Contacts of the helix formed by residues 323 - 333 (chain A) in PDB entry 1QCY
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 ILE 323 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A PHE* 4.1 10.8 - - + -
279A ILE* 3.9 28.9 - - + -
312A PHE* 3.7 36.6 - - + -
313A ASN 5.9 1.1 - - - +
314A VAL* 4.1 26.2 - - + -
319A ALA 4.7 0.9 - - - +
320A LEU* 3.1 18.8 - - + +
322A THR* 1.3 86.6 - - - +
324A VAL* 1.3 56.8 + - - +
325A LYS 3.3 2.9 - - - -
326A THR* 3.1 8.3 + - - +
327A LEU* 2.7 38.2 + - + +
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Residues in contact with VAL 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A PHE* 3.8 42.4 - - + +
167A ASP* 3.6 36.8 - - + +
168A LEU* 3.8 11.4 - - + +
171A ARG* 3.0 22.7 + - - +
321A VAL* 3.6 18.6 - - - +
322A THR 3.5 1.2 - - - -
323A ILE* 1.3 78.7 - - - +
325A LYS* 1.3 58.3 + - - +
327A LEU* 4.6 3.8 - - - -
328A GLY* 2.7 25.6 + - - -
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Residues in contact with LYS 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ARG* 2.9 28.6 + - - +
322A THR 5.0 3.2 + - - +
323A ILE 3.3 0.8 - - - -
324A VAL* 1.3 77.7 - - - +
326A THR* 1.3 64.1 + - - +
328A GLY* 3.3 0.3 + - - -
329A GLU* 2.9 51.4 + - - +
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Residues in contact with THR 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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312A PHE* 4.0 11.2 - - + -
322A THR 5.2 2.6 + - - -
323A ILE* 3.1 10.9 + - - -
325A LYS* 1.3 80.2 - - - +
327A LEU* 1.3 66.4 + - - +
329A GLU* 3.3 14.0 + - + +
330A ARG* 2.9 67.7 + - + +
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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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164A PHE* 4.0 21.8 - - + -
168A LEU* 3.9 27.1 - - + -
249A VAL* 4.3 10.3 - - + -
277A PHE* 3.6 42.4 - - + -
279A ILE* 4.3 7.6 - - + -
312A PHE* 4.0 21.7 - - + -
323A ILE* 2.7 24.7 + - + +
324A VAL* 4.1 2.0 - - - +
326A THR* 1.3 71.1 - - - +
328A GLY* 1.3 65.4 + - - +
330A ARG* 3.0 3.4 + - - +
331A ILE* 2.8 41.9 + - + +
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Residues in contact with GLY 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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168A LEU* 3.8 15.9 - - - +
171A ARG* 4.4 6.1 - - - -
172A MET* 6.1 0.2 - - - -
324A VAL 2.7 24.5 + - - -
325A LYS 3.6 0.7 - - - -
327A LEU* 1.3 76.7 - - - +
329A GLU* 1.3 60.9 + - - +
330A ARG 3.3 0.2 + - - -
331A ILE* 3.3 4.5 + - - +
332A PHE* 3.1 30.5 - - - -
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Residues in contact with GLU 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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171A ARG* 5.1 0.6 - - - +
325A LYS* 2.9 45.6 + - - +
326A THR* 3.3 19.2 + - - +
328A GLY* 1.3 72.6 - - - -
330A ARG* 1.3 55.4 + - + +
332A PHE* 4.7 3.6 - - - +
333A ALA* 2.7 41.1 + - + +
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Residues in contact with ARG 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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275A GLN* 5.0 3.6 + - - -
277A PHE* 3.9 19.8 - - + -
308A GLU 3.7 6.9 + - - -
309A LYS* 2.9 73.4 + - + +
311A PHE 5.0 0.8 + - - -
312A PHE* 3.4 23.1 - - - -
326A THR* 2.9 42.7 + - + +
327A LEU* 3.0 3.6 + - - +
329A GLU* 1.3 78.2 - - + +
331A ILE* 1.3 64.5 + - - +
332A PHE 3.0 1.3 - - - -
333A ALA 2.7 23.6 - - - +
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Residues in contact with ILE 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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143A LEU* 3.7 18.2 - - + +
145A ILE* 3.7 32.1 - - + -
168A LEU* 4.4 15.5 - - + -
172A MET* 5.1 2.9 - - + -
247A VAL* 4.2 13.5 - - + +
249A VAL* 4.2 18.4 - - + -
275A GLN* 4.4 9.5 - - - +
277A PHE* 3.9 17.5 - - + -
327A LEU* 2.8 52.3 + - + +
328A GLY* 3.7 5.4 - - - +
330A ARG* 1.3 76.5 - - - +
332A PHE* 1.3 67.9 + - + +
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Residues in contact with PHE 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A LEU* 3.8 21.6 - - + +
145A ILE* 4.6 2.7 - - + -
171A ARG 5.4 2.2 - - - -
172A MET* 3.8 42.2 - - + -
173A ASP 6.1 0.2 - - - -
179A THR* 3.7 23.1 - - - -
328A GLY* 3.1 28.8 + - - +
329A GLU* 4.2 2.7 - - - +
330A ARG 3.0 0.4 - - - -
331A ILE* 1.3 92.3 - - + +
333A ALA* 1.3 62.1 + - + +
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Residues in contact with ALA 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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329A GLU* 2.7 25.3 + - + +
330A ARG* 2.7 28.6 - - - +
332A PHE* 1.3 76.1 - - + +
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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