Contacts of the helix formed by residues 242 - 259 (chain A) in PDB entry 1UA4
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 TYR 242 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A LEU* 4.0 14.8 - - + -
238A THR 3.1 20.9 + - - +
239A LYS* 3.5 25.4 - - - -
241A ASN* 1.3 79.5 - - - +
243A LYS* 1.3 107.6 + - + +
245A PRO* 3.3 2.6 - - - +
246A PHE* 3.0 48.5 + + + -
274A LYS* 3.6 24.2 + - + -
275A VAL* 3.9 15.3 - - + -
278A GLU* 3.5 35.8 + - + -
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Residues in contact with LYS 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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239A LYS 5.5 2.7 - - - +
241A ASN 3.5 1.8 - - - -
242A TYR* 1.3 117.0 + - + +
244A GLU* 1.3 67.3 + - + +
246A PHE* 3.6 3.8 - - - +
247A GLU* 3.2 28.0 + - - +
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Residues in contact with GLU 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A ASN 4.6 1.2 + - - +
243A LYS* 1.3 78.0 - - + +
245A PRO* 1.3 72.8 - - + +
247A GLU* 3.2 16.5 + - - +
248A ILE* 3.3 17.3 + - - +
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Residues in contact with PRO 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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208A THR 3.5 21.1 - - - +
209A LEU* 3.7 34.5 - - + +
211A ILE* 4.6 1.5 - - + +
237A LEU* 4.0 6.1 - - + -
241A ASN 3.2 22.9 - - - +
242A TYR 3.3 6.3 - - - +
244A GLU* 1.3 95.0 - - + +
246A PHE* 1.3 61.9 + - - +
248A ILE* 3.1 10.8 + - + +
249A VAL* 3.0 27.0 + - - +
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Residues in contact with PHE 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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234A LEU* 3.9 19.1 - - + -
237A LEU* 3.7 24.2 - - + -
242A TYR* 3.0 44.8 + + + +
243A LYS* 3.6 6.1 - - - +
245A PRO* 1.3 78.4 - - - +
247A GLU* 1.3 58.1 + - - +
249A VAL* 3.3 8.0 + - + +
250A LYS* 2.9 42.6 + - + +
275A VAL* 4.2 8.1 - - + -
278A GLU* 3.7 38.1 - - + -
279A ILE* 3.8 26.9 - - + -
282A VAL* 4.4 15.9 - - + -
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Residues in contact with GLU 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A LYS* 3.2 15.6 + - + +
244A GLU* 3.2 11.0 + - - +
246A PHE* 1.3 78.2 - - - +
248A ILE* 1.3 65.4 + - + +
250A LYS* 2.9 35.3 + - - +
251A SER* 3.0 27.6 + - - -
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Residues in contact with ILE 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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211A ILE* 3.6 36.8 - - + -
215A PHE 4.8 1.6 - - - +
216A ARG* 4.1 37.0 - - + +
244A GLU 3.6 13.5 - - - +
245A PRO* 3.1 10.7 + - + +
247A GLU* 1.3 79.6 - - + +
249A VAL* 1.3 62.7 + - - +
251A SER* 3.1 9.5 + - - +
252A ASN* 3.0 32.3 + - - +
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Residues in contact with VAL 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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29A TYR* 3.7 40.2 - - + +
209A LEU* 3.9 19.3 - - + -
211A ILE* 4.3 3.1 - - + -
231A LEU* 4.6 5.2 - - + -
234A LEU* 4.6 20.4 - - + -
245A PRO 3.0 14.0 + - - +
246A PHE* 3.7 10.5 - - + +
248A ILE* 1.3 77.2 - - - +
250A LYS* 1.3 57.2 + - + +
252A ASN* 3.1 4.0 + - - +
253A LEU* 2.8 44.9 + - + +
282A VAL* 6.3 1.8 - - + -
286A PHE* 5.0 3.6 - - + -
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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
----------------------------------------------------------
246A PHE* 2.9 35.9 + - + +
247A GLU* 2.9 33.5 + - - +
249A VAL* 1.3 77.6 - - + +
251A SER* 1.3 57.2 + - - +
253A LEU* 3.2 11.8 + - + +
254A GLU* 2.9 35.5 + - + +
282A VAL* 4.1 28.3 - - + +
285A MET* 4.0 15.7 - - + +
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Residues in contact with SER 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A GLU 3.0 15.7 + - - -
