Contacts of the helix formed by residues 138 - 150 (chain H) in PDB entry 2HOI
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 GLU 138 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136H ALA* 3.5 8.2 - - + +
137H PHE* 1.3 74.4 - - - +
139H ARG* 1.3 62.3 + - - +
140H THR* 3.3 12.7 + - + +
141H ASP* 3.0 18.2 + - - +
142H PHE* 2.9 28.2 + - - +
168H TYR* 3.9 4.0 - - - -
294H GLY* 3.7 22.0 - - - +
297H ARG* 2.8 35.7 + - - -
298H ASP* 3.7 11.0 - - - +
301H ARG* 2.9 29.2 + - - +
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Residues in contact with ARG 139 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338A LEU* 2.8 30.1 + - - +
339A LEU* 3.5 43.3 + - - +
341A ASP 4.6 10.5 - - - -
138H GLU* 1.3 70.5 - - - +
140H THR* 1.3 70.2 + - + +
142H PHE* 3.2 6.4 + - - +
143H ASP* 2.9 54.3 + - - +
146H ARG* 5.9 2.8 - - - +
168H TYR* 3.3 23.0 + - - +
298H ASP* 2.9 17.8 + - + +
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Residues in contact with THR 140 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138H GLU* 4.3 11.4 + - + +
139H ARG* 1.3 82.0 - - + +
141H ASP* 1.3 71.5 + - - +
143H ASP* 3.4 7.6 + - - +
144H GLN* 3.0 25.6 + - - +
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Residues in contact with ASP 141 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136H ALA 3.4 10.7 - - - +
137H PHE* 4.0 7.6 - - + -
138H GLU* 3.0 35.8 + - - +
140H THR* 1.3 86.7 + - - +
142H PHE* 1.3 61.1 + - - +
144H GLN* 3.4 11.4 + - - +
145H VAL* 3.1 28.8 + - - +
272H ILE* 5.1 0.2 - - - +
273H TYR* 4.0 12.1 + - - -
286H TRP* 3.3 34.1 - - + -
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Residues in contact with PHE 142 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339A LEU* 4.1 27.1 - - + -
137H PHE* 3.6 28.6 - + + -
138H GLU 2.9 13.9 + - - +
139H ARG* 3.2 11.4 + - - +
141H ASP* 1.3 76.5 - - - +
143H ASP* 1.3 59.1 + - - +
145H VAL* 3.3 2.3 + - + +
146H ARG* 2.8 67.8 + - - +
161H LEU* 4.5 14.1 - - + -
164H LEU* 4.2 6.3 - - + -
165H GLY* 3.6 33.7 - - - -
168H TYR* 4.4 14.1 - + + -
217H VAL* 4.3 9.2 - - + -
220H LEU* 4.0 8.1 - - + -
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Residues in contact with ASP 143 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139H ARG* 2.9 53.9 + - - +
140H THR* 3.8 6.5 - - - +
142H PHE* 1.3 79.3 - - - +
144H GLN* 1.3 56.4 + - - +
146H ARG* 3.7 20.8 + - - +
147H SER* 3.0 31.5 + - - -
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Residues in contact with GLN 144 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140H THR 3.0 17.3 + - - +
141H ASP* 3.7 12.6 - - - +
142H PHE 3.3 0.2 - - - -
143H ASP* 1.3 73.6 - - - +
145H VAL* 1.3 64.9 + - - +
147H SER* 3.4 7.6 + - - +
148H LEU* 3.1 34.4 + - + +
272H ILE* 3.5 33.4 - - + +
273H TYR* 4.2 13.4 + - - -
286H TRP* 5.9 0.2 - - - -
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Residues in contact with VAL 145 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137H PHE* 4.2 12.8 - - + -
141H ASP 3.1 18.1 + - - +
142H PHE* 3.7 5.8 - - + +
144H GLN* 1.3 72.6 - - - +
146H ARG* 1.3 61.4 + - - +
148H LEU* 3.1 6.0 + - - +
149H MET* 2.8 35.9 + - + +
161H LEU* 4.0 17.9 - - + -
164H LEU* 4.0 11.7 - - + -
268H THR* 3.4 35.2 - - + -
271H LEU* 5.9 3.8 - - + -
272H ILE* 3.6 19.3 - - + -
286H TRP* 4.6 0.7 - - + -
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Residues in contact with ARG 146 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339A LEU* 5.7 6.7 + - - +
139H ARG* 5.9 2.8 - - - +
142H PHE* 2.8 50.9 + - - +
143H ASP* 3.7 18.6 + - - +
145H VAL* 1.3 77.7 - - - +
147H SER* 1.3 56.1 + - - +
150H GLU* 2.8 57.3 + - + +
161H LEU* 4.0 16.4 - - + +
216H GLY* 4.0 31.8 + - - -
217H VAL* 5.4 1.3 - - - -
220H LEU* 3.9 20.3 - - + +
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Residues in contact with SER 147 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143H ASP 3.0 20.4 + - - -
144H GLN* 3.4 11.1 + - - +
146H ARG* 1.3 75.4 - - - +
148H LEU* 1.3 59.3 + - - +
150H GLU* 3.8 18.9 - - - +
151H ASN* 4.9 8.7 + - - -
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Residues in contact with LEU 148 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144H GLN* 3.1 27.8 + - + +
145H VAL* 3.1 6.8 + - - +
147H SER* 1.3 84.0 - - - +
149H MET* 1.3 74.1 + - - +
150H GLU 3.7 0.4 - - - -
151H ASN* 5.1 6.8 + - - +
152H SER 5.6 0.3 + - - -
271H LEU* 4.4 15.0 - - + +
272H ILE* 3.8 31.2 - - + -
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Residues in contact with MET 149 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145H VAL* 2.8 20.6 + - + +
148H LEU* 1.3 90.2 - - - +
150H GLU* 1.3 64.2 + - - +
151H ASN 3.2 3.1 - - - -
152H SER* 3.3 25.7 + - - +
154H ARG* 5.9 0.2 - - - +
157H ASP* 3.8 42.4 - - + +
161H LEU* 4.2 20.9 - - + +
223H ARG* 5.3 0.2 + - - -
271H LEU* 3.8 36.8 - - + -
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Residues in contact with GLU 150 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146H ARG* 2.8 49.6 + - + +
147H SER* 3.8 16.0 + - - +
148H LEU 3.7 0.4 - - - -
149H MET* 1.3 75.5 - - - +
151H ASN* 1.3 67.9 + - - +
152H SER 3.4 0.2 + - - -
161H LEU* 4.1 10.6 - - + +
220H LEU* 5.8 3.8 - - + -
223H ARG* 3.2 27.0 + - - -
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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