Contacts of the helix formed by residues 145 - 156 (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 VAL 145 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A VAL* 3.5 26.0 - - - +
141A ILE 3.9 8.5 - - - +
142A SER 3.2 11.4 - - - +
143A ASN* 3.1 16.4 + - - +
144A PRO* 1.3 67.3 - - - +
146A ASP* 1.3 71.3 + - - +
149A THR* 2.7 36.7 + - - +
165A GLY* 4.2 1.1 - - - -
166A THR* 4.0 4.9 - - - +
167A GLY* 3.8 25.4 - - - +
198A HIS* 3.6 37.4 + - + +
274A SER* 5.1 0.7 - - - -
330A NAD 3.9 3.6 - - - +
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Residues in contact with ASP 146 (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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144A PRO* 3.2 1.6 + - + +
145A VAL* 1.3 82.5 - - - +
147A VAL* 1.3 63.2 + - + +
149A THR* 3.4 2.8 + - - -
150A ALA* 3.2 20.1 + - - +
167A GLY* 4.8 0.2 - - - -
196A GLY 4.3 0.7 - - - +
197A GLU* 3.5 9.6 - - + +
198A HIS* 3.1 30.2 + - - +
274A SER* 2.7 35.9 + - - +
283A TYR* 4.0 7.6 - - - +
284A LEU* 3.7 9.8 - - - -
285A SER* 4.0 4.5 + - - -
318A ILE* 3.7 34.8 - - + -
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Residues in contact with VAL 147 (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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112A PHE* 4.4 14.4 - - + -
115A LEU* 4.1 13.9 - - + -
144A PRO* 3.1 15.5 + - + +
146A ASP* 1.3 75.3 - - + +
148A ILE* 1.3 64.1 + - - +
150A ALA* 3.2 7.4 + - - +
151A LEU* 3.0 24.8 + - + +
197A GLU* 5.8 0.4 - - - +
282A MET* 4.8 0.4 - - - -
318A ILE* 3.9 30.7 - - + +
321A ARG* 4.1 14.1 - - + -
322A PHE* 4.0 22.9 - - + +
325A ILE* 4.1 16.4 - - + -
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Residues in contact with ILE 148 (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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97A LEU* 6.2 0.4 - - + -
115A LEU* 4.0 20.2 - - + -
118A THR* 3.5 30.5 - - - +
119A SER* 4.0 12.6 - - - +
122A VAL* 3.9 9.0 - - + -
140A VAL* 3.9 8.7 - - + -
142A SER* 3.8 20.0 - - - +
143A ASN 3.9 9.4 - - - +
144A PRO* 2.9 20.7 + - + +
145A VAL 4.1 0.2 - - - +
147A VAL* 1.3 71.9 - - - +
149A THR* 1.3 67.0 + - - +
151A LEU* 3.9 10.3 - - + +
152A PHE* 3.0 46.5 + - + +
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Residues in contact with THR 149 (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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140A VAL* 3.5 23.5 - - + +
145A VAL* 2.7 26.4 + - - +
146A ASP* 3.7 6.2 - - - -
148A ILE* 1.3 78.1 - - - +
150A ALA* 1.3 61.4 + - - +
152A PHE* 3.2 2.9 + - - +
153A GLN* 3.0 19.4 + - - +
163A VAL* 3.7 11.9 - - + +
164A ILE 3.6 24.2 - - - +
165A GLY* 3.7 11.6 - - - +
274A SER* 4.5 1.7 + - - +
283A TYR* 3.6 31.9 - - + -
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Residues in contact with ALA 150 (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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146A ASP 3.2 2.7 + - - +
147A VAL 3.2 9.1 + - - +
149A THR* 1.3 78.6 - - - +
151A LEU* 1.3 57.7 + - - +
153A GLN* 3.2 5.7 + - - +
154A HIS* 2.9 27.2 + - - +
282A MET* 3.2 35.7 - - + -
283A TYR* 3.6 20.6 - - + -
322A PHE* 3.7 15.0 - - + -
