Contacts of the strand formed by residues 244 - 255 (chain A) in PDB entry 1XEH
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 244 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135A LYS* 5.3 5.0 + - - -
237A ASP* 3.0 8.7 - - - +
238A VAL* 2.8 34.6 + - + +
242A SER* 3.3 17.1 + - - +
243A LEU* 1.3 84.2 - - - +
245A LYS* 1.3 65.4 + - - +
246A TYR* 4.4 25.3 + - + +
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Residues in contact with LYS 245 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235A ILE* 3.4 33.7 - - + +
236A THR 3.9 2.7 - - - +
237A ASP* 3.5 20.4 - - - +
244A ASP* 1.3 80.5 + - - +
246A TYR* 1.3 73.5 + - - +
247A THR* 4.6 5.9 + - - +
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Residues in contact with TYR 246 (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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126A LEU* 4.9 15.3 - - + +
135A LYS* 3.3 35.3 + - - +
235A ILE* 3.7 3.8 - - - +
236A THR* 2.9 53.0 + - + +
238A VAL* 3.4 28.4 - - + +
244A ASP* 4.4 20.3 + - + +
245A LYS* 1.3 77.8 - - - +
247A THR* 1.3 68.8 + - - +
283A GLY* 4.8 22.7 - - - +
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Residues in contact with THR 247 (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 ASP* 4.8 13.9 - - + +
234A GLN 3.6 12.6 - - - +
235A ILE* 4.1 18.9 - - + +
245A LYS* 4.6 7.3 + - - +
246A TYR* 1.3 82.4 + - - +
248A LYS* 1.3 73.9 + - - +
319A LYS* 5.9 2.9 - - - -
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Residues in contact with LYS 248 (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 ASP* 3.8 3.8 - - - -
234A GLN* 3.1 29.5 + - + +
247A THR* 1.3 83.5 - - - +
249A THR* 1.3 82.4 + - - +
250A VAL* 3.5 4.6 + - - +
281A LYS* 4.4 25.8 - - + +
282A ARG* 4.6 19.7 - - + +
283A GLY 4.7 9.2 - - - +
284A LEU* 4.8 8.7 - - + -
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Residues in contact with THR 249 (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 SER* 4.2 9.2 - - - -
232A VAL 3.9 1.3 - - - +
233A ASP* 3.5 22.5 + - - +
248A LYS* 1.3 90.8 + - - +
250A VAL* 1.3 59.2 + - - +
251A PHE 3.3 25.6 - - - +
252A ILE* 4.3 13.0 - - + -
281A LYS* 3.4 21.3 - - - -
321A ARG* 6.2 0.4 - - - +
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Residues in contact with VAL 250 (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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232A VAL* 3.1 21.1 + - + +
234A GLN* 4.3 8.7 - - + +
248A LYS 3.9 6.7 - - - +
249A THR* 1.3 77.3 - - - +
251A PHE* 1.3 69.0 + - - +
273A PRO* 4.8 11.0 - - + +
274A ILE 5.4 2.8 + - - +
277A ALA* 5.2 3.1 - - - +
278A SER* 5.0 11.7 - - - -
281A LYS* 4.6 11.3 + - + +
284A LEU* 3.5 37.0 - - + -
297A LEU* 5.1 6.1 - - + -
318A TYR* 3.6 37.0 - - + +
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Residues in contact with PHE 251 (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 SER* 3.5 1.6 - - - -
232A VAL* 3.4 32.8 + - + -
249A THR* 3.3 17.6 - - - +
250A VAL* 1.3 81.3 - - - +
252A ILE* 1.3 80.2 + - + +
271A VAL* 3.8 23.6 - - + -
272A THR* 2.9 48.9 - - - -
273A PRO* 4.0 7.0 - - + -
274A ILE 5.7 0.4 - - - -
277A ALA* 5.5 13.2 - - + -
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Residues in contact with ILE 252 (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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229A LYS* 4.8 16.2 - - + -
230A ILE 3.8 7.0 - - - +
231A SER* 3.5 23.6 - - - -
249A THR* 4.3 10.8 - - + -
251A PHE* 1.3 93.3 - - + +
253A GLN* 1.3 76.3 + - - +
254A GLU* 4.7 6.5 - - + +
271A VAL* 5.8 2.2 - - - +
321A ARG* 4.9 6.3 - - - +
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Residues in contact with GLN 253 (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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229A LYS* 3.5 3.3 - - - +
230A ILE* 3.1 62.0 + - + +
252A ILE* 1.3 79.7 - - - +
254A GLU* 1.3 66.1 + - - +
255A PHE* 3.3 45.8 + - + -
269A PHE* 4.2 4.7 - - - +
270A ALA 4.6 4.9 + - - +
271A VAL* 4.4 15.5 - - + +
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Residues in contact with GLU 254 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227A LYS* 3.1 42.9 + - + +
228A ILE 4.1 1.8 - - - +
229A LYS* 3.1 37.2 + - + +
252A ILE* 4.3 6.3 - - + +
253A GLN* 1.3 74.5 - - - +
255A PHE* 1.3 69.6 + - - +
256A THR* 4.1 2.5 + - + +
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Residues in contact with PHE 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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227A LYS* 3.2 5.3 - - - +
228A ILE* 3.0 36.1 + - + +
230A ILE* 5.6 1.6 - - + -
253A GLN* 3.3 41.7 + - + +
254A GLU* 1.3 81.0 - - - +
256A THR* 1.3 61.4 + - - +
257A GLU* 2.8 45.3 + - + +
267A GLN* 5.5 0.4 - - - -
269A PHE* 3.9 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