Contacts of the strand formed by residues 225 - 237 (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 225 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189A VAL* 3.2 18.1 + - - +
190A ASP 4.2 0.5 - - - +
191A VAL* 4.1 11.4 - - - +
200A TRP* 3.6 27.5 - - - +
201A SER 4.2 2.4 + - - -
224A TYR* 1.3 81.3 - - - +
226A ALA* 1.3 66.2 + - - +
257A GLY 4.5 0.2 - - - -
258A GLY 3.3 12.1 - - - -
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Residues in contact with ALA 226 (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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189A VAL* 3.8 19.3 - - + -
200A TRP* 3.5 3.0 - - - -
201A SER 3.5 9.4 - - - +
223A THR* 5.4 2.7 - - + -
225A GLY* 1.3 76.0 - - - +
227A ASP* 1.3 66.1 + - - +
229A ILE* 3.9 16.4 - - + -
231A PHE* 5.8 1.3 - - + -
258A GLY 3.0 8.9 + - - +
259A ILE* 3.1 18.0 - - + +
260A ARG 3.0 25.5 + - - -
262A ILE* 4.2 7.4 - - + -
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Residues in contact with ASP 227 (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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200A TRP* 2.8 29.8 + - - -
201A SER 3.2 5.7 + - - -
202A ARG* 2.9 44.8 + - + +
203A ASN 3.1 14.6 + - - -
226A ALA* 1.3 75.3 - - - +
228A ASN* 1.3 74.4 + - + +
229A ILE* 3.6 3.5 - - - +
260A ARG* 2.9 41.0 + - - +
261A ASN* 4.9 4.4 + - + +
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Residues in contact with ASN 228 (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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37A ASP* 3.1 25.8 + - - +
38A PHE* 3.5 24.8 - - - +
202A ARG* 5.7 2.0 - - + +
203A ASN* 2.8 43.6 + - - +
204A GLY 3.4 2.3 + - - -
227A ASP* 1.3 77.4 - - + +
229A ILE* 1.3 57.5 + - - +
260A ARG 3.2 13.3 + - - -
261A ASN* 3.3 21.3 - - + +
262A ILE* 4.3 0.2 - - - +
263A PHE* 5.1 3.1 - - - -
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Residues in contact with ILE 229 (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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38A PHE* 4.0 5.5 - - - -
170A TYR* 3.4 30.5 - - + +
189A VAL* 5.2 1.1 - - + -
201A SER* 4.1 6.1 - - - +
202A ARG* 4.1 2.2 - - - -
203A ASN 3.9 4.3 - - - +
204A GLY 3.4 29.4 - - - +
206A ILE* 4.5 5.2 - - + -
226A ALA* 3.9 23.6 - - + -
227A ASP 3.7 12.3 - - - +
228A ASN* 1.3 77.8 - - - +
230A LEU* 1.3 65.9 + - - +
231A PHE* 3.7 35.2 - - + -
261A ASN 3.7 3.2 + - - -
262A ILE* 3.7 9.0 - - + +
263A PHE 3.1 25.6 + - - +
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Residues in contact with LEU 230 (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 37.7 - - + +
35A ASP* 4.7 2.0 - - - +
38A PHE* 3.9 28.7 - - + -
204A GLY 3.0 10.0 + - - +
205A ILE* 3.4 16.9 - - + +
206A ILE 2.9 26.9 + - - +
229A ILE* 1.3 74.1 - - - +
231A PHE* 1.3 71.6 + - - +
232A ARG* 3.8 38.4 - - + +
263A PHE* 3.3 22.0 - - + +
264A ALA* 4.4 1.1 - - - +
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Residues in contact with PHE 231 (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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189A VAL* 4.4 7.9 - - + -
206A ILE* 3.3 39.7 - - + -
221A ILE* 3.8 19.1 - - + -
223A THR* 3.8 23.3 - - + -
226A ALA* 5.8 0.9 - - + -
