Contacts of the helix formed by residues 145 - 156 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140C VAL* 3.6 25.6 - - + +
142C SER* 3.5 31.0 + - - +
143C ASN* 4.6 0.6 + - - -
144C PRO* 1.3 70.3 - - - +
146C ASP* 1.3 60.1 + - - +
148C ILE* 4.1 0.2 - - - +
149C THR* 2.6 44.3 + - - +
165C GLY* 4.0 1.6 - - - -
166C THR* 4.0 4.9 - - - +
167C GLY* 3.9 25.6 - - - +
198C HIS* 3.6 40.7 + - + +
274C SER* 4.9 0.7 - - - -
330C NAD 4.8 1.8 - - - +
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Residues in contact with ASP 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C PRO* 3.4 2.5 - - + +
145C VAL* 1.3 81.6 - - - +
147C VAL* 1.3 61.9 + - + +
149C THR* 3.6 1.1 + - - -
150C ALA* 3.2 23.0 + - - +
196C GLY 4.2 1.7 - - - +
197C GLU* 3.6 10.6 - - - +
198C HIS 3.4 25.2 + - - +
274C SER* 2.5 35.2 + - - +
282C MET* 4.0 0.5 - - - +
283C TYR* 3.7 12.8 - - - +
284C LEU* 3.4 12.1 - - - -
285C SER* 3.8 3.9 + - - -
318C ILE* 3.7 32.1 - - + +
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Residues in contact with VAL 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C PRO* 3.4 27.3 + - + +
145C VAL 3.4 0.2 - - - -
146C ASP* 1.3 72.9 - - + +
148C ILE* 1.3 64.3 + - + +
150C ALA* 3.1 8.6 + - - +
151C LEU* 2.9 26.5 + - - +
197C GLU* 6.2 0.4 - - - +
282C MET* 4.6 3.8 - - - -
318C ILE* 4.2 19.1 - - + +
321C ARG* 3.8 28.0 - - + +
322C PHE* 4.0 12.8 - - + -
325C ILE* 3.7 34.1 - - + -
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Residues in contact with ILE 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C LEU 4.5 3.1 - - - +
98C GLY* 5.4 1.8 - - - -
118C THR* 3.8 29.6 - - + -
122C VAL* 4.4 13.0 - - + -
140C VAL* 4.1 2.5 - - + -
142C SER* 3.3 34.8 - - - +
143C ASN 4.5 1.8 - - - +
144C PRO* 3.1 29.2 + - + +
145C VAL 4.1 0.7 - - - +
147C VAL* 1.3 78.3 - - + +
149C THR* 1.3 62.9 + - - +
151C LEU* 3.4 7.3 + - + +
152C PHE* 3.1 44.3 + - + -
325C ILE* 4.6 13.7 - - + -
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Residues in contact with THR 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C VAL* 3.6 18.0 - - + +
145C VAL 2.6 27.1 + - - -
146C ASP* 3.7 6.3 - - - -
148C ILE* 1.3 77.7 - - - +
150C ALA* 1.3 61.9 + - - +
152C PHE* 3.2 4.9 + - - +
153C GLN* 3.0 20.6 + - - +
163C VAL* 3.8 10.4 - - + +
164C ILE 3.9 6.1 - - - +
165C GLY* 3.5 34.4 - - - +
274C SER* 4.5 0.8 + - - +
283C TYR* 3.5 31.6 - - + -
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Residues in contact with ALA 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146C ASP 3.2 4.7 + - - +
147C VAL 3.1 6.9 + - - +
149C THR* 1.3 78.5 - - - +
151C LEU* 1.3 57.9 + - - +
153C GLN* 3.3 4.7 + - - +
154C HIS* 2.9 27.9 + - - +
282C MET* 3.4 33.7 - - + -
283C TYR* 3.6 23.3 - - + -
322C PHE* 3.7 15.6 - - + -
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Residues in contact with LEU 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C SER* 4.0 24.7 - - - +
122C VAL* 3.9 24.9 - - + -
147C VAL 2.9 15.5 + - - +
148C ILE* 3.7 11.2 - - + +
150C ALA* 1.3 77.2 - - - +
152C PHE* 1.3 56.8 + - - +
154C HIS* 3.1 5.4 + - + +
155C VAL* 2.9 37.3 + - + +
322C PHE* 3.6 18.1 - - + -
325C ILE* 4.1 24.9 - - + -
326C VAL* 4.2 26.2 - - + -
329C LEU* 4.3 14.1 - - + -
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Residues in contact with PHE 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C ILE* 5.9 0.2 - - + -
95C SER* 3.7 26.2 - - - -
97C LEU* 5.3 7.6 - - + -
122C VAL* 4.0 27.1 - - + +
125C VAL* 4.0 27.4 - - + -
126C GLY* 4.1 21.1 - - - -
129C LEU* 5.1 4.0 - - + -
138C LEU* 4.0 28.5 - - + -
140C VAL* 3.9 17.0 - - + -
148C ILE* 3.1 39.3 + - + -
149C THR 3.6 8.1 - - - +
151C LEU* 1.3 71.3 - - - +
153C GLN* 1.3 58.1 + - - +
155C VAL* 4.6 1.6 - - - +
156C THR* 2.6 40.0 + - + +
163C VAL* 4.3 2.9 - - + -
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Residues in contact with GLN 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149C THR 3.0 10.7 + - - +
150C ALA 3.5 9.0 - - - +
151C LEU 3.2 0.2 - - - -
152C PHE* 1.3 78.4 - - - +
154C HIS* 1.3 65.7 + - - +
156C THR* 3.6 3.7 + - - -
157C GLY* 3.2 21.8 + - - -
158C PHE 2.8 28.4 + - - +
159C PRO* 4.5 1.0 - - - +
160C ALA* 3.7 13.9 - - - +
163C VAL* 4.1 10.7 - - + +
276C ARG* 3.7 30.1 + - - +
283C TYR* 3.5 29.3 - - + +
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Residues in contact with HIS 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C ALA 2.9 14.0 + - - +
151C LEU* 3.2 12.6 - - + +
153C GLN* 1.3 84.4 + - - +
155C VAL* 1.3 66.3 + - + +
157C GLY* 4.0 5.7 + - - -
322C PHE* 4.3 11.6 - + + -
326C VAL* 3.9 18.4 - - + +
329C LEU* 3.7 30.2 - - + +
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Residues in contact with VAL 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C VAL* 3.7 14.1 - - + +
123C GLN* 3.5 55.9 - - - +
126C GLY* 4.2 7.1 - - - +
127C THR* 4.3 7.9 + - - +
130C LYS* 4.3 10.2 + - - -
151C LEU* 2.9 25.3 + - + +
152C PHE* 4.3 2.9 - - - +
154C HIS* 1.3 84.1 - - + +
156C THR* 1.3 64.5 + - + +
157C GLY 3.7 0.2 + - - -
329C LEU* 4.4 12.3 - - + -
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Residues in contact with THR 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C GLY* 3.4 37.9 - - - +
129C LEU* 4.9 3.4 - - + -
130C LYS* 3.3 29.1 - - - +
138C LEU* 5.1 0.9 - - + -
152C PHE* 2.6 31.9 + - + +
153C GLN* 3.6 2.6 + - - -
155C VAL* 1.3 77.2 - - - +
157C GLY* 1.3 62.4 + - - +
158C PHE* 3.2 47.8 + - + +
163C VAL* 4.5 0.5 - - - +
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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