Contacts of the helix formed by residues 279 - 290 (chain A) in PDB entry 4KPD
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 279 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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277A ARG 4.9 3.8 - - - +
278A ALA* 1.4 74.4 - - - +
280A PRO* 1.4 74.9 - - - +
281A GLU* 3.4 15.1 + - - +
282A GLN* 2.9 40.3 + - - +
283A TYR* 2.9 20.8 + - - +
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Residues in contact with PRO 280 (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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279A THR* 1.4 87.7 - - - +
281A GLU* 1.4 69.9 + - - +
283A TYR* 3.4 10.5 + - + +
284A GLN* 3.3 25.3 + - - +
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Residues in contact with GLU 281 (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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279A THR* 3.1 15.7 + - - +
280A PRO* 1.4 89.6 - - - +
282A GLN* 1.3 62.5 + - + +
284A GLN* 3.5 9.3 + - - +
285A ILE* 3.4 28.9 + - + +
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Residues in contact with GLN 282 (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 ALA* 3.4 6.7 - - + -
279A THR* 2.9 45.6 + - - +
281A GLU* 1.3 74.8 - - + +
283A TYR* 1.3 64.5 + - - +
285A ILE* 3.3 16.9 + - + +
286A LEU* 3.1 18.4 + - - +
304A LEU* 3.5 39.6 - - + +
307A GLU* 3.8 24.4 + - - +
308A LEU* 3.4 23.3 - - - +
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Residues in contact with TYR 283 (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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185A LEU* 3.7 28.9 - - + +
186A VAL* 4.7 12.6 + - - +
275A LEU* 3.5 35.9 - - + -
278A ALA* 4.1 10.0 - - + +
279A THR 2.9 12.1 + - - +
280A PRO* 3.5 15.5 - - + +
282A GLN* 1.3 76.8 - - - +
284A GLN* 1.3 61.9 + - + +
286A LEU* 3.3 8.3 + - - +
287A LYS* 2.8 47.0 + - + +
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Residues in contact with GLN 284 (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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280A PRO 3.3 12.0 + - - +
281A GLU* 3.6 11.9 - - - +
282A GLN 3.3 0.6 - - - -
283A TYR* 1.3 84.4 - - + +
285A ILE* 1.3 59.1 + - + +
287A LYS* 3.3 33.4 + - - +
288A GLU* 2.9 58.9 + - - +
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Residues in contact with ILE 285 (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* 3.4 20.1 + - + +
282A GLN* 3.3 20.7 + - + +
284A GLN* 1.3 74.6 - - + +
286A LEU* 1.3 62.1 + - - +
288A GLU* 4.1 8.3 - - - +
289A ASN* 2.7 34.1 + - + +
300A ARG* 3.5 57.7 - - + +
301A VAL* 5.7 1.3 - - - +
304A LEU* 4.2 18.8 - - + -
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Residues in contact with LEU 286 (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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185A LEU* 4.1 8.1 - - + -
271A VAL* 3.9 17.7 - - + -
274A CYS* 4.0 25.8 - - - -
275A LEU* 3.8 36.3 - - + -
278A ALA* 6.0 0.9 - - + -
282A GLN 3.1 12.8 + - - +
283A TYR* 3.5 9.4 - - - +
285A ILE* 1.3 73.6 - - - +
287A LYS* 1.3 59.8 + - - +
289A ASN* 3.1 1.6 + - - -
290A TYR* 2.9 51.0 + - + +
301A VAL* 3.9 30.7 - - + -
304A LEU* 4.0 8.9 - - + +
305A TYR* 4.2 0.7 - - + -
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Residues in contact with LYS 287 (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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183A VAL* 3.8 42.1 - - + +
185A LEU* 3.8 21.1 - - + +
283A TYR* 2.8 32.0 + - + +
284A GLN* 3.5 33.5 - - - +
286A LEU* 1.3 71.9 - - - +
288A GLU* 1.3 63.2 + - + +
289A ASN 3.5 0.2 + - - -
290A TYR* 4.2 6.9 + - - +
292A GLN* 4.6 1.4 - - - +
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Residues in contact with GLU 288 (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 GLN* 2.9 43.1 + - - +
285A ILE* 4.1 6.9 + - - +
287A LYS* 1.3 76.4 - - + +
289A ASN* 1.3 68.9 + - - +
292A GLN* 2.9 15.2 + - - +
297A LYS* 3.8 14.9 + - - -
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Residues in contact with ASN 289 (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 ILE* 4.5 2.4 - - - +
285A ILE* 2.7 31.7 + - + +
288A GLU* 1.3 90.0 + - - +
290A TYR* 1.3 63.5 + - - +
291A GLY 4.1 0.3 + - - -
292A GLN* 3.6 9.5 + - - +
296A GLU 4.7 0.2 - - - +
297A LYS* 3.4 60.0 + - + +
298A VAL 4.5 0.3 + - - -
300A ARG* 3.7 26.5 - - + +
301A VAL* 3.7 12.2 - - + +
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Residues in contact with TYR 290 (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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183A VAL* 5.4 5.2 - - - +
185A LEU* 4.5 8.1 - - + -
188A PHE* 3.5 20.0 - + - -
261A ASP* 3.7 10.2 + - - +
262A ILE* 3.7 27.2 - - + +
265A ASN* 3.4 27.6 - - - +
266A LYS 2.5 30.7 + - - -
268A SER* 4.1 7.1 - - - -
271A VAL* 3.7 16.3 - - + +
286A LEU* 2.9 34.3 + - + +
287A LYS 4.2 5.5 + - - +
288A GLU 3.9 0.2 - - - -
289A ASN* 1.3 72.8 - - - +
291A GLY* 1.3 71.8 + - - +
292A GLN* 3.3 12.8 - - - +
301A VAL* 3.8 19.9 - - + +
305A TYR* 3.5 20.0 + - - -
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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