Contacts of the strand formed by residues 258 - 270 (chain A) in PDB entry 1KTW
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 258 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224A TYR 3.2 18.6 + - - -
225A GLY* 4.0 0.2 - - - -
226A ALA 3.0 17.8 + - - -
251A MET* 3.7 5.7 - - - -
257A GLY* 1.3 72.7 - - - -
259A ILE* 1.3 62.9 + - - -
260A ARG* 3.1 17.8 + - - -
283A MET* 3.8 14.7 - - - -
284A LYS 5.1 0.2 - - - -
285A ASN* 3.2 13.9 - - - -
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Residues in contact with ILE 259 (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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223A THR* 3.7 32.3 - - + +
224A TYR 4.0 10.5 - - - +
226A ALA* 3.1 24.7 - - + +
244A MET* 3.9 19.7 - - + -
246A THR* 4.3 4.7 - - + -
258A GLY* 1.3 76.3 - - - +
260A ARG* 1.3 58.6 + - - +
262A ILE* 4.0 23.1 - - + -
285A ASN* 2.9 14.7 + - - +
286A GLY* 2.8 32.1 + - - -
287A ASP 5.5 0.2 - - - -
288A VAL* 4.5 2.9 - - + -
375A PHE* 3.8 25.8 - - + -
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Residues in contact with ARG 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A TRP* 3.5 15.6 - - - +
226A ALA 3.0 6.3 + - - -
227A ASP* 2.9 45.4 + - - +
228A ASN 3.2 15.9 + - - -
257A GLY 2.9 23.6 + - - -
258A GLY* 3.1 28.9 + - - -
259A ILE* 1.3 77.4 + - - +
261A ASN* 1.3 78.1 + - - +
262A ILE* 3.5 4.8 - - - +
284A LYS 4.7 9.5 + - - -
285A ASN 4.8 0.2 - - - -
286A GLY* 3.9 21.5 - - - +
287A ASP 4.4 1.6 - - - -
460B VAL* 5.8 1.0 - - - +
461B ASN* 3.5 14.0 - - - +
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Residues in contact with ASN 261 (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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227A ASP* 4.9 4.0 + - - +
228A ASN* 3.3 35.0 - - + +
229A ILE 3.7 1.0 + - - -
260A ARG* 1.3 83.4 - - - +
262A ILE* 1.3 59.4 + - - +
263A PHE* 3.9 20.1 - - + -
287A ASP* 3.2 25.7 + - - +
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Residues in contact with ILE 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A THR* 6.5 0.2 - - + -
226A ALA* 4.1 27.4 - - + +
229A ILE* 3.7 18.6 - - + +
231A PHE* 3.7 31.0 - - + -
244A MET* 4.7 9.6 - - - -
259A ILE* 4.0 26.0 - - + -
260A ARG 3.5 20.0 - - - +
261A ASN* 1.3 75.9 - - - +
263A PHE* 1.3 70.2 - - - +
264A ALA* 5.6 1.6 - - + -
287A ASP 3.2 6.2 + - - +
288A VAL* 3.4 20.3 - - + -
289A GLN* 3.0 24.6 + - - +
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Residues in contact with PHE 263 (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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31A LYS* 3.6 42.2 - - + -
32A THR 5.7 0.7 - - - -
33A TYR* 3.9 25.6 - + + -
38A PHE* 3.8 28.7 - + + -
228A ASN* 5.1 3.1 - - - -
229A ILE 3.1 7.8 + - - +
230A LEU* 3.3 21.2 - - + -
231A PHE* 2.9 25.3 + - - -
261A ASN* 3.9 21.8 - - + -
262A ILE* 1.3 76.6 - - - +
264A ALA* 1.3 62.8 + - - +
289A GLN* 3.5 29.8 - - + -
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Residues in contact with ALA 264 (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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33A TYR* 4.9 4.7 + - - -
230A LEU* 4.6 1.1 - - - -
231A PHE* 3.0 14.8 - - + +
242A LEU* 3.8 29.8 - - + -
262A ILE* 5.6 1.3 - - + -
