Contacts of the helix formed by residues 250 - 264 (chain B) in PDB entry 1HYH
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 250 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35B ALA* 4.7 5.2 - - + -
245B LYS* 3.5 18.7 + - - -
247B TYR* 5.2 3.8 + - - -
249B SER* 1.3 84.6 + - - +
251B GLY* 1.3 60.1 + - - +
253B ALA* 4.0 3.3 - - - +
254B THR* 2.7 33.8 + - - +
34D ALA* 3.1 30.9 + - - +
38D HIS* 3.7 39.0 - + + +
62D ASP* 3.6 9.2 + - - -
65D ASP* 3.2 25.7 + - + +
66D PHE* 3.5 48.7 - + + -
69D ALA* 3.7 4.4 - - + +
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Residues in contact with GLY 251 (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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170B LEU* 3.6 19.0 - - - +
250B TYR* 1.3 76.7 - - - +
252B VAL* 1.3 59.3 + - - +
254B THR* 3.5 2.9 + - - -
255B SER* 2.9 26.9 + - - -
65D ASP* 3.2 26.2 + - - -
68D ASP* 4.2 2.8 - - - +
69D ALA* 4.0 13.8 - - - -
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Residues in contact with VAL 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B VAL* 3.5 26.9 - - + -
141B ILE* 3.9 12.9 - - + +
166B THR* 4.3 11.9 - - - +
170B LEU* 3.7 18.4 - - + +
248B THR* 4.6 2.1 + - - +
249B SER* 3.5 10.7 + - - +
251B GLY* 1.3 72.0 - - - +
253B ALA* 1.3 69.3 + - - +
255B SER* 3.3 4.6 + - - -
256B ALA* 3.1 23.0 + - - +
330B NAD 3.5 53.6 - - + +
65D ASP* 5.1 0.2 + - - -
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Residues in contact with ALA 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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32B VAL* 4.3 2.5 - - + +
35B ALA* 3.7 24.7 - - + +
36B VAL* 3.7 29.1 - - + +
249B SER 2.9 19.9 + - - +
250B TYR* 4.0 4.5 - - - +
252B VAL* 1.3 80.6 - - - +
254B THR* 1.3 57.6 + - - +
256B ALA* 3.5 3.5 + - - +
257B ILE* 3.1 33.8 + - + +
38D HIS* 5.3 2.7 - - + -
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Residues in contact with THR 254 (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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250B TYR* 2.7 23.4 + - - +
251B GLY 3.8 3.8 - - - -
253B ALA* 1.3 75.3 - - - +
255B SER* 1.3 63.5 + - - +
257B ILE* 3.4 11.9 + - + +
258B ARG* 3.0 22.9 + - - +
38D HIS* 4.8 9.5 + - - -
69D ALA* 3.6 17.3 - - + +
72D ASN* 3.5 27.7 - - + +
73D LEU* 3.7 30.9 - - + +
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Residues in contact with SER 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B THR* 4.4 8.5 - - - -
169B LEU* 3.6 25.5 - - - +
170B LEU* 4.1 13.2 - - - +
173B ALA* 5.0 0.2 - - - +
251B GLY 2.9 15.0 + - - -
252B VAL* 3.6 11.2 - - - -
254B THR* 1.3 77.4 - - - +
256B ALA* 1.3 62.6 + - - +
258B ARG* 3.2 11.5 + - - +
259B ILE* 3.3 17.8 + - - +
72D ASN* 2.8 26.9 + - - +
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Residues in contact with ALA 256 (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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36B VAL* 4.3 8.3 - - + -
94B ILE* 4.6 15.4 - - + +
139B VAL* 4.7 6.7 - - + +
141B ILE* 3.4 32.5 - - + -
166B THR* 4.0 12.2 - - + +
252B VAL 3.1 6.0 + - - +
253B ALA 3.6 9.0 - - - +
254B THR 3.3 0.2 - - - -
255B SER* 1.3 76.0 - - - +
257B ILE* 1.3 54.9 + - - +
259B ILE* 3.3 7.0 + - - +
260B ALA* 3.0 28.2 + - - +
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Residues in contact with ILE 257 (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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35B ALA 4.8 0.9 - - - +
36B VAL* 3.7 34.5 - - + +
39B GLY* 3.9 22.2 - - - -
40B LEU* 4.0 19.7 - - + +
43B GLN* 4.4 9.2 - - - +
94B ILE* 5.7 0.4 - - + -
253B ALA* 3.1 20.1 + - + +
254B THR* 3.7 12.6 - - + +
256B ALA* 1.3 73.9 - - - +
258B ARG* 1.3 65.6 + - - +
260B ALA* 3.7 6.9 - - - +
261B LYS* 3.1 46.4 + - + +
38D HIS* 5.9 0.9 - - - +
74D GLU* 5.6 0.9 - - - +
