
87A PHE* 3.7 23.0 - - + -
342A LYS* 1.3 70.4 - - - +
344A SER* 1.3 64.3 + - - +
346A TRP* 3.2 8.0 + - - +
347A LEU* 3.2 26.0 + - - +
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Residues in contact with SER 344 (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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19A SER* 6.1 0.2 - - - -
79A GLU* 6.3 2.2 - - - -
83A ASP* 3.5 25.7 + - - -
342A LYS* 3.7 20.8 + - - +
343A ALA* 1.3 78.1 - - - +
345A THR* 1.3 63.9 + - - +
347A LEU* 3.4 15.3 + - - +
348A ASN* 3.4 20.2 + - - +
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Residues in contact with THR 345 (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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341A ILE* 4.6 0.7 - - - -
342A LYS* 3.1 38.2 + - - +
344A SER* 1.3 75.8 + - - +
346A TRP* 1.3 66.6 + - - +
348A ASN* 3.0 20.5 + - - +
349A HIS* 3.1 29.7 + - + -
542A LEU* 3.9 17.3 - - + -
545A ALA* 4.5 9.4 - - + +
546A SER* 3.9 17.3 - - - +
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Residues in contact with TRP 346 (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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22A LEU* 3.9 35.2 - - + -
87A PHE* 3.4 24.4 - + + -
341A ILE* 4.3 1.7 - - + +
342A LYS 3.0 11.9 + - - +
343A ALA 3.5 8.3 - - - +
345A THR* 1.3 77.2 - - - +
347A LEU* 1.3 59.3 + - + +
349A HIS* 3.0 5.9 + - - +
350A PHE* 2.8 43.0 + + + +
351A ASP 3.2 21.8 + - - -
354A SER* 3.7 8.5 - - - -
355A LEU* 3.7 25.0 - - + +
372A LEU* 4.8 6.7 - - + -
374A LEU* 4.9 6.5 - - + -
377A PHE* 3.3 46.0 - + - -
542A LEU* 3.7 39.4 - - + +
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Residues in contact with LEU 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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82A THR 5.2 0.7 - - - +
83A ASP* 4.3 9.2 - - - +
86A GLY* 3.9 39.0 - - - +
87A PHE* 3.8 30.5 - - + -
343A ALA 3.2 15.0 + - - +
344A SER* 3.8 11.0 - - - +
345A THR 3.2 0.4 - - - -
346A TRP* 1.3 78.1 - - + +
348A ASN* 1.3 63.6 + - - +
349A HIS 3.2 0.2 - - - -
350A PHE 3.4 18.8 + - - +
351A ASP* 4.9 0.7 - - - -
352A ALA* 4.1 14.8 - - + +
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Residues in contact with ASN 348 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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344A SER 3.4 15.7 + - - +
345A THR* 3.0 17.0 + - - +
347A LEU* 1.3 80.8 + - - +
349A HIS* 1.3 72.4 + - + +
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Residues in contact with HIS 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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345A THR* 3.1 21.5 + - + -
346A TRP 3.0 3.6 + - - +
347A LEU 4.7 0.2 - - - -
348A ASN* 1.3 92.9 - - + +
350A PHE* 1.3 87.7 + - + +
538A GLN* 3.7 19.1 + - + +
541A ALA* 3.7 25.0 + - + +
542A LEU* 3.5 29.1 - - + +
545A ALA* 3.7 22.9 - - + +
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Residues in contact with PHE 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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346A TRP* 2.8 58.5 + + + +
347A LEU* 3.4 19.1 - - - +
349A HIS* 1.3 88.7 - - + +
351A ASP* 1.3 64.8 + - - +
354A SER* 3.9 4.3 - - - +
377A PHE* 4.2 15.5 - + - -
534A ILE* 4.3 19.1 - - + -
538A GLN* 3.7 46.0 - - + -
539A VAL* 3.7 24.7 - - + -
542A LEU* 3.9 22.0 - - + -
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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