Contacts of the helix formed by residues 138 - 150 (chain B) in PDB entry 2HOF
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136B ALA* 3.9 18.9 - - + +
137B PHE* 1.3 75.0 - - - +
139B ARG* 1.3 61.4 + - - +
140B THR* 3.3 8.0 - - - +
141B ASP* 3.0 20.3 + - - +
142B PHE* 2.9 27.4 + - - +
168B TYR* 3.8 6.1 - - - -
294B GLY* 3.7 19.3 - - - +
297B ARG* 4.0 15.6 + - - -
298B ASP* 3.3 18.6 - - - +
301B ARG* 3.2 21.4 + - - -
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Residues in contact with ARG 139 (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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138B GLU* 1.3 72.1 - - - +
140B THR* 1.3 54.7 + - - +
142B PHE* 3.2 8.7 + - - +
143B ASP* 2.7 66.6 + - - +
146B ARG* 4.5 7.9 - - - +
168B TYR* 3.3 31.5 + - - +
298B ASP* 2.8 16.7 + - + +
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Residues in contact with THR 140 (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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138B GLU* 3.3 6.3 - - - +
139B ARG* 1.3 78.1 - - - +
141B ASP* 1.3 61.2 + - - +
143B ASP* 3.3 10.2 + - + +
144B GLN* 2.8 60.2 + - + +
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Residues in contact with ASP 141 (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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136B ALA 3.9 5.4 - - - +
137B PHE* 3.8 13.4 - - + -
138B GLU* 3.0 35.5 + - - +
140B THR* 1.3 74.5 - - - +
142B PHE* 1.3 60.7 + - - +
144B GLN* 3.3 10.6 + - - +
145B VAL* 2.9 36.4 + - - +
272B ILE* 6.1 0.4 - - - -
273B TYR* 3.6 14.0 + - - -
286B TRP* 3.5 35.7 - - + -
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Residues in contact with PHE 142 (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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137B PHE* 3.7 26.8 - + + -
138B GLU 2.9 13.1 + - - +
139B ARG* 3.5 14.6 - - - +
141B ASP* 1.3 75.8 - - - +
143B ASP* 1.3 58.7 + - - +
145B VAL* 4.5 2.0 - - + -
146B ARG* 2.9 60.6 + - + +
161B LEU* 4.2 21.3 - - + -
164B LEU* 4.5 5.2 - - + -
165B GLY* 3.6 34.1 - - - -
168B TYR* 4.2 23.1 - + + -
217B VAL* 4.2 13.9 - - + -
220B LEU* 3.8 17.9 - - + -
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Residues in contact with ASP 143 (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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139B ARG* 2.7 51.2 + - - +
140B THR* 3.4 9.5 - - + +
142B PHE* 1.3 73.7 - - - +
144B GLN* 1.3 57.2 + - + +
146B ARG* 2.8 33.6 + - - +
147B SER* 3.0 29.6 + - - -
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Residues in contact with GLN 144 (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 THR* 2.8 45.8 + - + +
141B ASP* 3.7 9.4 + - - +
143B ASP* 1.3 71.8 - - + +
145B VAL* 1.3 64.8 + - - +
147B SER* 2.7 23.1 + - - -
148B LEU* 3.2 16.8 + - + +
272B ILE* 4.5 17.8 - - + +
273B TYR* 4.2 14.2 + - - -
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Residues in contact with VAL 145 (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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137B PHE* 4.2 9.6 - - + -
141B ASP 2.9 23.5 + - - +
142B PHE* 3.9 6.1 - - + +
144B GLN* 1.3 73.7 - - - +
146B ARG* 1.3 59.7 + - - +
148B LEU* 3.2 5.4 + - - +
149B MET* 2.8 56.0 + - + +
161B LEU* 4.1 7.4 - - + -
164B LEU* 3.8 20.6 - - + -
268B THR* 3.5 22.0 - - + -
271B LEU* 6.2 1.3 - - + -
272B ILE* 3.8 20.9 - - + -
286B TRP* 4.4 2.9 - - + -
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Residues in contact with ARG 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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139B ARG* 4.5 9.3 - - - +
142B PHE* 2.9 41.3 + - + +
143B ASP* 2.8 32.3 + - - +
145B VAL* 1.3 78.0 - - - +
147B SER* 1.3 61.9 + - - +
150B GLU* 3.0 51.7 + - + +
161B LEU* 3.7 22.4 - - + -
216B GLY* 4.9 15.4 - - - -
217B VAL* 5.1 1.4 - - - +
220B LEU* 4.2 23.5 - - + +
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Residues in contact with SER 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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143B ASP 3.0 15.7 + - - -
144B GLN* 2.7 23.9 + - - -
146B ARG* 1.3 75.8 - - - +
148B LEU* 1.3 62.2 + - - +
150B GLU* 4.2 10.9 - - - +
151B ASN* 3.5 20.6 + - - -
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Residues in contact with LEU 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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144B GLN* 3.2 14.9 + - + +
145B VAL* 3.6 6.1 - - - +
146B ARG 3.1 0.2 - - - -
147B SER* 1.3 87.6 + - - +
149B MET* 1.3 66.9 + - + +
150B GLU 3.6 0.3 + - - -
151B ASN* 4.0 12.6 + - - +
152B SER* 4.7 2.1 + - - -
271B LEU* 4.7 14.4 - - + +
272B ILE* 4.1 28.5 - - + -
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Residues in contact with MET 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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145B VAL* 2.8 44.0 + - - +
148B LEU* 1.3 73.5 - - + +
150B GLU* 1.3 57.8 + - - +
151B ASN 3.1 3.4 - - - -
152B SER* 3.0 29.9 + - - +
157B ASP* 3.5 46.9 - - + +
158B ILE* 6.0 0.7 - - - +
160B ASN* 3.8 22.7 - - + +
161B LEU* 4.0 17.7 - - + +
164B LEU* 4.9 1.3 - - - -
223B ARG* 4.8 1.0 + - - -
268B THR* 4.6 13.7 - - - +
271B LEU* 4.3 23.1 - - + -
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Residues in contact with GLU 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B ARG* 3.0 39.8 + - + +
147B SER* 4.2 12.3 - - - +
148B LEU 3.5 0.2 - - - -
149B MET* 1.3 76.7 - - - +
151B ASN* 1.3 72.2 + - - +
152B SER 3.3 1.3 - - - -
161B LEU* 3.7 17.4 - - + +
220B LEU* 5.3 5.4 - - + +
223B ARG* 3.1 25.7 + - - +
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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