Contacts of the helix formed by residues 244 - 262 (chain A) in PDB entry 1UOU
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 ASN 244 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236A PHE* 4.5 0.9 - - - -
242A PHE 2.7 15.1 + - - +
243A PRO* 1.3 84.2 - - - +
245A GLN* 1.3 67.5 + - - +
246A GLU* 3.2 8.3 + - + +
247A GLN* 3.3 26.4 + - + +
248A ALA* 3.3 6.4 + - - +
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Residues in contact with GLN 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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236A PHE* 3.7 44.4 - - + -
243A PRO 3.7 3.4 + - - -
244A ASN* 1.3 71.7 - - - +
246A GLU* 1.3 61.8 + - - +
248A ALA* 3.4 2.6 + - - +
249A ARG* 3.1 52.8 + - + +
270A LEU* 6.2 0.4 - - + -
473A PHE* 5.5 4.7 - - - -
475A GLU* 5.6 0.3 - - - +
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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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244A ASN* 3.2 6.4 + - + +
245A GLN* 1.3 77.5 - - - +
247A GLN* 1.3 61.3 - - + +
249A ARG* 3.5 10.9 + - - +
250A GLU* 3.3 20.1 + - - +
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Residues in contact with GLN 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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211A LEU* 4.2 15.2 - - - +
242A PHE* 3.5 46.4 - - + -
244A ASN* 3.3 20.9 + - + +
246A GLU* 1.3 76.7 - - + +
248A ALA* 1.3 61.8 + - - +
250A GLU* 3.2 20.4 + - - +
251A LEU* 2.9 28.8 + - - +
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Residues in contact with ALA 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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234A VAL* 3.5 19.2 - - + +
235A LYS 4.3 2.9 - - - +
236A PHE* 3.8 27.8 - - + -
242A PHE* 4.1 8.1 - - + +
244A ASN 3.3 4.0 + - - +
245A GLN 3.4 8.0 + - - +
247A GLN* 1.3 77.6 - - - +
249A ARG* 1.3 57.8 + - - +
251A LEU* 3.3 7.0 + - - +
252A ALA* 2.9 25.3 + - - +
270A LEU* 3.6 20.2 - - + -
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Residues in contact with ARG 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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236A PHE* 6.3 0.6 - - - -
245A GLN* 3.1 41.8 + - + +
246A GLU* 3.7 9.4 - - - +
247A GLN 3.2 0.4 - - - -
248A ALA* 1.3 75.9 - - - +
250A GLU* 1.3 62.5 + - - +
252A ALA* 3.2 4.1 + - - +
253A LYS* 3.1 28.5 + - - +
270A LEU* 3.8 29.8 - - + +
473A PHE* 6.2 0.8 - - - -
475A GLU* 2.6 38.4 + - - +
477A VAL* 5.1 5.3 - - - +
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Residues in contact with GLU 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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211A LEU* 3.3 29.1 - - + +
246A GLU 3.3 10.4 + - - +
247A GLN* 3.2 19.8 + - - +
249A ARG* 1.3 80.7 - - - +
251A LEU* 1.3 56.9 - - - +
253A LYS* 3.3 31.3 + - - +
254A THR* 2.5 36.8 + - - +
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Residues in contact with LEU 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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118A THR* 4.0 25.6 - - + +
211A LEU* 3.8 22.5 - - + +
214A ILE* 4.0 26.0 - - + -
215A THR* 4.0 19.1 - - - +
234A VAL* 4.5 8.3 - - + -
241A VAL* 5.5 1.3 - - + -
242A PHE* 3.8 24.2 - - + -
247A GLN 2.9 12.9 + - - +
248A ALA* 3.5 9.0 - - - +
250A GLU* 1.3 77.4 - - - +
252A ALA* 1.3 52.6 + - - +
254A THR* 3.1 4.6 + - - -
255A LEU* 2.8 53.5 + - + +
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Residues in contact with ALA 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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234A VAL* 4.1 15.9 - - + +
248A ALA 2.9 13.4 + - - +
249A ARG* 3.2 12.3 + - - +
251A LEU* 1.3 76.5 - - - +
253A LYS* 1.3 57.6 + - - +
255A LEU* 3.6 3.3 + - - +
256A VAL* 3.1 33.8 + - - +
268A ALA* 3.9 20.2 - - + -
270A LEU* 4.4 5.4 - - + -
477A VAL* 4.3 18.8 - - + -
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Residues in contact with LYS 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 ARG* 3.1 18.4 + - - +
250A GLU* 3.3 40.6 - - - +
252A ALA* 1.3 75.7 - - - +
254A THR* 1.3 59.9 + - - +
