Contacts of the helix formed by residues 151 - 166 (chain A) in PDB entry 1OFY
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 LEU 151 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A THR 3.6 4.9 + - - +
150A LEU* 1.3 79.0 - - - +
152A PRO* 1.3 66.4 - - + +
153A GLY* 4.1 6.7 - - - +
154A ASP* 2.5 45.8 + - - +
155A ASN* 2.9 9.3 + - - -
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Residues in contact with PRO 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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150A LEU 3.6 6.9 - - - +
151A LEU* 1.3 90.7 - - + +
153A GLY* 1.3 53.7 + - - +
155A ASN* 3.5 11.3 - - + +
156A GLU* 2.7 40.1 + - - +
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Residues in contact with GLY 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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151A LEU* 2.9 5.9 + - - +
152A PRO* 1.3 79.3 - - - +
154A ASP* 1.3 63.6 + - - +
156A GLU* 3.0 21.4 - - - +
157A ALA* 3.3 21.8 + - - +
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Residues in contact with ASP 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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141A GLN* 4.9 13.7 + - - +
144A LYS* 5.8 1.7 + - - -
150A LEU* 3.9 21.8 - - + +
151A LEU* 2.5 40.7 + - - +
153A GLY* 1.3 73.0 - - - -
155A ASN* 1.3 64.9 + - - +
157A ALA* 3.2 6.5 + - - +
158A LEU* 3.0 27.6 + - - +
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Residues in contact with ASN 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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13A ALA 4.6 0.2 - - - +
14A ILE* 3.8 12.6 - - - +
15A VAL* 2.9 52.3 + - - +
17A PHE* 3.7 16.8 - - - -
150A LEU* 3.8 17.7 - - + +
151A LEU 2.9 4.8 + - - +
152A PRO* 3.5 17.9 - - + +
154A ASP* 1.3 79.5 - - - +
156A GLU* 1.3 58.8 + - - +
158A LEU* 3.3 0.8 + - - +
159A ALA* 2.9 24.4 + - - +
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Residues in contact with GLU 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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3A LEU* 5.7 0.3 - - - +
11A PRO* 5.3 10.7 - - + +
13A ALA 4.4 9.4 - - - +
152A PRO* 2.7 17.0 + - - +
153A GLY* 3.0 26.9 + - - +
155A ASN* 1.3 76.4 - - - +
157A ALA* 1.3 61.6 + - - +
159A ALA* 3.7 6.1 - - - +
160A ALA* 2.8 31.0 + - - +
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Residues in contact with ALA 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 GLY 3.3 13.2 + - - +
154A ASP* 3.2 8.6 + - - +
155A ASN 3.2 0.6 - - - -
156A GLU* 1.3 81.1 - - + +
158A LEU* 1.3 66.8 + - + +
160A ALA* 3.2 4.6 + - - +
161A GLU* 3.0 26.1 + - - +
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Residues in contact with LEU 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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15A VAL* 4.0 13.9 - - + -
17A PHE* 4.8 2.2 - - + -
133A ILE* 4.7 1.8 - - + -
134A THR* 3.5 14.4 - - + +
136A SER* 4.5 2.9 - - - -
137A MET* 3.8 50.9 - - + +
141A GLN* 3.8 30.7 - - + +
150A LEU* 4.4 15.7 - - + -
154A ASP 3.0 17.4 + - - +
155A ASN* 3.6 6.7 - - - +
157A ALA* 1.3 77.2 - - + +
159A ALA* 1.3 61.5 + - - +
161A GLU* 4.5 8.3 - - - +
162A THR* 3.0 30.0 + - - -
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Residues in contact with ALA 159 (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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13A ALA* 3.5 37.2 - - + +
14A ILE 3.8 3.6 - - - +
15A VAL* 3.8 12.8 - - + +
34A VAL* 3.8 14.8 - - + -
155A ASN 2.9 16.3 + - - +
156A GLU 3.7 2.0 - - - +
157A ALA 3.1 0.2 - - - -
158A LEU* 1.3 78.3 - - - +
160A ALA* 1.3 62.0 + - - +
162A THR* 3.4 1.7 + - - -
163A VAL* 3.0 28.4 + - - +
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Residues in contact with ALA 160 (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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2A ALA* 5.7 2.9 - - + -
3A LEU* 3.8 35.1 - - + +
156A GLU 2.8 21.8 + - - +
157A ALA* 3.9 4.9 - - - +
159A ALA* 1.3 74.0 - - - +
161A GLU* 1.3 58.7 + - - +
163A VAL* 4.5 0.2 - - - -
164A LEU* 2.8 45.0 + - + +
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Residues in contact with GLU 161 (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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134A THR* 3.6 15.5 + - + +
136A SER* 2.5 37.0 + - - -
157A ALA 3.0 17.7 + - - +
158A LEU* 3.7 10.3 - - - +
160A ALA* 1.3 75.9 - - - +
162A THR* 1.3 66.9 + - - +
164A LEU* 3.8 5.8 - - - +
165A ALA* 2.9 27.1 + - + +
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Residues in contact with THR 162 (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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34A VAL* 3.8 18.6 - - + -
132A ASN 3.2 26.5 - - - +
133A ILE* 3.8 4.9 - - - +
134A THR* 2.9 38.5 + - - +
158A LEU 3.0 11.4 + - - -
159A ALA 3.7 4.0 - - - -
161A GLU* 1.3 77.1 - - - +
163A VAL* 1.3 64.0 + - - +
165A ALA* 3.0 14.7 + - - +
166A GLN* 3.1 29.4 + - + +
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Residues in contact with VAL 163 (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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3A LEU* 3.9 25.1 - - + -
13A ALA* 3.9 19.1 - - + -
34A VAL* 4.0 12.1 - - + -
36A ASN* 4.3 22.2 - - + +
159A ALA 3.0 21.0 + - - +
160A ALA 3.9 2.0 - - - +
162A THR* 1.3 75.0 - - - +
164A LEU* 1.3 68.1 + - + +
166A GLN* 2.9 39.4 + - - +
1295A HEC 6.1 0.4 - - - +
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Residues in contact with LEU 164 (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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1A ALA 5.1 10.5 - - - +
2A ALA* 5.5 7.9 - - - +
3A LEU* 3.7 22.9 - - + -
160A ALA* 2.8 37.0 + - + +
161A GLU* 4.0 5.6 - - - +
163A VAL* 1.3 77.9 - - + +
165A ALA* 1.3 60.3 + - - +
166A GLN 3.6 3.7 + - - +
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Residues in contact with ALA 165 (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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134A THR* 6.0 2.2 - - - -
135A PRO* 6.3 2.2 - - + -
161A GLU* 2.9 21.0 + - + +
162A THR* 3.0 7.5 + - - +
164A LEU* 1.3 75.9 - - - +
166A GLN* 1.3 65.0 + - - +
167A LYS* 3.6 11.8 + - - +
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Residues in contact with GLN 166 (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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34A VAL* 5.1 2.8 + - - +
36A ASN* 5.7 0.9 + - - -
132A ASN* 3.3 29.8 - - + +
162A THR* 3.1 24.9 + - + +
163A VAL* 2.9 36.9 + - - +
164A LEU 4.4 3.3 - - - +
165A ALA* 1.3 78.5 - - - +
167A LYS* 1.3 64.2 + - - +
1295A HEC 4.0 21.6 + - - +
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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