Contacts of the helix formed by residues 250 - 264 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A ALA* 4.7 4.3 - - + -
245A LYS* 3.5 19.0 + - - -
247A TYR* 5.4 3.3 + - - -
249A SER* 1.3 84.2 + - - +
251A GLY* 1.3 61.1 + - - +
253A ALA* 4.4 3.8 - - - -
254A THR* 2.8 32.3 + - - +
34C ALA* 3.2 31.2 + - - +
35C ALA* 5.2 0.2 - - - -
38C HIS* 3.5 42.0 - + + +
62C ASP* 3.8 6.6 + - - -
65C ASP* 3.2 29.6 + - + +
66C PHE* 3.5 48.9 - + + -
69C ALA* 3.6 5.1 - - + +
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Residues in contact with GLY 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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170A LEU* 3.6 18.6 - - - +
174A ARG* 5.8 0.2 - - - -
248A THR* 6.4 0.2 - - - -
250A TYR* 1.3 76.8 - - - +
252A VAL* 1.3 59.9 + - - +
254A THR* 3.9 2.9 - - - -
255A SER* 3.0 24.1 + - - -
65C ASP* 3.0 26.0 + - - -
68C ASP* 4.1 3.4 - - - +
69C ALA* 4.1 14.1 - - - -
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Residues in contact with VAL 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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32A VAL* 3.6 23.6 - - + -
141A ILE* 3.9 18.2 - - + -
166A THR* 4.2 12.2 - - + +
170A LEU* 3.7 13.4 - - + +
248A THR* 4.4 6.3 + - - +
249A SER 3.6 7.3 + - - +
251A GLY* 1.3 72.9 - - - +
253A ALA* 1.3 67.4 + - - +
255A SER* 3.2 6.7 + - - -
256A ALA* 3.1 21.3 + - - +
330A NAD 3.5 53.8 - - + +
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Residues in contact with ALA 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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32A VAL* 4.5 1.6 - - - +
35A ALA* 3.9 13.0 - - + +
36A VAL* 3.7 40.0 - - + +
249A SER 3.0 21.3 + - - +
250A TYR* 4.0 4.3 - - - +
252A VAL* 1.3 78.2 - - - +
254A THR* 1.3 59.6 + - - +
256A ALA* 3.4 4.3 + - - +
257A ILE* 3.1 34.1 + - + +
38C HIS* 5.1 2.7 - - + -
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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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250A TYR* 2.8 22.6 + - - +
251A GLY 3.9 3.8 - - - -
253A ALA* 1.3 77.0 - - - +
255A SER* 1.3 57.4 + - - +
257A ILE* 3.4 13.5 + - + +
258A ARG* 3.0 27.4 + - - +
38C HIS* 4.9 8.8 + - - -
69C ALA* 3.5 29.2 - - - +
72C ASN* 3.4 26.3 - - + +
73C LEU* 3.7 19.7 - - + +
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Residues in contact with SER 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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166A THR* 4.5 8.1 - - - -
169A LEU* 3.6 22.2 - - - +
170A LEU* 4.1 13.3 - - - +
251A GLY 3.0 13.4 + - - -
252A VAL* 3.2 13.6 + - - -
254A THR* 1.3 76.5 - - - +
256A ALA* 1.3 59.1 + - - +
258A ARG* 3.4 4.2 + - - +
259A ILE* 3.2 28.5 + - - +
72C ASN* 2.9 28.9 + - - +
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Residues in contact with ALA 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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36A VAL* 4.5 8.3 - - + -
94A ILE* 4.5 16.1 - - + +
139A VAL* 4.9 5.8 - - + +
141A ILE* 3.6 31.0 - - + -
166A THR* 4.1 11.7 - - + +
252A VAL 3.1 5.2 + - - +
253A ALA 3.6 8.7 - - - +
254A THR 3.3 0.2 - - - -
255A SER* 1.3 72.2 - - - +
257A ILE* 1.3 59.7 + - - +
259A ILE* 3.3 6.5 + - - +
260A ALA* 2.8 30.4 + - - +
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Residues in contact with ILE 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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35A ALA 4.8 0.9 - - - +
36A VAL* 3.8 28.0 - - + +
39A GLY* 4.0 21.8 - - - -
40A LEU* 4.0 24.0 - - + -
43A GLN* 4.2 9.4 - - - +
94A ILE* 5.7 0.7 - - + -
253A ALA* 3.1 23.1 + - + +
254A THR* 3.8 12.1 - - + +
255A SER 3.4 0.2 - - - -
256A ALA* 1.3 75.5 - - - +
258A ARG* 1.3 63.5 + - - +
260A ALA* 3.3 6.3 + - - +
261A LYS* 3.0 49.8 + - - +
