Contacts of the strand formed by residues 254 - 268 (chain A) in PDB entry 1XKW
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 THR 254 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249A ASP* 3.4 4.0 - - - +
250A LEU* 2.9 48.5 + - + -
251A SER* 3.0 23.0 + - - +
252A PRO 3.6 0.2 - - - -
253A ASP* 1.3 79.0 - - - +
255A LEU* 1.3 61.5 + - - +
309A LEU* 3.7 28.9 - - + -
310A GLU 3.4 6.1 - - - +
311A GLN* 2.8 26.7 + - - +
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Residues in contact with LEU 255 (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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59A SER* 4.5 13.9 - - - -
218A ARG* 3.6 15.9 - - - +
247A GLU* 3.9 24.7 - - + +
248A PHE 3.7 5.6 - - - +
249A ASP* 3.5 21.8 - - - +
253A ASP 4.3 0.4 + - - -
254A THR* 1.3 73.2 - - - +
256A LEU* 1.3 63.0 + - - +
257A THR* 4.2 13.8 + - - +
308A SER* 3.7 1.6 + - - +
309A LEU* 3.3 5.9 - - - -
310A GLU* 2.9 59.4 + - + +
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Residues in contact with LEU 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A GLU* 3.2 5.0 - - - +
248A PHE* 2.8 64.0 + - + +
250A LEU* 3.9 30.0 - - + +
254A THR 4.2 0.6 - - - -
255A LEU* 1.3 74.0 - - - +
257A THR* 1.3 63.3 + - - +
258A VAL* 4.0 22.2 - - + -
307A GLY* 6.0 0.2 - - - -
308A SER 3.5 16.8 - - - +
309A LEU* 4.1 13.0 - - + -
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Residues in contact with THR 257 (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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182A ARG* 3.7 31.2 + - - +
245A VAL* 3.9 14.8 - - + -
246A THR 3.3 9.6 - - - +
247A GLU* 3.6 18.2 + - + +
255A LEU* 4.2 10.7 + - - +
256A LEU* 1.3 75.5 - - - +
258A VAL* 1.3 70.6 + - - +
306A PHE* 4.5 5.6 - - + -
307A GLY* 3.0 3.8 - - - -
308A SER* 2.8 48.9 + - - +
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Residues in contact with VAL 258 (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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245A VAL* 3.5 4.1 - - - -
246A THR* 2.8 49.1 + - - +
248A PHE* 4.8 5.8 - - + -
256A LEU* 4.0 25.8 - - + -
257A THR* 1.3 81.5 - - - +
259A GLY* 1.3 66.7 - - - +
306A PHE 3.5 8.7 - - - +
307A GLY* 4.8 3.1 - - - -
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Residues in contact with GLY 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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244A GLY 3.1 13.5 - - - -
245A VAL* 4.0 0.7 - - - -
258A VAL* 1.3 81.4 - - - +
260A ALA* 1.3 63.9 + - - +
305A ALA* 3.4 2.4 - - - +
306A PHE* 2.9 53.9 + - - +
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Residues in contact with ALA 260 (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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243A TYR* 3.4 7.2 - - - -
244A GLY* 2.8 32.4 + - - +
259A GLY* 1.3 76.9 - - - +
261A GLN* 1.3 62.4 + - - +
304A ARG 3.2 13.2 - - - +
305A ALA* 4.4 4.9 - - + -
306A PHE* 3.6 4.1 - - - -
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Residues in contact with GLN 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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149A ASP 5.2 1.4 + - - -
152A ILE* 3.3 27.7 - - - +
153A TYR* 5.2 0.4 + - - -
180A ARG* 5.1 2.9 + - - +
241A LEU* 3.4 29.7 - - + +
242A LEU 3.4 11.9 - - - +
243A TYR* 4.1 10.1 - - + -
260A ALA* 1.3 78.3 - - - +
262A TYR* 1.3 69.9 + - - +
263A GLN* 4.3 13.2 + - - +
302A THR* 3.8 1.5 - - - +
303A TYR* 3.5 4.5 - - - +
