Contacts of the helix formed by residues 252 - 265 (chain A) in PDB entry 1U5U
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 252 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111A ASP* 3.0 12.8 - - - -
250A PRO* 3.7 16.1 - - - +
251A ASP* 1.3 74.5 + - + +
253A TYR* 1.3 62.5 + - - +
255A ARG* 3.3 27.4 + - + +
256A LYS* 2.8 60.3 + - + +
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Residues in contact with TYR 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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111A ASP* 3.3 10.7 + - + -
112A ALA* 3.6 31.6 - - + -
183A ALA* 2.9 23.4 - - - -
184A PRO* 2.6 33.3 + - - +
185A ASP 4.7 5.2 - - - -
249A ARG* 3.6 47.1 - - + -
250A PRO* 3.0 37.9 + - + +
252A ASP* 1.3 78.6 + - - +
254A LEU* 1.3 73.8 + - + +
256A LYS* 3.4 6.0 + - - +
257A GLU* 2.8 31.7 + - + +
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Residues in contact with LEU 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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105A ASN* 4.4 0.2 - - - +
111A ASP* 3.0 16.9 + - + +
117A ARG* 3.6 24.7 - - - +
184A PRO* 3.4 39.5 - - + +
185A ASP 3.8 3.8 - - - +
186A THR* 3.5 28.5 - - - +
187A PHE* 3.5 43.1 - - + +
253A TYR* 1.3 85.8 - - + +
255A ARG* 1.3 65.7 + - - +
257A GLU* 3.2 13.2 + - + +
258A TYR* 3.3 13.3 + - - +
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Residues in contact with ARG 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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69A VAL* 3.6 26.5 - - - +
70A GLY* 3.5 43.1 - - - +
71A THR* 3.6 21.7 + - + -
105A ASN* 5.7 0.4 - - - +
109A PRO* 2.9 26.9 + - - +
111A ASP* 3.0 18.3 + - - +
187A PHE* 4.3 9.2 - - + -
251A ASP* 3.0 20.0 + - - +
252A ASP* 3.4 25.9 - - + +
254A LEU* 1.3 79.3 - - - +
256A LYS* 1.3 61.9 + - + +
258A TYR* 3.6 1.2 + - - +
259A VAL* 3.5 23.7 + - - +
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Residues in contact with LYS 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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250A PRO* 5.6 5.3 - - + +
252A ASP* 2.8 49.7 + - + +
253A TYR* 3.8 6.7 - - - +
255A ARG* 1.3 75.5 - - + +
257A GLU* 1.3 66.1 + - - +
259A VAL* 3.3 8.1 + - - +
260A GLU* 2.9 25.6 + - - +
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Residues in contact with GLU 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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185A ASP 3.6 15.7 - - - +
186A THR* 2.7 29.1 + - - -
187A PHE 4.5 0.3 + - - -
253A TYR* 2.8 19.7 + - + +
254A LEU* 3.2 10.7 + - + +
256A LYS* 1.3 77.8 - - - +
258A TYR* 1.3 64.3 + - - +
260A GLU* 3.3 16.1 + - - +
261A ARG* 2.8 60.2 + - - +
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Residues in contact with TYR 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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71A THR* 3.8 29.2 - - + -
72A GLY* 4.0 27.1 - - - -
101A LEU* 4.1 2.1 - - + +
103A HIS* 3.6 17.1 - + - -
187A PHE* 4.2 12.3 - - + -
188A ALA* 4.5 8.7 - - + -
254A LEU 3.3 6.7 + - - +
255A ARG 3.8 9.2 - - - +
256A LYS 3.2 0.4 - - - -
257A GLU* 1.3 87.6 + - - +
259A VAL* 1.3 58.0 + - + +
261A ARG* 3.2 5.0 + - - +
262A LEU* 2.8 44.1 + - + +
267A VAL* 3.6 28.0 - - + +
269A TYR* 2.6 36.1 + - - -
308A ILE* 3.7 13.5 - - + +
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Residues in contact with VAL 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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71A THR* 3.8 13.2 - - - +
72A GLY 5.7 2.2 - - - +
255A ARG 3.5 14.5 + - - +
256A LYS* 3.3 9.9 + - - +
258A TYR* 1.3 77.1 - - + +
260A GLU* 1.3 65.3 + - - +
262A LEU* 3.1 9.5 + - + +
263A GLN* 3.1 38.3 + - - +
311A PRO* 5.1 17.0 - - + +
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Residues in contact with GLU 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 LYS 2.9 16.7 + - - +
257A GLU* 3.5 15.4 - - - +
259A VAL* 1.3 77.8 - - - +
261A ARG* 1.3 60.4 + - - +
263A GLN* 3.0 34.4 - - - +
264A LYS* 3.1 35.9 + - + +
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Residues in contact with ARG 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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185A ASP* 5.8 0.4 + - - -
186A THR* 3.4 27.1 + - - +
188A ALA* 4.0 17.4 - - - +
189A HIS* 3.8 26.6 + - - -
257A GLU* 2.8 49.3 + - - +
258A TYR* 3.6 7.0 - - - +
260A GLU* 1.3 74.2 - - - +
262A LEU* 1.3 63.7 + - - +
264A LYS* 3.1 20.7 + - + +
265A GLY 3.1 14.8 + - - +
266A PRO 5.8 0.7 - - - +
267A VAL* 4.0 19.3 - - + +
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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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72A GLY 3.7 15.9 - - - +
258A TYR* 2.8 25.6 + - + +
259A VAL* 3.1 8.9 + - + +
261A ARG* 1.3 78.6 - - - +
263A GLN* 1.3 58.8 + - - +
265A GLY* 3.1 19.6 + - - +
267A VAL* 3.8 15.9 - - + -
308A ILE* 3.4 37.9 - - + +
309A LYS 3.9 13.6 - - - +
310A THR 3.7 4.3 - - - +
311A PRO* 3.5 44.7 - - + +
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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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259A VAL* 3.1 26.1 + - - +
260A GLU* 3.0 32.8 + - - +
262A LEU* 1.3 77.8 - - - +
264A LYS* 1.3 62.4 + - + +
265A GLY 3.3 0.4 + - - -
311A PRO* 5.8 4.9 - - + +
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Residues in contact with LYS 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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260A GLU* 3.1 39.6 + - + +
261A ARG* 3.1 12.0 + - - +
263A GLN* 1.3 81.6 - - + +
265A GLY* 1.3 56.9 + - - +
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Residues in contact with GLY 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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261A ARG* 3.1 16.6 + - - +
262A LEU* 3.1 15.7 + - - +
263A GLN 3.3 3.4 - - - -
264A LYS* 1.3 81.1 - - - +
266A PRO* 1.3 77.7 - - - +
267A VAL* 4.2 0.7 - - - +
309A LYS 5.5 0.7 - - - -
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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