Contacts of the helix formed by residues 145 - 156 (chain D) 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 VAL 145 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140D VAL* 3.2 28.2 - - + +
142D SER* 3.4 30.7 - - - +
143D ASN* 3.3 5.1 - - - +
144D PRO* 1.3 71.2 - - - +
146D ASP* 1.3 60.7 + - - +
149D THR* 2.5 42.8 + - - +
165D GLY* 4.1 0.9 - - - -
166D THR* 4.0 15.5 - - - +
167D GLY* 3.9 16.6 - - - +
198D HIS* 3.5 37.9 + - + -
274D SER* 4.9 0.7 - - - -
330D NAD 4.4 1.6 - - - +
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Residues in contact with ASP 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144D PRO* 3.3 2.2 - - + +
145D VAL* 1.3 80.9 - - - +
147D VAL* 1.3 63.3 + - + +
149D THR* 3.7 2.2 - - - -
150D ALA* 3.1 24.8 + - - +
167D GLY* 4.9 0.2 - - - -
196D GLY 4.0 1.4 - - - +
197D GLU* 3.6 8.4 - - - +
198D HIS 3.3 26.9 + - - +
274D SER* 2.6 31.8 + - - +
283D TYR* 3.8 9.6 - - - +
284D LEU* 3.4 14.2 - - - -
285D SER* 3.9 3.6 + - - -
318D ILE* 3.7 33.1 - - + +
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Residues in contact with VAL 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144D PRO* 3.3 32.0 + - + -
146D ASP* 1.3 72.9 - - + +
148D ILE* 1.3 67.5 + - + +
150D ALA* 3.2 7.7 + - - +
151D LEU* 2.9 28.7 + - + +
197D GLU* 6.5 0.4 - - + -
282D MET* 4.7 4.0 - - - -
318D ILE* 4.1 22.0 - - + +
321D ARG* 4.0 24.5 - - + +
322D PHE* 4.0 9.9 - - - -
325D ILE* 3.7 30.5 - - + -
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Residues in contact with ILE 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D LEU 4.6 3.6 - - - +
98D GLY* 5.6 3.1 - - - -
118D THR* 3.8 28.7 - - + -
121D MET* 6.0 0.9 - - + -
122D VAL* 4.2 15.0 - - + -
140D VAL* 4.2 2.9 - - + -
142D SER* 3.5 32.8 - - - +
143D ASN 4.6 1.6 - - - +
144D PRO* 3.0 30.9 + - + +
145D VAL 4.3 0.4 - - - +
147D VAL* 1.3 76.7 - - + +
149D THR* 1.3 61.3 + - - +
151D LEU* 3.3 5.9 + - + +
152D PHE* 3.0 47.0 + - + +
325D ILE* 4.5 12.3 - - + -
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Residues in contact with THR 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D VAL* 3.6 17.8 - - + +
145D VAL 2.5 24.6 + - - -
146D ASP* 3.7 6.5 - - - -
148D ILE* 1.3 76.4 - - - +
150D ALA* 1.3 58.6 + - - +
152D PHE* 3.3 3.5 + - - +
153D GLN* 3.0 26.7 + - - +
163D VAL* 3.7 10.9 - - + +
164D ILE 3.8 5.8 - - - +
165D GLY* 3.5 33.9 - - - +
274D SER* 4.5 1.0 + - - +
283D TYR* 3.4 31.9 - - + -
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Residues in contact with ALA 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D ASP 3.1 10.8 + - - +
147D VAL 3.2 3.8 + - - +
149D THR* 1.3 78.7 - - - +
151D LEU* 1.3 54.0 + - - +
153D GLN* 3.3 4.9 + - - +
154D HIS* 2.9 28.2 + - - +
282D MET* 3.4 34.1 - - + -
283D TYR* 3.6 22.9 - - + -
322D PHE* 3.7 15.3 - - + -
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Residues in contact with LEU 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D SER* 4.2 16.4 - - - +
122D VAL* 3.9 23.6 - - + -
147D VAL 2.9 16.2 + - - +
148D ILE* 3.5 11.2 - - + +
150D ALA* 1.3 72.8 - - - +
152D PHE* 1.3 58.4 + - - +
154D HIS* 3.1 6.5 + - + +
155D VAL* 2.9 35.5 + - + +
322D PHE* 3.7 14.1 - - + -
325D ILE* 3.8 34.8 - - + +
326D VAL* 4.4 18.8 - - + -
329D LEU* 4.2 26.7 - - + -
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Residues in contact with PHE 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D ILE* 6.2 0.2 - - + -
95D SER* 3.7 29.2 - - - -
97D LEU* 4.9 8.1 - - + -
122D VAL* 3.9 23.7 - - + +
125D VAL* 3.8 30.1 - - + -
126D GLY* 3.9 20.9 - - - -
129D LEU* 5.1 4.5 - - + -
138D LEU* 4.0 26.0 - - + -
140D VAL* 4.0 12.8 - - + -
148D ILE* 3.0 38.7 + - + +
149D THR* 3.5 9.2 - - - +
151D LEU* 1.3 70.6 - - - +
153D GLN* 1.4 58.0 + - - +
155D VAL* 4.5 1.6 - - - +
156D THR* 2.6 41.2 + - + +
163D VAL* 4.5 3.4 - - + -
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Residues in contact with GLN 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149D THR 3.0 14.0 + - - +
150D ALA* 3.5 12.3 - - - +
151D LEU 3.2 0.2 - - - -
152D PHE* 1.4 75.8 - - - +
154D HIS* 1.3 63.2 + - - +
156D THR* 3.3 5.0 + - - -
157D GLY* 3.0 29.4 + - - -
158D PHE 2.8 28.0 + - - +
159D PRO* 4.6 0.4 - - - +
160D ALA* 3.8 21.1 - - - +
163D VAL* 4.2 11.4 - - + +
276D ARG* 3.8 18.3 + - - +
283D TYR* 3.4 25.5 - - + +
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Residues in contact with HIS 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150D ALA 2.9 13.3 + - - +
151D LEU* 3.1 13.7 - - + +
153D GLN* 1.3 85.9 + - - +
155D VAL* 1.3 64.6 + - + +
157D GLY* 3.9 6.1 + - - -
322D PHE* 4.5 11.7 - + + -
326D VAL* 3.7 24.9 - - + +
329D LEU* 3.9 26.4 - - + +
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Residues in contact with VAL 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122D VAL* 4.0 12.3 - - + +
123D GLN* 3.5 52.3 - - + +
126D GLY* 4.3 8.2 - - - +
127D THR* 4.3 7.1 + - - +
130D LYS* 4.8 6.4 + - - +
151D LEU* 2.9 28.2 + - + +
152D PHE* 4.1 3.8 - - - +
154D HIS* 1.3 77.4 - - + +
156D THR* 1.3 61.6 + - - +
157D GLY* 4.7 0.3 - - - -
329D LEU* 4.3 23.6 - - + -
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Residues in contact with THR 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D GLY* 3.7 34.3 - - - +
129D LEU* 4.8 4.0 - - + -
130D LYS* 3.6 28.0 - - - +
138D LEU* 4.9 1.6 - - + -
152D PHE* 2.6 34.5 + - + +
153D GLN* 3.3 3.8 + - - -
155D VAL* 1.3 77.1 - - - +
157D GLY* 1.3 62.8 + - - +
158D PHE* 3.2 50.7 + - + +
163D VAL* 4.5 0.2 - - - +
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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