304A ARG* 2.9 75.8 + - + +
306A PHE* 5.5 2.0 - - + -
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Residues in contact with TYR 262 (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 ARG* 5.0 6.7 - - + -
241A LEU* 3.4 5.9 - - - +
242A LEU* 2.9 47.7 + - + +
261A GLN* 1.3 75.1 - - - +
263A GLN* 1.3 72.8 + - - +
264A HIS* 3.4 23.7 + - + +
301A ASP* 2.8 29.7 + - - -
302A THR 3.4 6.1 - - - -
303A TYR* 3.5 39.0 + + + +
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Residues in contact with GLN 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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146A SER* 3.4 11.9 + - - -
147A PRO 3.1 24.0 + - - -
148A GLN* 3.9 12.3 + - - +
149A ASP* 3.0 32.6 + - - +
239A THR* 4.9 3.1 - - + -
240A ARG 3.5 7.2 - - - +
241A LEU* 4.1 12.1 - - + +
261A GLN* 4.3 17.1 + - - +
262A TYR* 1.3 79.2 - - - +
264A HIS* 1.3 61.0 + - - +
265A ILE* 3.8 16.5 - - + +
300A TRP 3.7 1.2 - - - +
301A ASP* 3.5 2.9 - - - -
302A THR* 2.9 51.2 + - + +
304A ARG* 5.5 1.5 + - - +
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Residues in contact with HIS 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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238A GLY 5.2 0.7 - - - -
239A THR* 3.5 3.5 - - - +
240A ARG* 2.8 59.4 + - + +
262A TYR* 3.4 24.6 + - + +
263A GLN* 1.3 71.4 - - - +
265A ILE* 1.3 72.4 + - - +
266A ASP* 3.7 25.9 + - + +
299A LYS* 4.5 18.6 - - + -
300A TRP 3.4 3.4 + - - -
301A ASP* 2.6 29.1 + - - -
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Residues in contact with ILE 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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146A SER* 3.8 5.6 - - - +
147A PRO* 3.3 40.2 - - + +
148A GLN* 5.2 0.2 - - - -
149A ASP* 5.3 2.0 - - + +
237A GLN* 3.6 33.7 - - + +
238A GLY 3.4 4.7 - - - +
239A THR* 4.3 15.3 - - + +
263A GLN* 3.8 20.9 - - + +
264A HIS* 1.3 82.0 - - - +
266A ASP* 1.3 62.9 + - - +
299A LYS* 3.1 4.2 - - - +
300A TRP* 2.6 62.9 + - + +
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Residues in contact with ASP 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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236A ASP* 4.6 1.2 - - - +
237A GLN* 3.3 1.4 - - - +
238A GLY* 2.7 41.2 + - - +
240A ARG* 6.3 0.9 - - - +
264A HIS* 3.7 21.3 + - + +
265A ILE* 1.3 73.7 - - - +
267A SER* 1.3 71.4 + - - +
297A ARG* 2.9 39.3 + - - -
298A PHE 3.9 1.6 - - - -
299A LYS* 3.8 15.2 - - - +
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Residues in contact with SER 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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230A TYR* 5.7 0.2 - - - -
236A ASP* 3.1 21.1 - - - -
237A GLN* 4.0 13.9 - - - -
266A ASP* 1.3 78.5 + - - +
268A ILE* 1.3 61.9 + - - +
269A THR* 3.9 8.1 + - - -
297A ARG* 3.3 11.9 - - - +
298A PHE* 2.8 59.2 + - - +
300A TRP* 3.7 10.7 - - - -
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Residues in contact with ILE 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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230A TYR* 5.4 0.2 - - - -
234A VAL* 3.8 24.2 - - + +
235A ALA* 3.2 8.2 - - - +
236A ASP* 3.1 54.6 + - - +
267A SER* 1.3 71.0 - - - +
269A THR* 1.3 60.4 + - - +
290A TYR* 3.8 19.1 - - - +
294A ASP 3.9 19.3 - - - +
296A ASP* 3.7 17.0 - - + +
297A ARG* 3.6 28.5 - - - +
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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