248A ILE* 3.4 13.0 - - - +
250A LYS* 1.3 72.5 - - - +
252A ASN* 1.3 68.6 + - - +
254A GLU* 3.2 19.1 + - - +
255A VAL* 3.2 26.6 + - - +
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Residues in contact with ASN 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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29A TYR* 2.6 41.2 + - - +
215A PHE* 3.3 23.0 + - - +
216A ARG 4.5 1.9 - - - +
219A PHE* 3.6 36.5 - - + +
231A LEU* 5.3 0.7 - - + -
248A ILE* 3.0 24.9 + - - +
249A VAL 3.1 7.2 + - - +
251A SER* 1.3 79.3 - - - +
253A LEU* 1.3 57.3 + - - +
255A VAL* 3.2 4.2 + - - +
256A LEU* 2.9 36.5 + - + +
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Residues in contact with LEU 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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231A LEU* 4.0 7.4 - - + -
249A VAL* 2.8 30.2 + - + +
250A LYS* 3.5 13.0 - - + +
251A SER 3.2 0.2 - - - -
252A ASN* 1.3 74.3 - - - +
254A GLU* 1.3 55.2 + - - +
256A LEU* 3.7 2.6 - - + +
257A ASN* 2.7 43.4 + - - +
263A VAL* 4.0 28.9 - - + -
282A VAL* 4.8 3.8 - - + +
285A MET* 3.8 39.7 - - + +
286A PHE* 3.7 39.9 - - + -
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Residues in contact with GLU 254 (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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250A LYS* 2.9 28.5 + - + +
251A SER* 3.2 20.6 + - - +
253A LEU* 1.3 75.4 - - - +
255A VAL* 1.3 60.1 + - + +
257A ASN* 3.9 7.9 - - - +
258A GLU* 2.9 30.1 + - - +
285A MET* 4.3 11.4 - - + +
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Residues in contact with VAL 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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219A PHE* 4.0 13.7 - - + -
220A SER* 3.9 24.9 - - - +
223A ILE* 3.4 25.1 - - + -
251A SER* 3.2 14.6 + - - +
252A ASN 3.6 6.5 - - - +
254A GLU* 1.3 76.3 - - + +
256A LEU* 1.3 64.9 + - - +
258A GLU* 3.3 5.8 + - - +
259A ARG* 3.2 36.1 + - + +
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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
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26A LEU* 4.3 5.6 - - + -
219A PHE* 4.0 16.6 - - + -
223A ILE* 3.6 25.6 - - + -
226A VAL* 5.1 1.1 - - + -
229A ALA* 4.0 15.7 - - + -
231A LEU* 4.3 12.6 - - + -
252A ASN* 2.9 24.8 + - + +
253A LEU* 3.7 5.8 - - - +
255A VAL* 1.3 75.7 - - - +
257A ASN* 1.3 61.4 + - - +
259A ARG 3.2 3.1 + - - -
260A GLU 3.1 4.0 + - - -
261A ILE* 3.0 51.1 + - + +
263A VAL* 3.5 34.8 - - + -
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Residues in contact with ASN 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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253A LEU* 2.7 35.9 + - - +
254A GLU* 3.9 5.8 - - - +
256A LEU* 1.3 73.4 - - - +
258A GLU* 1.3 57.0 + - - +
260A GLU* 2.9 25.2 + - - +
261A ILE 4.9 2.6 - - - +
263A VAL* 4.8 7.4 - - - +
285A MET* 3.1 48.5 + - - +
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Residues in contact with GLU 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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254A GLU 2.9 19.0 + - - +
255A VAL* 3.6 8.3 - - - +
256A LEU 3.3 0.2 - - - -
257A ASN* 1.3 75.8 - - - +
259A ARG* 1.3 64.4 + - + +
260A GLU* 3.1 9.1 + - - +
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Residues in contact with ARG 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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220A SER* 2.8 52.0 + - - -
223A ILE* 3.5 20.7 - - - +
224A LYS* 3.4 36.0 - - - +
255A VAL* 3.2 19.5 + - + +
256A LEU 3.9 3.6 - - - +
258A GLU* 1.3 81.1 - - + +
260A GLU* 1.3 71.3 + - - +
261A ILE* 3.3 20.5 + - + +
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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