Contacts of the helix formed by residues 326 - 337 (chain A) in PDB entry 5T0I
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 326 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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278A ASP 5.2 1.6 - - - +
281A GLY* 2.3 38.2 + - - +
282A GLY* 4.1 4.9 - - - -
283A ALA* 3.2 29.0 - - + +
324A PRO 3.6 0.8 - - - +
325A ASP* 1.3 90.7 + - + +
327A LEU* 1.3 70.9 + - - +
328A ASP 3.4 0.2 - - - -
329A PRO* 3.1 19.2 - - - +
330A ALA* 3.2 23.4 + - - +
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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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283A ALA* 4.9 1.5 - - + +
325A ASP* 5.9 2.0 - - + -
326A THR* 1.3 80.9 - - + +
328A ASP* 1.3 58.6 + - - +
330A ALA* 3.1 6.7 + - - +
331A LEU* 2.8 41.4 + - + +
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Residues in contact with ASP 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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283A ALA* 4.0 12.4 - - + +
284A ARG* 4.2 20.1 + - + -
299A MET* 3.4 13.6 - - + +
300A LEU* 3.3 27.0 - - - +
326A THR* 4.2 0.8 + - - -
327A LEU* 1.3 78.8 - - - +
329A PRO* 1.3 67.8 - - + +
331A LEU* 3.3 20.4 + - + +
332A MET* 3.1 38.1 + - - +
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Residues in contact with PRO 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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277A ILE* 4.8 14.4 - - + -
281A GLY* 4.2 7.6 - - - +
299A MET* 3.7 26.2 - - + -
303A ILE* 4.7 21.7 - - + +
325A ASP 5.8 0.4 - - - +
326A THR* 3.1 37.2 - - - +
328A ASP* 1.3 91.4 - - + +
330A ALA* 1.3 58.6 + - - +
332A MET* 4.0 7.1 - - + +
333A ARG* 3.3 26.1 + - - +
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Residues in contact with ALA 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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324A PRO* 4.1 13.7 - - + +
326A THR 3.2 19.1 + - - +
327A LEU* 3.1 9.5 + - - +
329A PRO* 1.3 79.7 - - - +
331A LEU* 1.3 58.3 + - - +
333A ARG* 3.2 30.2 + - - +
334A PRO* 3.1 21.3 - - - +
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Residues in contact with LEU 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 LEU* 2.8 31.6 + - + +
328A ASP* 3.4 25.1 - - + +
330A ALA* 1.3 71.1 - - - +
332A MET* 1.3 77.0 + - + +
334A PRO* 3.3 14.5 - - - +
335A GLY 4.6 2.3 + - - -
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Residues in contact with MET 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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300A LEU* 6.1 1.3 - - + -
303A ILE* 3.9 22.9 - - + -
307A ASP* 3.3 29.8 - - - +
328A ASP* 3.1 32.0 + - - +
329A PRO* 4.0 6.3 - - + +
330A ALA 3.4 0.2 - - - -
331A LEU* 1.3 91.3 - - + +
333A ARG* 1.3 63.7 + - - +
335A GLY* 3.4 12.1 + - - -
336A ARG* 3.8 8.5 + - - +
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Residues in contact with ARG 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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213A LEU* 3.3 37.3 - - - +
215A PHE* 4.9 7.1 - - - -
303A ILE* 5.7 4.0 - - + +
324A PRO* 6.1 2.4 - - - +
329A PRO 3.3 12.9 + - - +
330A ALA* 3.2 37.4 + - - +
332A MET* 1.3 76.8 - - - +
334A PRO* 1.3 64.5 - - + +
336A ARG 2.8 3.5 + - - -
337A LEU* 2.4 66.9 + - + +
338A ASP* 6.2 1.4 - - - +
340A LYS* 3.2 47.7 - - - +
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Residues in contact with PRO 334 (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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330A ALA 3.1 21.8 - - - +
331A LEU* 3.3 17.3 - - - +
333A ARG* 1.3 100.7 - - + +
335A GLY* 1.3 59.7 + - - +
336A ARG 3.4 0.7 + - - -
337A LEU 3.8 11.6 - - - +
340A LYS* 5.3 8.5 - - - +
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Residues in contact with GLY 335 (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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331A LEU 4.6 2.2 + - - -
332A MET 3.4 8.4 + - - -
333A ARG 3.1 1.4 - - - -
334A PRO* 1.3 79.1 - - - +
336A ARG* 1.3 59.4 + - - +
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Residues in contact with ARG 336 (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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210A LYS* 2.5 57.5 + - + +
211A GLY* 4.1 1.2 - - - -
306A LEU* 2.3 38.5 + - - +
307A ASP* 3.5 27.3 - - - +
308A GLY 4.6 1.6 + - - +
312A ARG* 2.6 54.8 + - - +
317A VAL* 4.2 7.5 - - - +
332A MET 3.8 4.4 + - - +
333A ARG 2.8 4.4 + - - +
334A PRO 4.8 0.2 - - - +
335A GLY* 1.3 79.9 - - - +
337A LEU* 1.3 95.9 + - + +
338A ASP* 5.0 0.7 - - - +
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Residues in contact with LEU 337 (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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211A GLY* 3.8 14.1 - - - +
212A VAL 3.2 31.6 - - - +
213A LEU* 5.3 3.1 - - + -
303A ILE* 5.7 6.5 - - + -
306A LEU* 4.4 14.1 - - + -
307A ASP* 5.5 0.9 - - - +
317A VAL* 5.4 1.6 - - + -
319A MET* 4.2 16.2 - - + -
333A ARG* 2.4 53.1 + - + +
334A PRO* 3.8 12.0 - - - +
336A ARG* 1.3 118.1 - - + +
338A ASP* 1.3 66.0 + - - +
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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