256A VAL* 4.1 6.2 - - - +
257A GLY* 2.9 25.7 + - - -
477A VAL* 4.9 11.0 - - + -
480A PRO* 6.0 4.5 - - + +
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Residues in contact with THR 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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85A LEU* 4.3 16.2 - - + +
88A THR* 5.2 4.9 - - + +
211A LEU* 4.9 13.6 - - + +
212A PRO 5.7 0.2 - - - -
215A THR* 3.5 20.5 - - + +
250A GLU* 2.5 30.5 + - - +
251A LEU* 3.4 7.0 - - - -
253A LYS* 1.3 80.5 - - - +
255A LEU* 1.3 64.3 + - - +
256A VAL 3.2 0.2 - - - -
257A GLY 4.5 0.2 - - - +
258A VAL* 2.9 44.7 + - + +
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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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118A THR* 4.2 4.5 - - + -
215A THR* 3.9 17.9 - - - +
218A ILE* 4.3 20.0 - - + -
219A LEU* 3.3 34.5 - - + +
232A VAL* 3.9 36.6 - - + -
234A VAL* 3.9 15.0 - - + -
251A LEU* 2.8 42.7 + - + +
252A ALA* 3.8 4.9 - - - +
254A THR* 1.3 75.4 - - - +
256A VAL* 1.3 58.6 + - - +
259A GLY* 3.0 26.9 + - - -
266A VAL* 4.4 3.6 - - + +
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Residues in contact with VAL 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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252A ALA 3.1 19.5 + - - +
253A LYS* 4.1 5.2 - - - +
255A LEU* 1.3 77.6 - - + +
257A GLY* 1.3 59.8 + - - +
259A GLY* 3.9 0.2 - - - -
260A ALA* 3.0 28.2 + - - +
266A VAL* 3.9 22.8 + - + +
267A ALA* 4.0 3.8 - - - -
268A ALA* 3.9 28.9 - - + +
477A VAL* 4.1 7.6 - - + +
478A LEU 3.6 5.4 - - - +
479A PRO* 3.4 39.5 - - + -
480A PRO* 4.2 5.6 - - + -
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Residues in contact with GLY 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 LYS 2.9 19.7 + - - -
254A THR* 5.1 0.2 - - - -
256A VAL* 1.3 77.5 - - - +
258A VAL* 1.3 63.7 + - - +
260A ALA* 3.4 5.4 + - - +
261A SER* 3.1 23.0 + - - -
480A PRO* 5.4 6.7 - - - -
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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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85A LEU* 4.1 22.9 - - + +
88A THR* 4.5 7.2 - - + -
89A SER* 4.1 29.6 - - - +
92A THR* 4.5 4.9 - - - +
215A THR* 4.0 22.9 - - + -
219A LEU* 4.9 3.6 - - + -
254A THR* 2.9 35.0 + - + +
257A GLY* 1.3 73.6 - - - +
259A GLY* 1.3 66.3 + - - +
261A SER* 2.8 20.3 + - - -
262A LEU* 3.4 18.4 + - + +
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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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219A LEU* 3.6 21.1 - - - +
255A LEU 3.0 20.5 + - - -
256A VAL 3.9 0.9 - - - -
258A VAL* 1.3 77.4 - - - +
260A ALA* 1.3 55.6 + - - +
262A LEU* 3.0 20.5 + - - +
264A LEU* 3.1 25.2 + - - +
266A VAL* 4.1 6.3 - - - -
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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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256A VAL 3.0 19.2 + - - +
257A GLY* 3.4 7.2 + - - +
259A GLY* 1.3 75.4 - - - +
261A SER* 1.3 61.1 + - - +
263A GLY* 3.2 13.5 + - - -
264A LEU 3.4 13.1 + - - +
266A VAL 5.9 0.4 - - - +
479A PRO* 4.5 18.2 - - + -
480A PRO* 6.2 0.7 - - + -
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Residues in contact with SER 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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89A SER* 4.6 7.2 + - - -
257A GLY 3.1 11.4 + - - -
258A VAL* 2.8 29.1 + - - +
260A ALA* 1.3 74.2 - - - +
262A LEU* 1.3 63.8 + - - +
263A GLY 3.4 1.7 + - - -
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Residues in contact with LEU 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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89A SER* 4.0 23.3 - - - +
92A THR* 4.1 26.9 - - + -
93A GLN* 3.5 35.4 - - + +
219A LEU* 5.6 0.4 - - + -
223A LEU* 4.1 31.9 - - + +
258A VAL* 3.4 18.4 + - + +
259A GLY* 3.0 11.2 + - - +
261A SER* 1.3 79.8 + - - +
263A GLY* 1.3 60.9 + - - +
264A LEU 3.3 2.0 + - - -
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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