Contacts of the helix formed by residues 292 - 301 (chain A) in PDB entry 3K5N
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 292 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A TRP* 4.3 1.3 - - - +
290A SER* 3.3 12.6 + - - -
291A PHE* 1.3 77.9 - - - +
293A LEU* 1.3 60.9 + - - +
294A GLU* 3.7 19.8 - - - +
295A THR* 3.1 24.9 + - - -
296A VAL* 2.3 35.7 + - - +
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Residues in contact with LEU 293 (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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156A ASP* 5.4 2.9 - - - +
223A TRP* 3.7 38.6 - - + +
292A SER* 1.3 69.1 - - - +
294A GLU* 1.3 81.4 + - - +
296A VAL* 3.9 2.5 - - - -
297A ALA* 3.1 26.5 + - + +
335A ASN* 3.9 35.9 - - + +
338A LEU* 4.0 23.4 - - + +
339A VAL* 4.0 11.4 - - + +
342A ILE* 3.7 29.8 - - + -
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Residues in contact with GLU 294 (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 SER* 3.7 18.2 - - - +
293A LEU* 1.3 90.2 + - - +
295A THR* 1.3 63.2 + - - +
297A ALA* 3.9 2.7 - - - +
298A GLN* 3.6 21.5 + - - +
303A GLU* 5.5 0.9 - - - +
304A GLY 5.4 3.8 - - - -
311A TRP* 5.7 13.5 - - + +
338A LEU* 5.8 2.4 - - - +
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Residues in contact with THR 295 (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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288A PHE* 4.6 0.2 - - + -
289A SER* 4.0 6.5 + - - +
290A SER* 3.6 27.1 - - - +
292A SER* 3.1 20.5 + - - -
294A GLU* 1.3 81.7 - - - +
296A VAL* 1.3 67.2 + - - +
298A GLN* 3.1 10.7 + - - +
299A GLU* 2.9 50.5 + - + +
311A TRP* 5.5 6.6 + - - -
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Residues in contact with VAL 296 (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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223A TRP* 3.7 33.2 - - + -
281A LEU* 4.6 2.7 - - + -
288A PHE* 3.6 37.8 - - + -
290A SER 4.2 1.6 - - - +
291A PHE* 3.7 14.8 - - - -
292A SER 2.3 40.2 + - - +
293A LEU* 3.9 2.2 - - - +
295A THR* 1.3 74.0 - - - +
297A ALA* 1.3 68.0 - - - +
298A GLN 3.2 0.5 + - - -
299A GLU* 3.3 3.3 + - - +
300A LEU* 3.1 30.2 + - + +
342A ILE* 4.6 6.7 - - + -
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Residues in contact with ALA 297 (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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293A LEU* 3.1 17.3 + - + +
294A GLU* 3.9 3.8 - - - +
296A VAL* 1.3 81.5 - - - +
298A GLN* 1.3 51.3 + - - +
301A LEU* 2.5 44.6 + - + +
303A GLU* 4.4 7.9 - - + -
338A LEU* 3.8 34.3 - - + -
342A ILE* 4.1 15.2 - - + +
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Residues in contact with GLN 298 (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 GLU 3.6 11.0 + - - +
295A THR* 3.1 12.0 + - - +
296A VAL 3.1 0.6 - - - -
297A ALA* 1.3 79.6 - - - +
299A GLU* 1.3 60.9 + - + +
300A LEU 3.0 5.2 - - - -
302A GLY* 3.6 12.5 + - - -
303A GLU* 2.2 62.0 + - + +
304A GLY* 3.2 18.3 - - - -
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Residues in contact with GLU 299 (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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288A PHE* 3.6 30.8 - - + +
289A SER* 2.8 28.6 + - - -
295A THR* 2.9 37.3 + - + +
296A VAL* 3.3 3.8 + - - +
298A GLN* 1.3 81.1 - - + +
300A LEU* 1.3 60.3 + - - +
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Residues in contact with LEU 300 (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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281A LEU* 5.4 0.4 - - + -
286A TRP* 3.9 14.6 - - + -
288A PHE* 3.5 33.0 - - + -
296A VAL* 3.1 15.9 - - + +
297A ALA 4.1 0.2 - - - +
299A GLU 1.3 85.8 - - - +
301A LEU* 1.3 73.2 + - + +
302A GLY 3.7 0.4 - - - -
342A ILE* 4.1 10.8 - - + -
345A LYS* 3.3 60.5 + - + -
346A THR* 3.9 22.7 - - + -
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Residues in contact with LEU 301 (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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297A ALA* 2.5 24.8 + - - +
300A LEU* 1.3 97.4 - - + +
302A GLY* 1.3 55.7 + - - -
303A GLU* 3.3 16.3 - - - +
338A LEU* 4.1 19.1 - - + +
341A GLN* 3.6 43.3 - - + +
342A ILE* 4.1 14.4 - - + -
345A LYS* 4.0 26.1 + - + +
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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