Contacts of the helix formed by residues 326 - 333 (chain J) in PDB entry 2QC8
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 PRO 326 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61I ASN* 5.9 1.1 - - - +
76I ASP* 3.7 7.4 - - - +
255J ASN* 5.1 0.4 - - - +
324J ARG* 3.5 36.0 - - + +
325J ILE* 1.3 87.0 - - + +
327J ARG* 1.3 67.2 + - - +
328J THR* 3.2 7.2 - - - +
329J VAL* 3.0 21.6 + - + +
330J GLY* 3.1 8.7 + - - -
336J TYR* 3.8 47.1 - - + +
337J PHE* 4.5 1.8 - - - -
338J GLU* 5.0 4.5 - - + -
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Residues in contact with ARG 327 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61I ASN* 6.5 0.7 - - + -
74I ASN* 2.8 31.9 + - - +
76I ASP* 3.0 52.0 + - + +
78I TYR* 3.1 41.4 - - + +
104I TYR* 3.4 30.7 + - - +
316J VAL* 4.2 17.9 - - + +
317J ALA* 3.4 19.1 - - + +
325J ILE 3.6 1.4 + - - -
326J PRO* 1.3 69.5 - - - +
328J THR* 1.3 65.2 + - - +
330J GLY* 3.0 2.3 + - - -
331J GLN* 2.8 36.6 + - + +
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Residues in contact with THR 328 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61I ASN* 4.7 11.5 + - - +
78I TYR* 5.6 7.6 - - - -
326J PRO* 3.2 5.5 - - - +
327J ARG* 1.3 78.4 - - - +
329J VAL* 1.3 65.2 + - + +
331J GLN* 3.4 4.7 + - - +
332J GLU* 2.9 57.5 + - - +
334J LYS 5.7 0.4 - - - +
336J TYR* 6.1 2.2 - - + -
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Residues in contact with VAL 329 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267J LEU* 4.4 5.7 - - + +
270J ILE* 3.7 19.5 - - + -
325J ILE* 3.9 13.0 - - + -
326J PRO* 3.0 19.7 + - + +
328J THR* 1.3 81.8 - - + +
330J GLY* 1.3 57.5 + - - +
333J LYS* 2.9 26.9 + - - -
334J LYS 3.1 25.7 + - - +
335J GLY* 4.2 2.5 - - - -
336J TYR* 3.3 49.4 - - + +
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Residues in contact with GLY 330 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267J LEU* 4.4 10.7 - - - +
316J VAL* 4.8 11.9 - - - -
325J ILE* 4.0 10.8 - - - +
326J PRO 3.1 8.1 + - - -
327J ARG 3.0 7.1 + - - -
329J VAL* 1.3 76.7 - - - +
331J GLN* 1.3 65.7 + - - +
333J LYS* 3.8 14.7 + - - +
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Residues in contact with GLN 331 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78I TYR* 3.8 22.0 + - + +
104I TYR 5.4 3.0 + - - -
327J ARG* 2.8 34.0 + - + +
328J THR* 3.8 5.8 - - - +
330J GLY* 1.3 76.0 - - - +
332J GLU* 1.3 65.6 + - + +
333J LYS* 3.6 10.0 + - - +
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Residues in contact with GLU 332 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264J GLU* 5.3 3.5 - - - +
265J ASN 5.3 1.4 + - - -
328J THR* 2.9 42.5 + - - +
331J GLN* 1.3 80.3 - - + +
333J LYS* 1.3 70.4 + - - +
334J LYS* 3.3 40.0 + - + +
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Residues in contact with LYS 333 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265J ASN* 3.2 30.0 - - - +
266J GLY 3.1 9.2 + - - -
267J LEU* 2.9 42.8 + - + -
329J VAL 2.9 11.8 + - - -
330J GLY 3.8 12.5 + - - +
331J GLN 3.4 9.4 - - - +
332J GLU* 1.3 78.5 - - - +
334J LYS* 1.3 57.2 + - - +
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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