Contacts of the helix formed by residues 268 - 280 (chain A) in PDB entry 3K3T
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 ASP 268 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177A PHE* 3.5 2.0 - - - -
266A LYS* 4.5 0.7 - - - +
267A THR* 1.3 80.3 + - - +
269A GLY* 1.3 69.0 + - - +
270A HIS* 3.3 12.6 + - - +
271A ALA* 3.1 33.4 + - + +
272A PHE* 2.9 24.4 + - - +
274A ARG* 4.6 2.6 + - - -
296A ASN* 5.4 3.5 + - - +
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Residues in contact with GLY 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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177A PHE* 3.4 13.4 - - - -
268A ASP* 1.3 74.9 + - - +
270A HIS* 1.3 57.2 + - - +
272A PHE* 3.3 3.3 + - - +
273A ALA* 3.0 27.9 + - - +
292A ALA* 4.3 4.0 - - - -
295A ILE* 3.7 37.4 - - - +
296A ASN* 4.9 9.9 + - - +
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Residues in contact with HIS 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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268A ASP* 3.3 11.5 + - - +
269A GLY* 1.3 75.9 - - - +
271A ALA* 1.3 58.0 + - - +
273A ALA* 3.2 4.0 + - - +
274A ARG* 2.8 67.2 + - - +
288A ALA* 3.6 35.6 - - + +
289A ASP* 2.8 28.3 + - - -
292A ALA* 3.8 19.8 - - + +
296A ASN* 5.1 1.2 + - - -
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Residues in contact with ALA 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A LYS* 3.8 27.5 - - + +
268A ASP* 3.1 27.3 + - + +
270A HIS* 1.3 75.4 - - - +
272A PHE* 1.3 58.0 + - - +
274A ARG* 3.4 30.4 + - - +
275A ALA* 3.0 28.6 + - - +
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Residues in contact with PHE 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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173A VAL* 4.2 11.2 - - + -
177A PHE* 3.5 51.6 - + + -
178A LEU* 4.1 14.1 - - + -
181A GLN* 3.7 11.7 - - - -
250A TYR* 3.8 9.2 - - - -
263A VAL* 3.7 31.0 - - + -
266A LYS* 4.1 11.3 - - + +
268A ASP 2.9 16.9 + - - +
269A GLY 3.4 2.5 - - - +
271A ALA* 1.3 78.3 - - - +
273A ALA* 1.3 57.6 + - - +
275A ALA* 3.2 6.1 + - - +
276A LEU* 3.0 55.0 + - + +
291A LEU* 4.0 7.2 - - + -
295A ILE* 3.9 12.8 - - + -
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Residues in contact with ALA 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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269A GLY 3.0 13.9 + - - +
270A HIS 3.2 7.6 + - - +
272A PHE* 1.3 73.6 - - - +
274A ARG* 1.3 59.4 + - - +
276A LEU* 3.2 6.3 + - - +
277A GLN* 3.0 28.1 + - - +
287A TYR* 4.3 5.6 - - + -
288A ALA* 3.6 33.4 - - - +
291A LEU* 3.7 29.6 - - + -
292A ALA 4.7 0.2 - - - +
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Residues in contact with ARG 274 (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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266A LYS* 5.9 1.0 - - - +
268A ASP* 4.6 2.4 + - - -
270A HIS* 2.8 61.1 + - + +
271A ALA* 3.5 37.6 + - - +
273A ALA* 1.3 71.4 - - - +
275A ALA* 1.3 57.5 + - - +
277A GLN* 3.2 8.5 + - - +
278A GLU* 2.9 29.5 + - - +
288A ALA* 4.0 8.1 - - + -
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Residues in contact with ALA 275 (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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259A ARG 4.6 2.4 - - - +
260A TYR* 4.5 1.4 - - - -
262A LYS* 3.5 43.1 - - + +
263A VAL* 3.6 14.5 - - - +
266A LYS* 4.7 1.6 - - + -
271A ALA 3.0 14.8 + - - +
272A PHE* 3.2 10.3 + - - +
274A ARG* 1.3 74.5 - - - +
276A LEU* 1.3 64.5 + - - +
278A GLU* 3.4 9.7 + - - +
279A GLY* 3.1 19.1 + - - -
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Residues in contact with LEU 276 (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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181A GLN* 3.5 37.5 - - - +
250A TYR* 4.0 12.6 - - - +
254A VAL* 4.6 7.0 - - + -
260A TYR* 3.6 18.3 - - + -
263A VAL* 4.0 16.2 - - + -
272A PHE* 3.0 39.8 + - + +
273A ALA 3.2 6.5 + - - +
275A ALA* 1.3 76.2 - - - +
277A GLN* 1.3 61.9 + - - +
279A GLY 3.3 1.9 + - - -
280A GLY 3.2 4.5 + - - -
281A TYR* 3.0 34.7 + - + +
287A TYR* 4.1 7.6 - - + +
291A LEU* 3.8 15.5 - - + -
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Residues in contact with GLN 277 (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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273A ALA 3.0 13.5 + - - +
274A ARG* 3.6 10.5 - - - +
276A LEU* 1.3 74.3 - - - +
278A GLU* 1.3 60.5 + - - +
280A GLY* 2.9 20.4 + - - -
281A TYR 4.6 0.2 - - - +
282A ALA 2.9 28.3 - - - +
283A THR* 3.6 9.7 + - - +
284A ASP 2.9 26.4 + - - +
285A PRO* 4.5 12.5 + - - +
287A TYR* 3.7 15.4 - - + +
288A ALA* 5.3 8.6 - - + +
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Residues in contact with GLU 278 (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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259A ARG* 4.1 17.6 + - - +
262A LYS* 3.4 32.8 - - + +
274A ARG 2.9 14.8 + - - +
275A ALA* 3.5 10.9 - - - +
277A GLN* 1.3 76.1 - - - +
279A GLY* 1.3 61.5 + - - +
280A GLY* 3.3 0.9 + - - -
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Residues in contact with GLY 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A ARG* 3.1 51.7 + - - +
260A TYR* 3.6 21.7 + - - -
275A ALA 3.1 10.1 + - - -
276A LEU 3.6 4.0 - - - -
277A GLN 3.2 0.6 - - - -
278A GLU* 1.3 75.8 - - - +
280A GLY* 1.3 59.2 - - - +
281A TYR 3.6 2.0 - - - -
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Residues in contact with GLY 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A ARG* 5.1 6.3 - - - -
260A TYR* 3.6 3.5 + - - -
277A GLN 2.9 15.2 + - - -
278A GLU 3.2 1.2 - - - -
279A GLY* 1.3 78.8 - - - +
281A TYR* 1.3 66.6 + - - +
282A ALA* 3.3 5.0 + - - -
283A THR* 5.1 12.0 - - - +
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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