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Residues in contact with ARG 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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169B LEU* 4.5 9.2 - - + +
176B GLN* 5.8 1.0 + - - -
254B THR 3.0 13.2 + - - +
255B SER* 3.2 9.8 + - - +
257B ILE* 1.3 77.3 - - - +
259B ILE* 1.3 62.5 + - - +
261B LYS* 3.4 9.5 + - - +
262B ALA* 3.2 21.1 + - - +
270B GLU 5.4 1.8 + - - -
271B LEU* 3.5 33.3 - - + +
71D ALA 4.1 10.4 + - - -
72D ASN* 2.8 47.6 + - + +
74D GLU* 5.7 4.5 - - - +
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Residues in contact with ILE 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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139B VAL* 3.8 21.1 - - + -
164B ILE* 3.7 26.2 - - + -
165B GLY 4.6 1.1 - - - +
166B THR* 4.1 24.5 - - + -
169B LEU* 3.8 21.3 - - + -
255B SER 3.3 10.2 + - - +
256B ALA 3.6 6.5 - - - +
258B ARG* 1.3 75.4 - - - +
260B ALA* 1.3 62.9 + - - +
262B ALA* 2.9 15.4 + - - +
263B VAL* 3.1 17.6 + - + +
271B LEU* 4.0 13.5 - - + -
273B VAL* 3.5 28.9 - - + -
290B ILE* 4.7 4.9 - - + -
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Residues in contact with ALA 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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24B ILE* 4.8 8.5 - - + -
40B LEU* 5.5 3.1 - - + -
92B VAL* 4.0 29.6 - - + +
94B ILE* 4.5 11.0 - - + -
139B VAL* 5.4 0.2 - - - -
256B ALA 3.0 16.3 + - - +
257B ILE* 3.7 9.2 - - - +
258B ARG 3.4 0.2 - - - -
259B ILE* 1.3 76.6 - - - +
261B LYS* 1.3 62.1 + - + +
263B VAL* 3.4 3.8 + - - +
264B MET* 3.1 36.2 + - + +
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Residues in contact with LYS 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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22B ARG* 6.6 0.2 - - - -
43B GLN* 3.1 29.9 + - - +
45B VAL* 3.6 36.2 - - + +
257B ILE* 3.1 32.6 + - + +
258B ARG* 3.6 7.2 - - - +
259B ILE 3.2 0.2 - - - -
260B ALA* 1.3 76.2 - - + +
262B ALA* 1.3 63.1 + - - +
264B MET* 3.8 7.7 + - + +
265B ALA* 3.1 28.4 + - - +
47C ASP* 5.0 0.2 - - - +
75C ALA* 6.3 2.9 - - + -
74D GLU* 3.1 29.2 + - - +
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Residues in contact with ALA 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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188A ARG* 5.9 1.8 - - - +
258B ARG 3.2 9.2 + - - +
259B ILE 2.9 10.5 + - - +
261B LYS* 1.3 75.8 - - - +
263B VAL* 1.3 59.6 + - - +
266B ASP* 3.0 8.0 + - - -
267B ALA* 2.9 36.6 + - + -
269B ALA* 4.3 18.4 - - + -
271B LEU* 4.2 17.5 - - + -
290B ILE* 4.2 11.0 - - + +
291B GLY* 3.9 5.0 - - - -
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Residues in contact with VAL 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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91B ASP* 4.3 6.1 - - + +
92B VAL* 3.5 23.3 - - + -
137B VAL* 3.8 38.1 - - + -
139B VAL* 5.5 0.4 - - + -
259B ILE* 3.1 20.3 + - + +
260B ALA* 3.5 7.6 - - - +
262B ALA* 1.3 71.9 - - - +
264B MET* 1.3 66.8 + - + +
266B ASP 2.9 12.5 + - - -
290B ILE* 3.9 12.8 - - + -
291B GLY 3.6 15.9 - - - +
292B ARG* 3.1 28.6 - - + +
294B GLY* 5.4 0.2 - - - -
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Residues in contact with MET 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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22B ARG* 3.7 33.7 - - + +
24B ILE* 4.2 24.7 - - + -
45B VAL* 3.9 27.6 - - + -
91B ASP* 3.7 31.2 - - + +
92B VAL* 4.2 5.8 - - + -
260B ALA* 3.1 21.7 + - + +
261B LYS* 4.1 12.3 - - + +
263B VAL* 1.3 79.6 - - - +
265B ALA* 1.3 55.2 + - - +
266B ASP 3.3 0.4 - - - -
292B ARG* 2.9 27.5 + - - +
21C ALA* 3.5 2.8 - - - +
47C ASP* 3.2 23.1 - - - +
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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