Contacts of the helix formed by residues 264 - 273 (chain A) in PDB entry 4KZK
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 264 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A PRO* 3.4 17.1 - - - +
46A TRP* 4.2 17.9 - - - -
49A ASP* 2.6 29.5 + - - -
236A ASP* 3.6 4.1 + - - -
262A ASN* 3.2 12.0 - - - -
263A GLY* 1.3 80.7 - - - +
265A GLN* 1.3 76.0 + - - +
266A VAL 3.2 2.5 - - - -
267A ALA 3.0 13.0 + - - -
268A LEU* 3.1 13.9 + - - +
328A ARG* 4.0 7.9 - - - +
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Residues in contact with GLN 265 (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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45A PRO* 3.7 22.8 - - + +
49A ASP* 5.0 7.7 - - - +
264A SER* 1.3 83.7 + - - +
266A VAL* 1.3 56.7 + - - +
267A ALA 3.3 0.2 - - - -
268A LEU* 3.5 30.9 - - - +
269A ASN* 2.9 43.4 + - - +
328A ARG* 4.1 11.4 + - - -
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Residues in contact with VAL 266 (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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43A ASP 5.8 0.2 - - - +
45A PRO* 3.8 21.0 - - + +
209A THR* 5.9 0.4 - - - +
236A ASP* 3.8 23.8 - - + +
237A ASP* 3.5 24.7 - - - +
240A VAL* 3.5 32.5 - - + -
264A SER 3.1 1.2 + - - -
265A GLN* 1.3 76.8 - - - +
267A ALA* 1.3 62.1 + - - +
269A ASN* 3.5 10.0 + - - +
270A GLU* 3.3 22.7 + - - +
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Residues in contact with ALA 267 (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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236A ASP* 3.5 17.8 + - - +
263A GLY* 4.0 7.6 - - - -
264A SER 3.0 9.9 + - - +
266A VAL* 1.3 78.3 - - - +
268A LEU* 1.3 64.8 + - + +
270A GLU* 3.1 5.9 + - - +
271A PHE* 3.0 35.9 + - + -
279A PHE* 3.7 26.0 - - + -
282A SER* 3.9 13.5 - - - -
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Residues in contact with LEU 268 (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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263A GLY 4.0 7.2 - - - +
264A SER 3.1 12.2 + - - +
265A GLN* 3.5 37.5 - - - +
267A ALA* 1.3 78.9 - - + +
269A ASN* 1.3 62.5 + - - +
271A PHE* 3.3 18.6 + - + +
272A ALA* 3.0 26.2 + - - +
319A ILE* 4.7 0.9 - - + -
324A GLU* 3.5 28.2 - - + +
328A ARG* 3.7 34.1 - - - +
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Residues in contact with ASN 269 (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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265A GLN* 2.9 36.9 + - - +
266A VAL* 3.7 9.9 - - - +
267A ALA 3.2 0.2 - - - -
268A LEU* 1.3 78.8 - - - +
270A GLU* 1.3 65.4 + - - +
272A ALA* 3.5 9.8 + - - +
273A LYS* 3.4 25.4 + - - +
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Residues in contact with GLU 270 (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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240A VAL* 3.9 14.4 - - + +
244A ARG* 2.8 40.1 + - - -
266A VAL* 3.3 13.5 + - - +
267A ALA 3.1 7.4 + - - +
269A ASN* 1.3 79.9 - - - +
271A PHE* 1.3 61.2 + - - +
273A LYS* 3.0 29.5 + - - +
277A THR* 2.7 29.8 + - - +
279A PHE* 3.7 37.4 - - + +
321A ARG* 3.0 17.5 + - - +
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Residues in contact with PHE 271 (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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267A ALA* 3.0 25.3 + - + +
268A LEU* 3.3 7.8 + - + +
270A GLU* 1.3 77.6 - - - +
272A ALA* 1.3 60.8 + - - +
273A LYS 3.5 3.6 + - - +
279A PHE* 3.9 22.9 - + - -
280A PHE 3.7 20.0 - - - -
281A GLY* 3.9 9.2 - - - -
282A SER 4.2 1.8 - - - -
319A ILE* 3.7 44.4 - - + -
320A THR* 4.0 3.8 - - - -
321A ARG* 3.7 44.9 + - + +
324A GLU* 3.6 38.4 - - + +
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Residues in contact with ALA 272 (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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268A LEU 3.0 16.5 + - - +
269A ASN* 4.0 7.0 - - - +
270A GLU 3.2 0.8 - - - -
271A PHE* 1.3 75.8 - - - +
273A LYS* 1.3 64.8 + - - +
274A PRO* 3.4 6.1 - - - +
325A LYS* 6.3 0.9 - - - +
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Residues in contact with LYS 273 (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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244A ARG* 3.5 19.0 - - - +
269A ASN* 3.4 22.6 + - - +
270A GLU* 3.0 35.3 + - - +
271A PHE 3.3 6.9 - - - +
272A ALA* 1.3 78.7 - - - +
274A PRO* 1.3 74.3 - - + +
275A LYS 3.2 19.0 + - - +
276A PRO* 4.2 4.0 - - - +
277A THR* 3.8 17.5 - - + +
321A ARG* 5.3 1.2 + - - -
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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