Contacts of the helix formed by residues 241 - 253 (chain A) in PDB entry 1UPX
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 241 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159A HIS* 2.8 35.1 + - - +
162A VAL* 3.6 22.7 - - - +
240A HIS* 1.3 75.6 - - - +
242A LEU* 1.3 62.5 + - - +
243A ARG* 3.1 13.7 + - - +
244A ASP* 2.9 56.9 + - - +
245A LEU 3.5 8.1 + - - -
265A MET* 3.5 10.5 - - - +
305A THR* 3.1 14.3 + - - +
306A THR* 4.7 1.3 - - + -
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Residues in contact with LEU 242 (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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163A LEU* 5.4 1.5 - - + +
213A ASN* 3.4 32.0 + - - +
217A TYR* 3.7 26.0 + - + -
240A HIS 3.2 12.5 + - - +
241A ASP* 1.3 71.7 + - - +
243A ARG* 1.3 60.8 + - - +
245A LEU* 3.2 6.6 + - + +
246A GLU 3.0 22.7 + - - -
265A MET* 4.2 7.9 - - + -
268A ALA* 3.7 34.5 - - + +
271A TYR* 3.6 30.1 - - + +
274A PHE* 3.6 11.9 - - + -
451A GLN* 4.3 12.8 - - - +
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Residues in contact with ARG 243 (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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162A VAL* 3.6 28.4 + - + +
163A LEU* 3.9 14.3 - - + +
217A TYR* 3.3 12.2 + - - +
241A ASP* 3.1 10.1 + - - +
242A LEU* 1.3 74.9 - - - +
244A ASP* 1.3 66.7 + - - +
246A GLU* 3.1 32.4 + - - +
247A MET* 3.1 52.4 + - + +
250A LYS* 4.9 4.6 - - - +
339A GLY* 3.0 30.0 + - - +
340A GLU 4.7 3.0 - - - -
341A HIS* 4.8 2.8 - - - +
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Residues in contact with ASP 244 (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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237A ILE* 4.1 4.0 - - + -
241A ASP* 2.9 28.5 + - - +
242A LEU 3.3 0.4 - - - -
243A ARG* 1.3 77.4 - - - +
245A LEU* 1.3 56.2 + - - +
247A MET* 3.4 9.4 + - - +
248A LEU* 2.9 29.5 + - - +
303A LEU* 5.0 0.4 - - + -
305A THR* 3.3 37.1 - - + +
323A THR* 3.5 8.8 - - - +
324A GLY* 5.8 0.2 - - - -
339A GLY* 6.0 0.3 - - - -
342A LYS* 2.7 42.9 + - - +
344A PHE* 3.7 11.9 - - + -
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Residues in contact with LEU 245 (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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237A ILE* 3.7 19.4 - - + +
241A ASP 3.5 3.0 + - - -
242A LEU* 3.2 8.2 + - + +
244A ASP* 1.3 78.8 - - - +
246A GLU* 1.3 57.8 + - - +
248A LEU* 3.1 2.7 + - + -
249A LEU* 2.8 49.2 + - + +
259A VAL* 3.9 22.7 - - + -
261A THR* 5.0 0.2 - - + -
265A MET* 3.8 17.9 - - + -
268A ALA* 3.2 34.8 - - + -
274A PHE* 4.0 18.8 - - + -
280A PHE* 3.8 16.4 - - + -
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Residues in contact with GLU 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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216A THR* 4.8 3.4 - - - +
217A TYR* 2.7 47.5 + - + +
242A LEU 3.0 8.3 + - - +
243A ARG* 3.1 29.9 + - - +
245A LEU* 1.3 75.6 - - - +
247A MET* 1.3 63.7 + - - +
249A LEU* 3.4 4.1 + - - +
250A LYS* 2.8 58.2 + - + +
274A PHE* 3.8 15.9 - - + -
277A TYR* 4.5 6.0 + - + +
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Residues in contact with MET 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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243A ARG* 3.1 57.2 + - + +
