Contacts of the helix formed by residues 298 - 308 (chain A) in PDB entry 1JD5
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 GLY 298 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293A VAL 3.3 1.6 + - - -
294A LYS* 3.0 22.1 + - - -
295A LEU 4.6 0.8 + - - -
296A MET 3.7 0.4 - - - -
297A LYS* 1.3 83.4 - - - +
299A GLN* 1.3 65.4 + - - -
300A LEU* 3.4 2.9 - - - -
301A TYR* 3.4 1.2 + - - +
302A ILE* 3.3 25.2 + - - +
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Residues in contact with GLN 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 SER 5.2 0.2 + - - -
294A LYS* 3.2 35.9 + - + +
298A GLY* 1.3 69.6 - - - -
300A LEU* 1.3 68.6 + - + +
302A ILE* 3.2 22.1 + - - +
303A ASP* 3.0 51.0 + - - +
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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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298A GLY 3.4 0.8 - - - -
299A GLN* 1.3 78.2 - - + +
301A TYR* 1.3 58.2 + - - +
303A ASP* 3.2 14.4 + - + +
304A THR* 2.8 35.7 + - - +
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Residues in contact with TYR 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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278A GLU* 5.1 1.0 + - - -
280A TRP* 3.4 11.8 - - - +
281A GLU* 3.3 36.2 + - + +
284A ALA* 3.9 17.9 - - + -
297A LYS* 3.5 67.4 + - + +
298A GLY 3.4 2.3 + - - +
300A LEU* 1.3 79.3 - - - +
302A ILE* 1.3 60.8 + - + +
304A THR* 3.1 7.8 + - - -
305A VAL* 2.8 52.1 + - + +
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Residues in contact with ILE 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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284A ALA* 4.1 17.1 - - + +
285A LEU* 6.0 0.2 - - - -
288A SER* 3.7 39.0 - - - +
293A VAL* 3.7 31.0 - - + -
294A LYS* 3.7 31.6 - - + -
298A GLY 3.3 14.6 + - - +
299A GLN* 3.2 25.9 + - - +
301A TYR* 1.3 77.6 - - + +
303A ASP* 1.3 65.0 + - - +
305A VAL* 3.7 3.6 + - - +
306A ALA* 3.5 18.4 + - - +
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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
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299A GLN* 3.0 43.5 + - - +
300A LEU* 3.5 16.9 - - + +
302A ILE* 1.3 75.5 - - - +
304A THR* 1.3 64.6 + - - +
306A ALA* 3.2 17.5 + - - +
307A ALA* 3.4 11.3 + - - +
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Residues in contact with THR 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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300A LEU* 2.8 25.7 + - - +
301A TYR* 3.6 9.4 - - + -
303A ASP* 1.3 72.7 - - - +
305A VAL* 1.3 64.3 + - + +
307A ALA* 3.0 19.3 + - + +
308A LYS* 3.4 19.1 + - + +
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Residues in contact with VAL 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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281A GLU* 3.5 33.4 - - + +
284A ALA* 4.3 2.9 - - + -
285A LEU* 3.9 19.5 - - + +
301A TYR* 2.8 61.2 + - + +
302A ILE 3.8 4.7 - - - +
304A THR* 1.3 71.9 - - - +
306A ALA* 1.3 60.4 + - - +
307A ALA 3.1 4.9 + - - -
308A LYS* 3.1 19.2 + - + +
311A LEU* 3.5 28.5 - - + +
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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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284A ALA 6.1 0.2 - - - +
285A LEU* 4.2 20.2 - - + +
302A ILE 3.5 9.1 + - - +
303A ASP* 3.2 12.1 + - - +
305A VAL* 1.3 78.7 - - + +
307A ALA* 1.3 57.7 + - - +
308A LYS 3.4 0.4 - - - -
312A ALA* 3.7 19.8 - - - +
315A LYS* 5.7 4.7 - - + -
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Residues in contact with ALA 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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303A ASP 3.4 8.4 + - - +
304A THR* 3.0 15.0 + - + +
306A ALA* 1.3 77.5 - - - +
308A LYS* 1.3 64.2 + - - +
309A PRO* 3.3 7.8 - - - +
312A ALA* 4.8 3.5 - - - +
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Residues in contact with LYS 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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281A GLU* 3.7 23.6 - - - +
304A THR* 3.4 18.4 + - + +
305A VAL* 3.1 15.7 + - + +
307A ALA* 1.3 76.3 - - - +
309A PRO* 1.3 63.7 - - + +
310A VAL* 3.4 13.3 - - + +
311A LEU* 3.0 30.6 + - + +
312A ALA* 2.7 32.9 + - - +
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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