Contacts of the helix formed by residues 306 - 314 (chain H) in PDB entry 2PUQ
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 MET 306 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274H ALA 6.1 0.2 - - - +
275H PHE* 4.2 13.7 - - + -
305H LEU* 1.4 74.4 - - - +
307H THR* 1.3 68.1 + - - +
308H GLN 3.1 1.9 + - - -
309H ASP* 3.2 10.4 + - - +
310H CYS 3.2 15.6 + - - -
74T ARG* 3.8 29.8 - - - +
76T PHE* 3.9 7.9 - - - -
91T GLU* 3.1 51.1 - - + +
92T PRO* 3.5 19.5 - - + +
94T TYR* 3.3 42.8 - - + +
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Residues in contact with THR 307 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305H LEU 3.7 1.6 + - - -
306H MET* 1.3 72.4 - - - +
308H GLN* 1.3 56.5 + - - +
310H CYS* 3.4 8.0 - - + +
311H LEU* 2.8 47.7 + - + +
323H ILE* 3.9 36.3 - - + +
324H THR 4.9 1.0 + - - -
327H MET 4.5 1.0 + - - -
328H PHE* 4.8 4.0 - - - -
379H ARG* 3.7 16.8 + - - -
89T ALA* 3.7 24.1 - - + +
91T GLU* 2.8 22.0 + - - -
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Residues in contact with GLN 308 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306H MET* 3.1 1.4 + - - +
307H THR* 1.3 78.1 - - - +
309H ASP* 1.4 57.5 + - - +
311H LEU* 3.4 11.2 + - + +
312H GLN* 3.0 28.3 + - - +
86T THR* 4.1 12.7 + - + +
89T ALA* 5.7 0.2 - - - +
91T GLU* 4.6 0.8 + - - -
92T PRO 3.9 5.3 + - - -
93T LEU* 3.5 42.9 - - - +
94T TYR* 3.2 45.0 - - + +
95T GLU* 5.2 2.6 - - - +
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Residues in contact with ASP 309 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305H LEU* 4.0 13.6 - - + -
306H MET 3.2 12.1 + - - +
308H GLN* 1.4 74.1 - - - +
310H CYS* 1.3 64.4 + - - +
312H GLN* 3.1 5.6 + - - +
313H GLN* 2.9 48.0 + - - +
45T TRP* 5.6 1.2 - - - -
74T ARG* 3.9 13.7 + - - -
94T TYR* 2.6 25.5 + - - -
96T ASN* 3.0 27.6 + - - +
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Residues in contact with CYS 310 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305H LEU* 4.1 8.6 - - + +
306H MET 3.2 12.5 + - - +
307H THR* 3.4 17.0 - - + +
309H ASP* 1.3 73.8 - - - +
311H LEU* 1.3 63.9 + - + +
313H GLN 4.0 0.3 - - - -
314H SER* 2.7 39.2 + - - -
323H ILE* 4.8 7.9 - - + -
329H CYS* 2.2 54.5 - - + -
374H PHE* 4.1 11.0 - - - -
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Residues in contact with LEU 311 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307H THR* 2.8 40.3 + - + +
308H GLN* 3.7 9.9 - - + +
310H CYS* 1.3 75.7 - - + +
312H GLN* 1.3 59.9 + - - +
313H GLN 3.6 0.2 + - - -
314H SER* 3.8 14.0 + - - +
323H ILE* 4.6 21.1 - - + +
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Residues in contact with GLN 312 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308H GLN 3.0 17.1 + - - +
309H ASP* 3.1 9.2 + - - +
311H LEU* 1.3 77.7 - - - +
313H GLN* 1.3 64.0 + - + +
314H SER 4.6 1.9 - - - +
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Residues in contact with GLN 313 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305H LEU* 4.2 6.2 - - - +
309H ASP* 2.9 40.3 + - - +
312H GLN* 1.3 83.3 - - + +
314H SER* 1.3 60.5 + - - +
315H ARG* 3.8 2.3 + - - +
333H SER* 4.7 8.8 + - - +
372H GLY* 3.9 8.5 - - - +
374H PHE* 3.8 31.2 - - + -
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Residues in contact with SER 314 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310H CYS* 2.7 27.7 + - - -
311H LEU* 3.8 12.2 + - - +
312H GLN 3.5 2.5 - - - +
313H GLN* 1.3 79.0 - - - +
315H ARG* 1.3 69.6 + - - +
316H LYS* 3.6 2.3 + - - -
372H GLY 3.2 11.6 + - - -
373H HIS* 4.6 8.7 - - - -
374H PHE* 3.9 16.5 + - - -
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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