Contacts of the helix formed by residues 274 - 282 (chain D) in PDB entry 3KC3
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 274 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271D ILE* 4.0 11.4 - - - +
272D SER 3.1 2.8 - - - +
273D PRO* 1.3 81.6 - - - +
275D MET* 1.3 55.3 + - - +
276D LYS 3.1 0.7 - - - -
277D THR* 3.3 9.8 + - - -
278D ARG* 2.7 42.1 + - - +
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Residues in contact with MET 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263D PHE* 3.4 38.1 - - + +
271D ILE* 3.2 30.9 - - - +
272D SER* 4.0 16.0 - - - +
274D GLY* 1.3 74.7 - - - +
276D LYS* 1.3 64.4 + - - +
278D ARG* 3.2 20.2 + - - +
279D ILE* 3.1 36.8 + - + +
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Residues in contact with LYS 276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272D SER 3.8 5.7 + - - +
273D PRO* 3.6 32.2 - - + +
275D MET* 1.3 79.3 - - - +
277D THR* 1.3 60.5 + - - +
279D ILE* 3.8 9.0 + - - +
280D ARG* 3.1 59.0 + - - +
96J GLN* 4.2 23.0 + - - +
131J ARG* 5.0 16.6 - - - +
181K ASN* 5.6 2.0 + - - -
235K LEU* 4.6 15.3 - - + +
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Residues in contact with THR 277 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273D PRO 3.1 15.1 + - - -
274D GLY* 3.1 11.4 + - - -
276D LYS* 1.3 76.9 - - - +
278D ARG* 1.3 64.8 + - - +
280D ARG* 3.5 21.2 + - + +
281D MET* 3.1 34.2 + - + +
283D GLN* 5.6 0.2 - - - -
129J ALA* 5.7 0.3 - - - +
131J ARG* 2.8 29.3 + - - +
178K HIS 5.8 0.2 - - - +
179K SER* 3.4 23.3 - - - +
181K ASN* 4.4 4.7 - - - +
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Residues in contact with ARG 278 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262D PRO 3.6 12.7 + - - -
263D PHE* 3.4 37.5 - - + +
274D GLY 2.7 29.4 + - - +
275D MET* 3.2 18.1 + - - +
277D THR* 1.3 69.5 - - - +
279D ILE* 1.3 68.5 + - - +
282D GLY 3.1 17.3 + - - -
283D GLN* 2.9 60.8 + - + +
284D TYR* 3.9 4.4 - - - +
285D GLU* 6.0 1.6 - - - +
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Residues in contact with ILE 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247D TRP* 3.9 24.4 - - + -
263D PHE* 3.5 37.6 - - + -
275D MET* 3.1 25.8 + - + +
276D LYS* 3.8 7.4 - - - +
278D ARG* 1.3 77.8 - - - +
280D ARG* 1.3 65.9 + - - +
281D MET 2.9 2.1 + - - -
282D GLY* 3.2 1.7 + - - -
308D THR* 3.1 21.8 - - - +
230K VAL 5.5 10.8 - - - +
231K ALA* 4.4 5.6 - - - -
232K PRO* 4.1 18.8 - - + -
235K LEU* 5.1 12.8 - - + -
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Residues in contact with ARG 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276D LYS* 3.1 71.6 + - - +
277D THR* 3.8 23.7 - - + +
278D ARG 3.4 0.4 - - - -
279D ILE* 1.3 80.6 - - - +
281D MET* 1.3 65.6 + - + +
308D THR* 4.0 12.2 - - - -
131J ARG* 5.3 0.2 - - - +
181K ASN* 3.4 34.9 + - - +
232K PRO* 5.1 9.2 - - + +
235K LEU* 4.0 40.0 + - + +
238K GLU* 4.2 16.6 + - - +
242K LYS* 4.7 5.6 + - - +
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Residues in contact with MET 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277D THR* 3.1 21.5 + - + +
278D ARG 3.9 2.7 - - - +
279D ILE 2.9 1.6 + - - -
280D ARG* 1.3 85.5 - - + +
282D GLY* 1.3 57.0 + - - +
283D GLN* 4.3 16.8 - - - +
308D THR* 3.1 15.2 + - - -
175K GLN* 5.2 6.7 - - - +
178K HIS* 3.4 30.1 - - + +
179K SER* 3.7 30.1 - - - -
242K LYS* 3.8 22.0 - - - +
315K THR* 4.2 13.9 + - - +
316K ILE* 4.5 11.8 - - + +
317K THR* 3.5 25.1 + - - +
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Residues in contact with GLY 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263D PHE* 4.6 3.4 - - - -
278D ARG 3.1 4.4 + - - -
279D ILE 3.2 3.7 + - - -
281D MET* 1.3 77.9 - - - +
283D GLN* 1.3 60.8 + - - +
284D TYR* 3.4 28.8 + - - +
306D LEU 5.3 1.3 - - - -
308D THR* 3.9 15.7 - - - -
317K THR* 3.9 15.2 - - - +
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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