Contacts of the helix formed by residues 268 - 282 (chain A) in PDB entry 1KT8
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 268 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ARG* 3.5 2.7 - - - -
242A ASN* 3.2 22.8 - - - +
266A LEU* 2.9 11.5 + - - -
267A PRO* 1.3 73.6 - - - +
269A VAL* 1.3 61.5 + - - -
270A VAL 3.4 2.0 - - - -
271A ARG* 3.3 6.3 + - - +
272A GLN* 3.0 29.1 + - - +
400A ILP 3.3 17.3 - - - -
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Residues in contact with VAL 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A PHE* 4.1 15.3 - - + -
92A ARG* 4.0 23.5 + - + +
95A LEU* 3.8 38.8 - - + -
96A ASN* 3.7 26.0 - - - +
99A ARG* 4.1 8.5 - - - +
267A PRO 3.5 1.5 + - - +
268A GLY* 1.3 69.4 - - - -
270A VAL* 1.3 66.2 + - + +
272A GLN* 3.4 6.5 + - - +
273A SER* 2.8 27.4 + - - -
313A THR* 5.3 2.7 - - - +
400A ILP 2.9 19.0 + - - +
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Residues in contact with VAL 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A PHE* 4.9 11.0 - - + -
269A VAL* 1.3 76.5 - - + +
271A ARG* 1.3 58.0 + - - +
273A SER* 3.0 8.7 + - - -
274A LEU* 2.8 41.6 + - + +
311A SER* 3.9 6.3 - - - -
312A GLY 3.5 26.7 - - - +
313A THR* 3.7 9.6 - - - +
316A GLN* 3.4 38.4 - - + +
349A LEU* 4.5 10.1 - - + -
400A ILP 3.0 15.8 + - - +
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Residues in contact with ARG 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A ASN* 3.4 37.0 - - - +
244A PHE* 3.6 24.6 - - + -
258A THR* 4.0 7.4 + - - +
259A PRO 3.0 26.9 + - - -
261A LEU* 3.5 36.3 - - - +
265A ILE* 4.2 3.6 - - - +
266A LEU 4.5 2.0 - - - -
267A PRO* 5.1 1.6 - - - +
268A GLY 3.3 16.1 + - - +
270A VAL* 1.3 78.3 - - - +
272A GLN* 1.3 74.4 + - - +
274A LEU 3.3 1.0 + - - -
275A LEU* 3.1 39.3 + - + +
288A GLU* 2.9 31.9 + - - +
311A SER* 3.7 14.0 + - - +
400A ILP 4.3 0.6 + - - -
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Residues in contact with GLN 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ARG* 4.3 7.4 - - - +
95A LEU* 4.6 12.1 - - + -
261A LEU* 5.1 7.5 - - - +
267A PRO* 6.4 0.2 - - - +
268A GLY 3.0 16.9 + - - +
269A VAL* 3.7 8.1 - - - +
271A ARG* 1.3 94.1 - - - +
273A SER* 1.3 56.9 + - - +
275A LEU* 3.5 13.8 + - - +
276A ASP* 2.9 63.6 + - - +
288A GLU* 5.6 2.4 + - - +
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Residues in contact with SER 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A PHE* 3.3 16.0 - - - -
92A ARG* 3.0 31.9 + - - +
269A VAL 2.8 18.0 + - - -
270A VAL* 3.0 11.5 + - - -
272A GLN* 1.3 75.2 - - - +
274A LEU* 1.3 61.7 - - - +
276A ASP 3.4 0.2 + - - -
277A MET* 2.9 32.2 + - - +
349A LEU* 4.9 5.6 - - - -
361A TRP* 3.5 20.7 - - - -
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Residues in contact with LEU 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A PHE* 4.0 12.1 - - + -
256A LEU* 5.4 0.4 - - - -
270A VAL* 2.8 24.5 + - + +
271A ARG 3.3 4.2 + - - +
273A SER* 1.3 78.7 - - - +
275A LEU* 1.3 57.4 + - - +
277A MET* 4.4 1.3 - - + -
278A ALA* 2.9 33.1 + - - +
309A PHE* 3.7 31.2 - - + -
311A SER* 3.8 22.0 - - - -
317A VAL* 4.5 6.7 - - + -
345A PHE* 3.6 41.7 - - + -
349A LEU* 4.0 27.1 - - + -
