Contacts of the helix formed by residues 326 - 333 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316A VAL* 4.6 0.2 - - - +
324A ARG* 3.6 29.4 - - + +
325A ILE* 1.3 86.2 - - + +
327A ARG* 1.3 68.5 + - - +
328A THR* 3.2 6.7 - - - +
329A VAL* 3.0 19.0 + - + +
330A GLY* 3.1 8.7 + - - -
336A TYR* 3.6 51.8 - - + +
337A PHE* 4.5 0.7 - - - -
338A GLU* 5.0 4.7 - - + -
61E ASN* 6.1 1.1 - - - +
76E ASP* 3.7 11.9 - - - +
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Residues in contact with ARG 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A VAL* 4.3 16.8 - - + +
317A ALA* 3.6 18.1 - - + +
325A ILE 3.7 1.2 + - - -
326A PRO* 1.3 69.8 - - - +
328A THR* 1.3 65.1 + - - +
330A GLY* 2.9 13.0 + - - -
331A GLN* 3.0 30.3 + - + +
61E ASN* 6.5 0.2 - - - -
74E ASN* 2.9 35.1 + - - +
76E ASP* 2.9 54.2 + - + +
77E MET 6.0 0.2 - - - -
78E TYR* 3.5 37.8 - - + +
104E TYR* 3.6 30.5 + - - +
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Residues in contact with THR 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A PRO* 3.1 5.4 + - - +
327A ARG* 1.3 78.0 - - - +
329A VAL* 1.3 64.0 + - + +
331A GLN* 3.5 6.2 + - - +
332A GLU* 2.9 55.2 + - - +
336A TYR* 6.1 2.5 - - + -
61E ASN* 4.1 15.2 + - - +
76E ASP* 5.0 0.2 + - - -
78E TYR* 5.4 9.1 - - - -
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Residues in contact with VAL 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A LEU* 4.4 4.6 - - + +
270A ILE* 3.7 15.9 - - + -
325A ILE* 3.9 11.7 - - + -
326A PRO* 3.0 18.9 + - + +
328A THR* 1.3 80.9 - - + +
330A GLY* 1.3 59.0 + - - +
333A LYS* 2.9 27.5 + - - -
334A LYS 3.3 28.4 + - - +
335A GLY* 4.3 0.7 - - - -
336A TYR* 3.5 51.4 - - + +
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Residues in contact with GLY 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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267A LEU* 4.1 12.8 - - - +
316A VAL* 5.1 11.9 - - - -
325A ILE* 4.0 9.5 - - - +
326A PRO 3.1 8.5 + - - -
327A ARG* 2.9 8.0 + - - -
329A VAL* 1.3 78.1 - - - +
331A GLN* 1.3 64.7 + - - +
333A LYS* 3.6 18.2 - - - +
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Residues in contact with GLN 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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327A ARG* 3.0 29.1 + - + +
328A THR* 3.7 8.3 - - - +
330A GLY* 1.3 80.1 - - - +
332A GLU* 1.3 64.0 + - + +
333A LYS* 3.2 11.8 + - - +
78E TYR* 4.1 20.7 + - - +
106E ARG* 5.6 4.0 + - - +
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Residues in contact with GLU 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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264A GLU* 4.2 8.7 - - - +
328A THR* 2.9 40.8 + - - +
331A GLN* 1.3 76.9 - - + +
333A LYS* 1.3 71.0 + - - +
334A LYS* 3.1 42.8 + - + +
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Residues in contact with LYS 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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264A GLU* 5.9 0.2 - - - +
265A ASN* 3.0 31.0 - - - +
266A GLY 3.0 19.9 + - - -
267A LEU* 3.1 28.0 + - + +
329A VAL 2.9 11.6 + - - -
330A GLY 3.6 14.6 - - - +
331A GLN 3.2 10.1 - - - +
332A GLU* 1.3 79.8 - - - +
334A LYS* 1.3 57.0 + - - +
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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