244A ASP* 3.8 24.0 - - - +
246A GLU* 1.3 79.0 - - - +
248A LEU* 1.3 63.1 + - - +
250A LYS* 3.4 8.4 + - + +
251A GLN* 3.0 36.5 + - - +
339A GLY* 4.4 1.3 - - - +
340A GLU 3.5 26.7 - - - +
341A HIS* 3.9 7.0 - - - +
342A LYS* 3.6 28.7 - - + +
344A PHE* 3.8 10.8 - - + -
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Residues in contact with LEU 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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235A ILE* 4.0 42.6 - - + -
237A ILE* 4.2 20.9 - - + -
244A ASP 2.9 17.5 + - - +
245A LEU* 3.6 5.2 - - + +
247A MET* 1.3 77.0 - - - +
249A LEU* 1.3 51.2 + - - +
251A GLN* 3.3 1.7 + - - -
252A THR* 2.7 41.9 + - + +
259A VAL* 4.0 27.8 - - + -
303A LEU* 4.3 6.1 - - + -
344A PHE* 3.6 37.2 - - + -
347A ILE* 4.5 2.5 - - + -
348A ILE* 4.7 0.7 - - + -
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Residues in contact with LEU 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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245A LEU* 2.8 36.6 + - + +
246A GLU 3.8 3.4 - - - +
248A LEU* 1.3 69.0 - - - +
250A LYS* 1.3 65.1 + - - +
252A THR* 3.2 1.5 + - - -
253A GLU* 3.2 6.2 + - - +
259A VAL* 3.8 27.1 - - + -
274A PHE* 3.7 29.8 - - + -
277A TYR* 3.8 28.8 - - + -
279A HIS* 2.9 36.7 + - + +
280A PHE* 3.8 32.1 - - + -
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Residues in contact with LYS 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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243A ARG* 4.9 4.7 - - - +
246A GLU* 2.8 53.0 + - + +
247A MET* 3.8 7.9 - - + +
249A LEU* 1.3 77.3 - - - +
251A GLN* 1.3 63.8 + - + +
253A GLU* 3.4 18.0 + - - +
277A TYR* 3.5 29.8 - - + +
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Residues in contact with GLN 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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247A MET* 3.0 29.2 + - - +
248A LEU* 4.0 3.1 - - - +
249A LEU 3.3 0.2 - - - -
250A LYS* 1.3 79.5 - - + +
252A THR* 1.3 58.4 + - - +
253A GLU 3.4 2.1 + - - +
255A THR* 3.4 15.8 - - - +
341A HIS* 3.5 19.3 - - + -
342A LYS 2.8 24.2 + - - -
343A ASP* 3.9 3.3 - - - +
344A PHE* 2.8 38.0 + - + +
345A SER* 4.0 1.9 + - - -
348A ILE* 3.5 18.6 - - + +
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Residues in contact with THR 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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235A ILE* 4.3 6.7 - - + -
248A LEU* 2.7 29.9 + - + +
249A LEU* 3.2 3.5 + - - -
250A LYS 3.3 0.2 - - - -
251A GLN* 1.3 75.0 - - - +
253A GLU* 1.3 64.5 + - - +
254A GLY 3.2 0.9 + - - -
255A THR* 2.7 29.2 + - - +
256A GLY 4.4 0.5 + - - -
257A VAL* 3.7 15.3 - - + +
259A VAL* 3.5 16.4 - - + +
279A HIS* 2.9 34.9 + - - -
348A ILE* 3.8 24.5 - - + -
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Residues in contact with GLU 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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249A LEU 3.2 10.3 + - - +
250A LYS* 3.4 16.3 - - - +
251A GLN 3.4 3.1 - - - +
252A THR* 1.3 77.5 - - - +
254A GLY* 1.3 70.9 + - - +
255A THR* 3.4 5.7 + - - +
276A LYS 5.3 1.0 - - - +
277A TYR* 4.0 15.4 - - + -
278A ALA* 5.1 1.7 + - - +
279A HIS* 3.3 25.7 + - - -
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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