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Residues in contact with LEU 151 (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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119A SER* 4.1 24.5 - - - -
122A VAL* 3.8 13.7 - - + -
147A VAL* 3.0 22.0 + - + +
148A ILE* 3.3 15.7 + - + +
150A ALA* 1.3 76.1 - - - +
152A PHE* 1.3 56.2 + - - +
154A HIS* 3.2 4.6 + - - +
155A VAL* 2.9 33.6 + - - +
322A PHE* 3.5 25.1 - - + -
325A ILE* 3.9 18.6 - - + -
326A VAL* 3.8 20.0 - - + +
329A LEU* 3.5 26.7 - - + -
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Residues in contact with PHE 152 (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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27A ILE* 5.9 0.4 - - + -
95A SER* 3.5 31.0 - - - -
97A LEU* 4.7 5.8 - - + -
122A VAL* 3.9 21.5 - - + +
125A VAL* 3.9 31.6 - - + -
126A GLY* 4.0 19.1 - - - -
129A LEU* 5.0 4.5 - - + -
138A LEU* 3.9 25.4 - - + -
140A VAL* 3.7 15.3 - - + -
142A SER* 5.1 0.9 - - - -
148A ILE* 3.0 36.1 + - + -
149A THR 3.5 8.5 - - - +
151A LEU* 1.3 72.8 - - - +
153A GLN* 1.3 67.6 + - - +
155A VAL* 3.2 0.6 + - - -
156A THR* 2.9 34.2 + - + +
163A VAL* 4.3 3.1 - - + -
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Residues in contact with GLN 153 (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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149A THR 3.0 10.6 + - - +
150A ALA 3.5 8.1 - - - +
152A PHE* 1.3 76.3 - - - +
154A HIS* 1.3 59.6 + - - +
156A THR* 3.5 5.1 + - - -
157A GLY* 3.0 29.1 + - - -
158A PHE 2.7 29.5 + - - +
159A PRO* 4.6 0.2 - - - +
160A ALA* 3.6 17.0 - - - +
163A VAL* 4.1 12.0 - - + +
276A ARG* 3.5 21.8 + - - +
283A TYR* 3.2 33.0 - - + +
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Residues in contact with HIS 154 (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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150A ALA 2.9 13.4 + - - +
151A LEU* 3.3 12.6 - - - +
153A GLN* 1.3 85.6 + - - +
155A VAL* 1.3 62.9 + - + +
157A GLY* 4.0 4.9 + - - -
322A PHE* 4.5 10.8 - + + -
326A VAL* 3.4 36.0 + - + +
329A LEU* 4.3 15.0 - - + -
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Residues in contact with VAL 155 (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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122A VAL* 3.8 19.7 - - + +
123A GLN* 3.4 47.6 - - - +
126A GLY* 4.0 7.6 - - - -
127A THR* 4.0 6.7 - - - +
130A LYS* 3.6 16.1 + - - -
151A LEU 2.9 22.4 + - - +
152A PHE 4.1 1.6 - - - +
154A HIS* 1.3 76.1 - - + +
156A THR* 1.3 65.7 + - - +
157A GLY* 4.5 0.3 - - - -
329A LEU* 3.6 26.9 - - + -
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Residues in contact with THR 156 (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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126A GLY* 3.6 31.6 - - - +
129A LEU* 4.6 6.5 - - + -
130A LYS* 3.4 29.9 - - - +
138A LEU* 4.9 1.8 - - + -
152A PHE* 2.9 31.0 + - + +
153A GLN* 3.5 2.6 + - - -
155A VAL* 1.3 77.5 - - - +
157A GLY* 1.3 63.8 + - - +
158A PHE* 3.2 49.2 + - + +
163A VAL* 4.5 1.0 - - - +
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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