Contacts of the helix formed by residues 300 - 311 (chain A) in PDB entry 3CKM
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 SER 300 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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299A ASN* 1.3 76.8 - - - +
301A VAL* 1.3 64.6 + - - +
302A GLN* 3.7 9.1 + - - +
303A ASP* 3.0 26.8 + - - +
304A ILE* 2.9 23.2 + - - +
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Residues in contact with VAL 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A LEU* 4.9 7.9 - - + -
296A THR* 5.0 8.3 - - + -
299A ASN 3.8 1.2 + - - +
300A SER* 1.3 72.4 - - - +
302A GLN* 1.3 64.2 + - - +
304A ILE* 3.2 8.5 + - - +
305A ILE* 3.0 44.3 + - + +
319A PRO* 4.7 6.7 - - + -
324A ASN* 3.7 45.5 - - + +
327A VAL* 3.9 26.6 - - + +
328A ILE* 4.1 15.9 - - + -
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Residues in contact with GLN 302 (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 SER* 3.2 7.8 + - - +
301A VAL* 1.3 80.4 - - - +
303A ASP* 1.3 63.0 + - - +
305A ILE* 3.5 2.9 + - - +
306A ALA* 3.2 20.6 + - - +
327A VAL* 4.4 9.8 - - + +
334A GLN* 3.7 24.6 - - - +
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Residues in contact with ASP 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A ASN* 3.9 12.1 + - + +
300A SER* 3.0 26.6 + - - +
302A GLN* 1.3 74.9 - - - +
304A ILE* 1.3 65.7 + - - +
306A ALA* 3.2 9.7 + - - +
307A GLN* 2.9 50.2 + - - +
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Residues in contact with ILE 304 (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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262A LEU* 3.7 23.3 - - + -
294A PHE* 3.6 42.1 - - + -
295A ASP 4.1 4.5 - - - +
296A THR* 3.8 31.6 - - + -
299A ASN* 3.7 29.2 - - + +
300A SER 2.9 22.3 + - - +
301A VAL* 3.6 6.5 - - - +
303A ASP* 1.3 77.0 - - - +
305A ILE* 1.3 64.0 + - - +
307A GLN* 3.1 10.2 + - - +
308A ALA* 2.8 22.7 + - + +
316A LEU* 6.0 0.2 - - + -
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Residues in contact with ILE 305 (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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262A LEU* 5.0 5.4 - - + -
301A VAL* 3.0 36.9 + - + +
302A GLN 3.9 4.0 - - - +
304A ILE* 1.3 75.0 - - - +
306A ALA* 1.3 58.6 + - - +
308A ALA* 3.2 6.7 + - - +
309A LYS* 2.9 34.2 + - - +
316A LEU* 4.4 13.5 - - + -
328A ILE* 4.1 8.5 - - + -
334A GLN* 3.7 46.9 - - + +
335A ILE* 3.8 20.6 - - + -
338A MSE 4.0 19.1 - - - -
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Residues in contact with ALA 306 (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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302A GLN 3.2 12.9 + - - +
303A ASP* 3.2 15.6 + - - +
304A ILE 3.2 0.2 - - - -
305A ILE* 1.3 76.3 - - - +
307A GLN* 1.3 61.0 + - - +
309A LYS* 3.5 9.6 + - - +
310A GLN* 3.1 43.8 + - - +
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Residues in contact with GLN 307 (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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292A GLN* 4.6 5.1 + - - +
294A PHE* 3.7 26.4 - - + -
299A ASN* 3.8 22.8 + - - +
303A ASP* 2.9 40.4 + - - +
304A ILE* 3.5 10.5 - - - +
306A ALA* 1.3 75.5 - - + +
308A ALA* 1.3 63.7 + - - +
310A GLN* 3.3 6.4 + - - +
311A ALA* 3.1 23.0 + - - +
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Residues in contact with ALA 308 (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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294A PHE* 4.2 18.1 - - + -
304A ILE* 2.8 17.2 + - + +
305A ILE* 3.6 6.3 - - - +
307A GLN* 1.3 77.8 - - - +
309A LYS* 1.3 63.9 + - - +
311A ALA* 3.1 8.0 + - - +
313A ILE* 3.0 36.5 + - + +
316A LEU* 4.0 27.6 - - + -
338A MSE 4.3 4.7 - - + -
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Residues in contact with LYS 309 (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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305A ILE* 2.9 27.4 + - + +
306A ALA* 3.7 8.3 - - - +
308A ALA* 1.3 76.4 - - - +
310A GLN* 1.3 61.9 + - + +
312A GLY* 3.0 19.8 + - - -
313A ILE 4.1 6.9 + - - +
333A ALA 4.9 1.0 + - - -
334A GLN* 2.7 40.3 + - - +
336A GLN 4.7 8.9 + - - -
338A MSE 4.2 20.2 - - + -
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Residues in contact with GLN 310 (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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306A ALA* 3.1 30.9 + - - +
307A GLN* 3.3 4.9 + - - +
308A ALA 3.2 0.2 - - - -
309A LYS* 1.3 79.0 - - + +
311A ALA* 1.3 57.7 + - - +
312A GLY 3.2 1.2 + - - -
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Residues in contact with ALA 311 (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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258A GLN* 3.1 20.0 + - - +
292A GLN* 4.0 20.9 - - - +
307A GLN 3.1 11.8 + - - +
308A ALA* 3.1 10.6 + - - +
310A GLN* 1.3 77.2 - - - +
312A GLY* 1.3 57.3 + - - +
313A ILE* 4.2 8.5 - - + -
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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