Contacts of the helix formed by residues 320 - 329 (chain C) in PDB entry 2QPA
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 THR 320 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318C VAL 5.1 3.6 - - - +
319C LEU* 1.3 78.9 - - - +
321C LYS* 1.3 57.9 + - - +
322C GLU* 3.6 16.4 - - - +
323C ASP* 2.5 46.3 + - - +
324C TYR* 3.5 6.6 + - - -
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Residues in contact with LYS 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309C GLU* 5.1 4.7 - - - +
320C THR* 1.3 71.3 - - - +
322C GLU* 1.3 64.4 + - - +
324C TYR* 2.9 27.5 + - - +
325C ARG* 3.1 12.1 + - - +
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Residues in contact with GLU 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320C THR* 2.7 19.8 + - - +
321C LYS* 1.3 76.5 - - - +
323C ASP* 1.3 57.7 + - - +
325C ARG* 3.5 7.6 + - - +
326C THR* 2.6 31.0 + - - +
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Residues in contact with ASP 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318C VAL 4.7 1.0 - - - +
319C LEU* 3.6 33.3 - - + +
320C THR* 2.5 41.4 + - - +
322C GLU* 1.3 73.5 - - - +
324C TYR* 1.3 50.7 + - + +
326C THR* 3.0 14.0 + - - +
327C LEU* 2.7 36.1 + - - +
403C ILE* 4.2 14.8 - - + +
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Residues in contact with TYR 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305C THR* 3.4 19.2 + - + -
308C PHE* 3.3 44.5 + + + -
309C GLU* 3.4 44.5 + - + +
312C VAL* 3.7 23.2 - - + +
319C LEU* 5.2 18.0 - - + +
320C THR 3.5 6.8 + - - -
321C LYS* 2.9 22.3 + - - +
323C ASP* 1.3 73.7 - - + +
325C ARG* 1.3 52.8 + - - +
326C THR 2.7 4.3 - - - -
327C LEU* 2.4 34.9 + - + +
328C GLY 2.6 17.2 + - - -
406C PHE* 5.5 2.2 - + - -
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Residues in contact with ARG 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301C LEU* 4.7 11.7 - - + +
305C THR* 3.7 14.8 + - + +
321C LYS 3.1 7.3 + - - +
322C GLU* 3.8 10.1 - - - +
324C TYR* 1.3 78.3 - - - +
326C THR* 1.3 59.3 + - - +
328C GLY 4.3 0.3 - - - -
329C ALA* 3.4 21.0 + - - +
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Residues in contact with THR 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322C GLU* 2.6 20.7 + - - +
323C ASP* 3.0 19.4 + - - +
324C TYR 2.7 0.4 - - - -
325C ARG* 1.3 79.6 - - - +
327C LEU* 1.3 56.3 + - - +
329C ALA* 4.0 2.9 - - - -
330C MET* 3.0 42.1 - - + +
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Residues in contact with LEU 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308C PHE* 3.9 29.6 - - + -
319C LEU* 5.0 9.4 - - + -
323C ASP 2.7 11.5 + - - +
324C TYR* 2.4 35.1 + - + +
326C THR* 1.3 67.4 - - - +
328C GLY* 1.3 57.5 + - - +
329C ALA 2.9 1.6 - - - -
330C MET* 2.7 32.8 + - + +
331C THR* 3.3 7.8 + - - -
403C ILE* 5.3 7.4 - - + +
406C PHE* 4.0 41.1 - - + -
407C LEU* 5.2 6.7 - - + +
410C ILE* 3.5 31.9 - - + -
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Residues in contact with GLY 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301C LEU* 4.1 7.2 - - - -
304C ARG* 3.0 21.4 + - - -
305C THR* 3.1 33.9 - - - -
308C PHE* 4.3 2.7 - - - -
324C TYR 2.6 14.1 + - - -
327C LEU* 1.3 73.2 - - - +
329C ALA* 1.3 57.8 + - - +
331C THR* 2.8 20.8 + - - -
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Residues in contact with ALA 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301C LEU* 4.0 19.7 - - + +
304C ARG* 5.0 0.7 - - - +
325C ARG 3.4 18.7 + - - +
326C THR* 3.8 1.8 - - - +
327C LEU 2.9 0.4 - - - -
328C GLY* 1.3 79.9 - - - +
330C MET* 1.3 80.4 + - + +
331C THR 3.1 1.4 + - - -
332C GLU* 3.9 15.3 + - - +
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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