38C HIS* 5.7 1.3 - - - +
74C GLU* 6.0 0.7 - - - +
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Residues in contact with ARG 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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169A LEU* 4.8 6.9 - - + +
176A GLN* 6.0 0.2 + - - -
254A THR 3.0 14.2 + - - +
255A SER* 3.5 10.1 - - - +
257A ILE* 1.3 78.8 - - - +
259A ILE* 1.3 61.4 + - - +
261A LYS* 3.6 8.4 + - + +
262A ALA* 3.2 21.3 + - - +
270A GLU 5.2 2.0 + - - -
271A LEU* 3.7 32.9 - - + +
71C ALA 3.9 12.1 + - - -
72C ASN* 2.9 46.0 + - + +
74C GLU* 6.0 2.5 - - - +
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Residues in contact with ILE 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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139A VAL* 4.1 19.5 - - + -
164A ILE* 3.8 26.0 - - + -
165A GLY 4.7 1.3 - - - +
166A THR* 4.1 25.1 - - + -
169A LEU* 3.8 17.3 - - + -
255A SER 3.2 15.8 + - - +
256A ALA* 3.7 5.4 - - - +
258A ARG* 1.3 76.3 - - - +
260A ALA* 1.3 63.2 + - - +
262A ALA* 3.0 13.3 + - - +
263A VAL* 3.1 18.9 + - + +
271A LEU* 4.0 13.0 - - + -
273A VAL* 3.6 28.3 - - + -
290A ILE* 4.6 5.4 - - + -
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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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24A ILE* 5.1 7.2 - - + -
40A LEU* 5.4 3.4 - - + -
92A VAL* 3.9 30.9 - - + +
94A ILE* 4.3 12.3 - - + -
139A VAL* 5.2 0.6 - - + +
256A ALA 2.8 20.7 + - - +
257A ILE* 3.7 7.9 - - - +
259A ILE* 1.3 73.1 - - - +
261A LYS* 1.3 60.6 + - + +
263A VAL* 3.5 3.1 + - - +
264A MET* 3.3 34.5 + - + +
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Residues in contact with LYS 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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40A LEU* 5.6 0.2 - - + -
43A GLN* 3.1 23.4 + - - +
45A VAL* 3.7 34.5 - - + +
257A ILE* 3.0 40.5 + - + +
258A ARG* 3.9 7.9 - - - +
260A ALA* 1.3 70.9 - - + +
262A ALA* 1.3 62.9 + - - +
264A MET* 4.1 8.5 - - + +
265A ALA* 3.2 27.9 + - - +
74C GLU* 2.8 31.0 + - - +
47D ASP* 4.9 0.3 - - - +
75D ALA* 6.3 3.1 - - + -
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Residues in contact with ALA 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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258A ARG 3.2 12.5 + - - +
259A ILE 3.0 9.5 + - - +
261A LYS* 1.3 74.5 - - - +
263A VAL* 1.3 63.2 + - - +
266A ASP* 3.1 2.9 + - - -
267A ALA* 3.1 34.5 + - + -
269A ALA* 4.3 18.2 - - + -
271A LEU* 4.2 18.2 - - + -
290A ILE* 4.3 11.7 - - + +
291A GLY* 4.0 3.6 - - - -
188B ARG* 6.0 1.3 - - - +
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Residues in contact with VAL 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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91A ASP* 4.3 6.5 - - + +
92A VAL* 3.7 20.9 - - + -
137A VAL* 3.9 37.9 - - + -
139A VAL* 5.5 0.9 - - + -
259A ILE* 3.1 20.2 + - + +
260A ALA 3.7 7.4 - - - +
261A LYS 3.3 0.2 - - - -
262A ALA* 1.3 72.8 - - - +
264A MET* 1.3 68.7 + - + +
266A ASP 2.9 11.6 + - - -
290A ILE* 3.8 19.1 - - + -
291A GLY 3.7 9.9 - - - +
292A ARG* 3.1 30.9 - - + +
294A GLY* 5.3 0.2 - - - -
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Residues in contact with MET 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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22A ARG* 3.7 33.0 - - + +
24A ILE* 4.1 23.8 - - + -
40A LEU* 5.7 0.2 - - + -
45A VAL* 3.7 30.1 - - + -
91A ASP* 3.8 29.8 - - + +
92A VAL* 4.0 5.8 - - + -
260A ALA* 3.3 21.8 + - + +
261A LYS* 4.1 11.0 - - + +
263A VAL* 1.3 76.0 - - - +
265A ALA* 1.3 49.8 + - - +
292A ARG* 2.5 36.3 + - - +
21D ALA* 3.6 5.2 - - + +
47D ASP* 3.3 20.2 - - - +
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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