229A ILE* 3.7 23.1 - - + -
230A LEU* 1.3 73.7 - - - +
232A ARG* 1.3 62.0 + - - +
234A LEU* 3.9 18.2 - - + -
242A LEU* 4.0 25.4 - - + -
244A MET* 5.9 0.2 - - - -
262A ILE* 3.7 33.4 - - + -
263A PHE 2.9 8.1 + - - -
264A ALA* 3.0 34.5 - - + +
265A ASP 3.0 5.4 + - - +
267A ILE* 4.0 3.0 - - + +
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Residues in contact with ARG 232 (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* 4.8 12.8 - - - -
35A ASP* 3.1 39.8 + - - -
171A LYS* 5.4 2.2 - - - +
205A ILE* 4.2 8.9 - - - +
206A ILE 3.1 7.3 + - - -
207A GLU* 2.7 40.2 + - + +
208A ARG 3.0 19.9 + - - -
230A LEU* 3.8 27.7 - - + +
231A PHE* 1.3 76.0 - - - +
233A ASN* 1.3 91.5 + - - +
234A LEU* 3.5 6.2 - - - +
265A ASP* 3.3 20.6 - - + +
267A ILE* 4.6 0.4 - - - -
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Residues in contact with ASN 233 (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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207A GLU* 5.1 0.2 + - - -
208A ARG* 3.2 43.2 + - + +
209A ILE 3.3 4.3 + - - +
232A ARG* 1.3 99.7 - - - +
234A LEU* 1.3 58.2 + - - +
265A ASP* 3.0 13.5 + - - +
266A ASN* 2.7 42.8 + - - +
268A ARG* 4.1 9.2 + - - +
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Residues in contact with LEU 234 (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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206A ILE* 4.1 6.1 - - + +
207A GLU* 3.9 11.9 - - - -
209A ILE* 3.5 32.3 - - + +
220A LEU* 3.9 11.4 - - + -
221A ILE* 3.9 27.4 - - + -
231A PHE* 3.9 26.7 - - + -
232A ARG 3.6 20.0 - - - +
233A ASN* 1.3 79.0 - - - +
235A HIS* 1.3 62.9 + - - +
241A ALA* 4.8 5.8 - - + +
242A LEU* 5.2 3.6 - - + -
266A ASN 3.1 5.6 + - - +
267A ILE* 3.4 18.0 - - + +
268A ARG* 2.8 26.9 + - - +
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Residues in contact with HIS 235 (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 3.1 8.2 + - - +
210A LYS* 3.4 33.9 - - + +
211A GLN 2.9 24.6 + - - -
220A LEU* 3.8 5.9 - - - +
234A LEU* 1.3 76.2 - - - +
236A SER* 1.3 89.0 + - - +
241A ALA* 4.6 0.7 - - - -
268A ARG* 3.2 55.5 + - + +
269A CYS 4.0 1.8 + - - -
270A SER* 3.1 33.0 + - - -
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Residues in contact with SER 236 (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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211A GLN* 3.7 8.1 - - - +
214A ALA* 4.0 9.5 - - - +
219A GLY* 4.0 1.2 - - - -
220A LEU* 3.9 19.7 + - - -
235A HIS* 1.3 81.8 - - - +
237A GLU* 1.3 61.1 + - - +
238A GLY 3.0 20.9 + - - +
239A GLY 5.4 0.4 - - - +
240A ILE 4.3 0.2 - - - -
241A ALA* 3.7 28.0 - - - +
268A ARG 3.2 4.8 + - - -
269A CYS* 3.6 7.3 - - - -
270A SER 3.2 19.9 + - - -
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Residues in contact with GLU 237 (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* 4.6 6.7 - - - -
211A GLN 2.9 17.7 + - - +
212A ASN* 3.7 14.1 - - - +
213A ASN* 2.8 29.0 + - - +
214A ALA* 3.0 26.3 + - - +
235A HIS* 4.3 0.4 - - - -
236A SER* 1.3 68.7 + - - +
238A GLY* 1.3 62.0 + - - +
270A SER* 3.2 25.7 + - - +
271A LYS* 4.5 16.2 + - + +
491A ARG* 3.9 30.4 + - - +
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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