263A PHE* 1.3 76.6 - - - +
265A ASP* 1.3 61.6 + - - +
267A ILE* 4.3 7.6 - - + -
288A VAL* 5.9 0.4 - - + -
289A GLN* 3.0 7.3 + - - +
290A VAL* 3.4 19.0 - - + -
291A THR* 3.0 24.7 + - - -
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Residues in contact with ASP 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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33A TYR* 3.7 18.2 - - - +
231A PHE 3.0 7.0 + - - +
232A ARG* 3.3 17.6 - - + +
233A ASN* 3.0 25.3 + - - +
264A ALA* 1.3 76.2 - - - +
266A ASN* 1.3 72.4 + - - +
267A ILE* 3.6 3.7 - - - +
291A THR* 2.7 28.1 + - - +
292A ASN* 2.9 24.2 + - - -
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Residues in contact with ASN 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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233A ASN* 2.7 28.2 + - - +
234A LEU 3.1 20.4 + - - -
265A ASP* 1.3 87.8 + - - +
267A ILE* 1.3 57.7 + - - +
268A ARG* 3.3 35.5 + - - +
291A THR 3.0 12.7 + - - -
292A ASN* 3.1 17.0 + - + +
294A SER* 5.2 0.5 + - - -
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Residues in contact with ILE 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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231A PHE 4.0 14.8 - - - +
234A LEU* 3.4 28.0 - - + +
241A ALA* 3.9 13.7 - - + -
242A LEU* 4.1 12.3 - - + -
264A ALA* 4.3 15.9 - - + -
265A ASP* 3.7 19.7 - - - +
266A ASN* 1.3 76.6 - - - +
268A ARG* 1.3 62.3 + - - +
275A ALA* 3.5 26.7 - - - +
276A VAL* 3.8 20.9 - - + -
290A VAL* 4.7 4.9 - - + -
292A ASN 3.3 4.2 + - - +
293A VAL* 3.5 8.8 - - + +
294A SER 3.1 22.5 + - - +
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Residues in contact with ARG 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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209A ILE 5.6 0.6 + - - -
210A LYS* 5.9 1.4 - - - +
233A ASN* 4.1 6.5 + - - +
234A LEU 2.8 19.0 + - - +
235A HIS* 3.2 45.5 + - + +
236A SER 3.2 21.7 + - - -
241A ALA* 3.5 8.7 - - - +
266A ASN* 3.3 48.4 + - - +
267A ILE* 1.3 77.8 - - - +
269A CYS* 1.3 60.9 + - - +
275A ALA* 3.9 3.6 - - - -
294A SER* 3.2 28.5 - - - +
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Residues in contact with CYS 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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235A HIS* 4.0 3.0 + - - -
236A SER 3.6 9.4 - - - +
239A GLY 4.3 2.9 - - - -
241A ALA* 5.4 1.1 - - + +
268A ARG* 1.3 73.8 - - - +
270A SER* 1.3 64.1 + - - +
272A GLY* 3.7 19.7 - - - -
273A LEU 4.1 0.2 - - - -
274A ALA 3.7 12.8 - - - +
275A ALA* 3.5 26.2 - - + +
294A SER 3.2 5.5 + - - -
295A SER* 3.3 7.3 - - - -
296A VAL* 3.1 23.2 + - - +
298A CYS* 2.1 44.6 - - - -
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Residues in contact with SER 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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210A LYS* 5.2 0.9 + - - -
235A HIS* 3.1 24.2 + - - -
236A SER 3.2 4.2 + - - -
237A GLU* 3.2 19.8 + - - +
238A GLY 3.0 17.8 + - - -
269A CYS* 1.3 77.5 - - - +
271A LYS* 1.3 73.2 + - - +
272A GLY 3.1 1.5 + - - -
296A VAL* 3.2 17.3 - - - -
298A CYS* 3.5 0.2 - - - -
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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