Contacts of the helix formed by residues 252 - 265 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B ASP* 3.0 13.0 - - - -
250B PRO* 3.7 14.4 - - - +
251B ASP* 1.3 75.0 + - + +
253B TYR* 1.3 57.2 + - - +
255B ARG* 3.3 26.7 + - + +
256B LYS* 2.9 69.0 + - + +
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Residues in contact with TYR 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B ASP* 3.4 11.0 + - + -
112B ALA* 3.6 30.1 - - + -
183B ALA* 2.9 24.1 - - - -
184B PRO* 2.6 31.8 + - - +
185B ASP 4.7 6.5 - - - -
249B ARG* 3.6 38.8 - - + -
250B PRO* 3.1 44.7 + - + +
252B ASP* 1.3 78.7 + - - +
254B LEU* 1.3 71.9 + - + +
256B LYS* 3.8 5.3 - - - +
257B GLU* 2.9 32.2 + - + +
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Residues in contact with LEU 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ASN* 4.4 0.9 - - - +
111B ASP* 3.1 16.9 + - + +
117B ARG* 3.5 24.5 - - - +
184B PRO* 3.4 36.1 - - + +
185B ASP 3.7 4.7 - - - +
186B THR* 3.6 28.3 - - - +
187B PHE* 3.5 42.1 - - + +
253B TYR* 1.3 85.6 - - + +
255B ARG* 1.3 65.7 + - - +
257B GLU* 3.3 5.0 + - - +
258B TYR* 3.2 21.1 + - - +
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Residues in contact with ARG 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B VAL* 3.5 27.6 - - - +
70B GLY* 3.6 41.3 + - - +
71B THR* 3.2 31.3 + - - -
105B ASN* 4.8 1.1 - - - +
109B PRO* 2.9 25.3 + - - +
111B ASP* 2.9 23.2 + - - +
187B PHE* 4.2 14.8 - - + -
251B ASP* 3.2 17.8 + - - +
252B ASP* 3.5 25.4 - - + +
254B LEU* 1.3 76.7 - - - +
256B LYS* 1.3 62.3 + - - +
258B TYR 3.5 6.1 + - - -
259B VAL* 3.7 4.7 + - - +
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Residues in contact with LYS 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B PRO* 6.0 2.4 - - + +
252B ASP* 2.9 51.9 + - + +
253B TYR* 3.9 5.6 - - - +
255B ARG* 1.3 74.5 - - + +
257B GLU* 1.3 66.0 + - - +
259B VAL* 3.2 10.1 + - - +
260B GLU* 3.1 38.8 + - + +
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Residues in contact with GLU 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B ASP 3.9 13.0 - - - +
186B THR* 2.9 28.1 + - - -
187B PHE 4.6 1.0 + - - -
253B TYR* 2.9 23.0 + - + +
254B LEU* 3.4 10.3 - - - +
255B ARG 3.3 0.2 - - - -
256B LYS* 1.3 77.0 - - - +
258B TYR* 1.3 64.7 + - - +
260B GLU* 3.3 11.7 + - + +
261B ARG* 2.8 60.2 + - - +
264B LYS* 5.3 4.2 + - - -
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Residues in contact with TYR 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B THR* 3.6 37.2 - - + -
72B GLY* 4.0 19.5 - - - -
73B GLY 4.6 0.4 - - - -
101B LEU* 3.8 4.4 - - + +
103B HIS* 3.6 15.9 - + - -
186B THR* 5.0 0.2 - - - -
187B PHE* 4.3 13.9 - - + -
188B ALA* 4.7 7.0 - - + -
254B LEU 3.2 6.2 + - - +
255B ARG 3.8 1.3 - - - +
256B LYS 3.2 0.2 - - - -
257B GLU* 1.3 88.2 + - - +
259B VAL* 1.3 62.9 + - - +
261B ARG* 3.3 5.0 + - - +
262B LEU* 3.1 50.2 + - + +
267B VAL* 4.0 18.5 - - + +
269B TYR* 2.7 30.5 + - - -
308B ILE* 3.6 25.8 - - - +
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Residues in contact with VAL 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B THR* 3.5 19.5 - - - +
72B GLY 5.3 3.1 - - - +
255B ARG 3.7 6.5 + - - +
256B LYS* 3.2 10.6 + - - +
258B TYR* 1.3 77.7 - - + +
260B GLU* 1.3 62.9 + - + +
262B LEU* 3.2 8.5 + - - +
263B GLN* 3.0 47.3 + - - +
311B PRO* 4.0 24.0 - - + -
312B LEU 5.9 2.2 - - - +
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Residues in contact with GLU 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256B LYS* 3.1 31.8 + - + +
257B GLU* 3.6 11.4 + - + +
258B TYR 3.2 0.2 - - - -
259B VAL* 1.3 75.3 - - + +
261B ARG* 1.3 63.6 + - - +
263B GLN* 3.3 26.8 + - - +
264B LYS* 3.1 32.8 + - - +
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Residues in contact with ARG 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B ASP* 5.0 1.0 + - - -
186B THR* 3.2 35.1 + - - +
188B ALA* 4.0 10.3 - - - -
189B HIS* 4.1 20.2 + - - -
218B ASP* 5.5 4.2 + - - +
257B GLU* 2.8 45.6 + - - +
258B TYR* 3.7 7.2 - - - +
260B GLU* 1.3 76.2 - - - +
262B LEU* 1.3 58.3 + - - +
264B LYS* 3.1 17.6 + - - +
265B GLY 2.8 28.1 + - - +
266B PRO 5.8 0.2 - - - +
267B VAL* 3.5 25.8 - - + -
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Residues in contact with LEU 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B GLY 4.2 3.8 - - - +
258B TYR* 3.1 37.8 + - + +
259B VAL* 3.4 9.2 - - - +
261B ARG* 1.3 79.2 - - - +
263B GLN* 1.3 60.5 + - - +
265B GLY* 3.2 15.5 + - - +
267B VAL* 3.3 32.8 - - + +
308B ILE* 3.7 34.3 - - + +
309B LYS 4.1 18.6 - - - +
311B PRO* 3.8 38.9 - - + +
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Residues in contact with GLN 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259B VAL* 3.0 31.4 + - + +
260B GLU* 3.6 24.5 - - - +
261B ARG 3.3 0.2 - - - -
262B LEU* 1.3 76.9 - - - +
264B LYS* 1.3 63.4 + - + +
311B PRO* 4.9 13.1 - - + +
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Residues in contact with LYS 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257B GLU* 5.3 4.0 + - - -
260B GLU* 3.1 38.1 + - - +
261B ARG* 3.1 14.7 + - - +
263B GLN* 1.3 82.3 - - + +
265B GLY* 1.3 56.5 + - - +
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Residues in contact with GLY 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261B ARG* 2.8 19.2 + - - +
262B LEU* 3.2 18.8 + - - +
264B LYS* 1.3 78.9 - - - +
266B PRO* 1.3 75.2 - - - +
267B VAL* 3.8 1.2 + - - +
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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