Contacts of the helix formed by residues 145 - 156 (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 VAL 145 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140B VAL* 3.3 28.3 - - + +
141B ILE 3.6 12.6 - - - +
142B SER 3.2 8.5 - - - +
143B ASN* 3.2 8.6 + - - +
144B PRO* 1.3 67.6 - - - +
146B ASP* 1.3 71.4 + - - +
149B THR* 2.9 31.3 + - - +
165B GLY* 4.3 0.9 - - - -
166B THR* 3.8 6.7 - - - +
167B GLY* 3.8 20.6 - - - +
198B HIS* 3.6 32.2 + - + +
274B SER* 5.0 0.2 - - - -
330B NAD 3.4 20.2 - - - +
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Residues in contact with ASP 146 (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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144B PRO* 3.1 1.6 + - - +
145B VAL* 1.3 80.5 - - - +
147B VAL* 1.3 58.1 + - + +
149B THR* 3.3 3.5 + - - -
150B ALA* 3.1 26.2 + - - +
167B GLY* 4.7 0.2 - - - -
196B GLY 4.1 1.2 - - - +
197B GLU* 3.5 10.6 - - + +
198B HIS 3.2 27.0 + - - +
274B SER* 2.7 32.3 + - - +
283B TYR* 3.9 9.0 - - - +
284B LEU* 3.7 10.4 - - - -
285B SER* 4.0 6.6 + - - -
318B ILE* 3.9 33.2 - - + -
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Residues in contact with VAL 147 (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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112B PHE* 5.1 5.4 - - + -
115B LEU* 4.2 13.0 - - + -
144B PRO* 3.1 20.0 + - + +
146B ASP* 1.3 72.9 - - + +
148B ILE* 1.3 60.7 + - - +
150B ALA* 3.3 7.4 + - - +
151B LEU* 3.0 32.2 + - + +
197B GLU* 5.3 3.4 - - - +
318B ILE* 4.2 29.2 - - + +
321B ARG* 4.4 15.9 - - + +
322B PHE* 4.1 10.8 - - + +
325B ILE* 4.0 27.1 - - + -
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Residues in contact with ILE 148 (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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97B LEU* 6.1 0.7 - - + -
115B LEU* 3.9 22.9 - - + -
118B THR* 3.5 30.1 - - - +
119B SER* 4.0 11.0 - - - +
122B VAL* 3.7 21.3 - - + -
140B VAL* 4.0 7.0 - - + -
142B SER* 3.8 23.8 - - - +
143B ASN 4.0 0.7 - - - +
144B PRO* 2.9 23.6 + - + +
145B VAL 4.1 0.2 - - - +
147B VAL* 1.3 74.3 - - - +
149B THR* 1.3 60.3 + - - +
151B LEU* 3.8 12.2 - - + +
152B PHE* 2.9 43.9 + - + +
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Residues in contact with THR 149 (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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140B VAL* 3.3 25.3 - - + +
145B VAL 2.9 22.8 + - - -
146B ASP* 3.5 7.1 - - - -
147B VAL 3.2 0.2 - - - -
148B ILE* 1.3 78.3 - - - +
150B ALA* 1.3 61.6 + - - +
152B PHE* 3.1 4.9 + - - +
153B GLN* 3.0 22.0 + - - +
163B VAL* 3.8 6.5 - - + +
164B ILE* 3.8 21.3 - - - -
165B GLY* 3.5 11.6 - - - +
274B SER* 4.3 2.1 + - - +
283B TYR* 3.3 35.4 - - + -
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Residues in contact with ALA 150 (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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146B ASP 3.1 6.0 + - - +
147B VAL 3.5 8.7 - - - +
148B ILE 3.3 0.2 - - - -
149B THR* 1.3 76.5 - - - +
151B LEU* 1.3 57.1 + - - +
153B GLN* 3.5 3.5 + - - +
154B HIS* 3.0 30.1 + - - +
282B MET* 3.3 35.4 - - + -
283B TYR* 3.7 17.0 - - + -
322B PHE* 3.7 18.1 - - + -
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Residues in contact with LEU 151 (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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119B SER* 4.1 17.3 - - - +
122B VAL* 3.7 18.4 - - + -
147B VAL* 3.0 23.4 + - + +
148B ILE* 3.9 23.1 - - + +
149B THR 3.3 0.2 - - - -
150B ALA* 1.3 75.8 - - - +
152B PHE* 1.3 54.1 + - - +
154B HIS* 3.3 8.2 + - + -
155B VAL* 2.7 43.3 + - + +
322B PHE* 3.7 20.0 - - + -
325B ILE* 3.9 26.9 - - + +
326B VAL* 4.3 17.0 - - - +
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Residues in contact with PHE 152 (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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27B ILE* 5.7 0.2 - - + -
95B SER* 3.3 31.6 - - - -
97B LEU* 4.9 4.9 - - + -
122B VAL* 4.0 22.9 - - + +
125B VAL* 3.7 31.9 - - + -
126B GLY* 4.1 18.4 - - - -
129B LEU* 5.1 4.7 - - + -
138B LEU* 3.9 24.7 - - + -
140B VAL* 3.8 15.3 - - + -
142B SER* 5.0 0.7 - - - -
148B ILE* 2.9 42.5 + - + +
149B THR 3.1 5.1 + - - +
151B LEU* 1.3 77.0 - - - +
153B GLN* 1.3 54.0 + - - +
155B VAL* 3.9 0.8 - - - +
156B THR* 2.5 41.9 + - + +
163B VAL* 4.4 2.9 - - + -
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Residues in contact with GLN 153 (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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149B THR 3.0 12.6 + - - +
150B ALA 3.7 4.7 - - - +
152B PHE* 1.3 76.6 - - - +
154B HIS* 1.3 63.4 + - - +
156B THR* 3.5 4.6 + - - -
157B GLY* 3.0 28.2 + - - -
158B PHE 2.7 25.5 + - - +
159B PRO* 4.6 0.6 - - - +
160B ALA* 3.6 23.0 - - - +
163B VAL* 3.7 12.7 - - + +
276B ARG* 4.9 7.8 + - - +
283B TYR* 3.0 36.4 - - + +
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Residues in contact with HIS 154 (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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150B ALA 3.0 19.3 + - - +
151B LEU* 3.5 12.8 - - + +
153B GLN* 1.3 86.5 + - - +
155B VAL* 1.3 64.7 + - + +
157B GLY* 4.0 5.2 + - - -
322B PHE* 4.0 20.2 - + + -
326B VAL 3.2 26.5 + - - -
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Residues in contact with VAL 155 (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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122B VAL* 3.8 22.4 - - + +
123B GLN* 3.6 54.7 - - + +
126B GLY* 4.3 9.3 - - - +
127B THR* 4.3 4.9 + - - +
130B LYS* 4.8 5.2 - - - +
151B LEU* 2.7 29.5 + - + +
152B PHE* 4.1 2.0 - - - +
154B HIS* 1.3 83.1 - - + +
156B THR* 1.3 63.0 + - - +
157B GLY 3.7 0.2 + - - -
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Residues in contact with THR 156 (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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126B GLY* 3.3 34.5 - - - +
129B LEU* 4.7 6.3 - - + -
130B LYS* 3.3 34.6 - - + +
138B LEU* 5.4 1.1 - - + -
152B PHE* 2.5 30.8 + - + +
153B GLN* 3.5 2.3 + - - -
155B VAL* 1.3 76.1 - - - +
157B GLY* 1.3 62.1 + - - +
158B PHE* 3.2 49.9 + - + +
163B VAL* 4.5 0.3 - - - +
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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