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Residues in contact with LEU 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A PHE* 3.6 25.6 - - + -
256A LEU* 4.9 3.8 - - + +
258A THR* 3.8 12.8 - - + -
271A ARG* 3.1 49.6 + - + +
272A GLN* 3.6 15.9 - - - +
274A LEU* 1.3 75.4 - - - +
276A ASP* 1.3 54.1 + - - +
278A ALA* 3.2 1.8 + - - +
279A GLN* 2.7 38.3 + - - +
286A VAL* 3.9 25.4 - - + +
287A VAL 5.0 3.1 - - - +
288A GLU* 4.0 23.6 - - + +
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Residues in contact with ASP 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ARG* 3.0 34.3 + - - -
272A GLN* 2.9 40.7 + - - +
273A SER 3.6 4.0 - - - +
275A LEU* 1.3 75.4 - - - +
277A MET* 1.3 58.3 + - - +
279A GLN* 3.6 6.5 - - - +
280A THR* 2.8 35.0 + - - +
361A TRP* 3.8 13.3 + - + -
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Residues in contact with MET 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A SER 2.9 15.2 + - - +
274A LEU* 3.7 4.9 - - + +
276A ASP* 1.3 77.7 - - - +
278A ALA* 1.3 62.2 + - - +
280A THR* 3.3 8.0 + - - -
281A TRP* 3.1 33.3 + - + +
345A PHE* 3.7 25.6 - - + +
348A GLU* 3.3 44.9 - - + +
349A LEU* 3.7 23.3 - - + -
352A ILE* 4.4 5.8 - - + -
361A TRP* 3.6 32.3 - - + -
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Residues in contact with ALA 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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256A LEU* 4.2 11.0 - - + -
274A LEU 2.9 18.5 + - - +
275A LEU 3.8 1.3 - - - +
277A MET* 1.3 72.7 - - - +
279A GLN* 1.3 69.9 + - - +
281A TRP* 3.3 15.8 + - + +
282A GLY* 3.3 15.1 + - - -
283A GLU 4.8 1.6 + - - -
284A PHE* 4.2 12.0 - - + +
286A VAL* 3.6 25.1 - - + +
345A PHE* 4.1 15.2 - - + -
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Residues in contact with GLN 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A LEU 2.7 23.6 + - - +
276A ASP* 3.6 6.7 - - - +
278A ALA* 1.3 74.2 - - - +
280A THR* 1.3 63.0 + - - +
282A GLY* 3.1 14.6 + - - -
284A PHE 5.4 2.2 + - - -
286A VAL* 3.9 31.6 + - + +
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Residues in contact with THR 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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276A ASP* 2.8 21.1 + - - +
277A MET* 3.4 12.4 - - - -
278A ALA 3.2 0.2 - - - -
279A GLN* 1.3 76.3 - - - +
281A TRP* 1.3 70.7 + - + +
282A GLY* 3.2 1.4 + - - -
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Residues in contact with TRP 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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277A MET* 3.1 25.2 + - + +
278A ALA* 3.3 13.6 + - - +
280A THR* 1.3 84.5 - - + +
282A GLY* 1.3 63.8 + - - +
283A GLU* 3.2 24.8 + - + +
284A PHE* 4.2 11.4 - + - -
341A LEU* 3.6 25.8 - - + -
344A ARG* 3.1 61.8 - - + +
345A PHE* 3.6 24.2 - + - -
348A GLU* 2.8 32.0 + - + -
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Residues in contact with GLY 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A ALA 3.3 4.3 + - - -
279A GLN* 3.1 20.2 + - - -
280A THR 4.1 1.1 - - - -
281A TRP* 1.3 79.3 - - - +
283A GLU* 1.3 62.1 + - - +
284A PHE 3.4 6.3 - - - -
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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