Contacts of the helix formed by residues 146 - 158 (chain A) in PDB entry 1HCR
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 LYS 146 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A ILE 2.8 14.3 + - - -
145A ASN* 1.4 64.2 - - - +
147A HIS* 1.3 62.5 + - - +
148A GLU 2.9 1.1 - - - -
149A GLN* 2.8 42.9 + - - +
150A GLU* 3.3 30.7 - - - +
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Residues in contact with HIS 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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145A ASN* 2.7 24.0 + - + -
146A LYS* 1.3 78.6 - - - +
148A GLU* 1.4 74.4 + - + +
150A GLU* 3.3 41.0 + - - +
151A GLN* 3.4 28.5 + - - +
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Residues in contact with GLU 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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144A ILE* 4.2 13.6 - - + +
145A ASN* 2.6 55.2 + - - +
146A LYS 2.9 1.2 - - - -
147A HIS* 1.4 88.8 + - - +
149A GLN* 1.3 57.8 + - - +
150A GLU 3.2 0.2 - - - -
151A GLN* 3.1 27.2 + - + +
152A ILE* 3.0 34.7 + - + +
169A PHE* 4.6 15.5 - - + -
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Residues in contact with GLN 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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142A ARG* 4.2 12.1 + - - +
144A ILE* 2.6 40.5 + - + +
146A LYS* 2.8 39.9 + - - +
148A GLU* 1.3 74.1 - - - +
150A GLU* 1.3 58.2 + - - +
152A ILE* 4.8 0.2 - - - -
153A SER* 2.8 34.8 + - - -
179A TYR* 3.1 34.4 + - + -
180A PHE* 3.6 18.1 - - + -
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Residues in contact with GLU 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 LYS* 3.3 24.4 + - - +
147A HIS* 3.3 29.3 + - - +
149A GLN* 1.3 73.3 - - - +
151A GLN* 1.3 66.6 - - - +
153A SER* 3.0 7.6 + - - -
154A ARG* 3.0 26.9 + - - +
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Residues in contact with GLN 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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147A HIS* 3.4 19.9 - - - +
148A GLU* 3.1 33.0 + - - +
150A GLU* 1.3 79.1 - - - +
152A ILE* 1.3 64.2 + - - +
154A ARG* 3.5 12.3 + - - +
155A LEU* 3.1 30.6 + - + +
169A PHE* 3.3 33.2 - - + -
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Residues in contact with ILE 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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144A ILE* 3.6 30.1 - - + -
148A GLU* 3.0 23.7 + - + +
151A GLN* 1.3 71.6 - - - +
153A SER* 1.3 66.5 + - - +
154A ARG 2.6 2.1 + - - -
155A LEU* 2.7 17.7 + - - -
156A LEU* 3.0 28.9 + - + -
165A LEU* 4.0 11.2 - - + -
169A PHE* 3.5 34.8 - - + -
171A ILE* 4.9 0.4 - - + -
176A LEU* 4.1 10.5 - - + -
180A PHE* 3.2 31.2 - - + -
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Residues in contact with SER 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 GLN 2.8 26.3 + - - -
150A GLU* 3.0 5.9 + - - -
152A ILE* 1.3 70.2 - - - +
154A ARG* 1.3 67.6 + - - +
156A LEU* 3.4 7.0 + - - +
157A GLU* 2.8 42.0 + - - +
180A PHE* 3.5 21.8 - - - -
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Residues in contact with ARG 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 GLU 3.0 9.3 + - - +
151A GLN* 3.5 15.3 + - - +
152A ILE 2.6 3.0 + - - -
153A SER* 1.3 82.3 - - - +
155A LEU* 1.3 100.7 + - - +
156A LEU 2.9 0.5 + - - -
157A GLU* 3.6 3.1 - - - +
158A LYS* 2.9 50.0 + - + +
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Residues in contact with LEU 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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151A GLN* 3.2 22.4 - - + +
152A ILE* 2.7 9.9 + - - +
154A ARG* 1.3 111.0 - - - +
156A LEU* 1.3 60.0 + - - +
158A LYS* 3.3 11.3 - - - +
160A HIS* 2.7 49.5 + - + +
165A LEU* 4.0 22.0 - - + -
169A PHE* 4.5 17.3 - - + -
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Residues in contact with LEU 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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152A ILE* 3.0 32.8 + - + +
153A SER* 4.0 9.9 - - - +
154A ARG 2.9 1.2 + - - -
155A LEU* 1.3 71.8 - - - +
157A GLU* 1.3 75.2 + - + +
158A LYS 3.1 1.3 - - - -
159A GLY* 3.0 16.8 + - - -
160A HIS* 3.2 27.3 + - - +
162A ARG* 4.0 42.8 - - + +
165A LEU* 3.6 12.5 - - + +
176A LEU* 4.9 0.9 - - + -
180A PHE* 4.0 24.0 - - + -
181A PRO 5.7 0.4 - - - +
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Residues in contact with GLU 157 (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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153A SER* 2.8 38.9 + - - +
154A ARG* 3.9 1.8 - - - +
156A LEU* 1.3 83.0 - - + +
158A LYS* 1.3 58.0 + - - +
159A GLY 3.2 3.5 + - - -
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Residues in contact with LYS 158 (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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154A ARG* 2.9 50.5 + - + +
155A LEU* 3.3 6.1 - - - +
157A GLU* 1.3 76.5 - - - +
159A GLY* 1.3 58.8 + - - +
160A HIS* 3.6 27.8 + - - -
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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