Contacts of the helix formed by residues 151 - 166 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144B LYS* 5.2 1.2 - - - +
149B THR 3.4 5.1 + - - +
150B LEU* 1.3 77.4 - - - +
152B PRO* 1.3 64.7 - - + -
153B GLY* 4.3 2.7 - - - +
154B ASP* 2.6 50.9 + - - +
155B ASN* 2.7 16.6 + - - -
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Residues in contact with PRO 152 (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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150B LEU 3.5 6.2 - - - +
151B LEU* 1.3 92.5 - - + +
153B GLY* 1.3 52.6 + - - +
155B ASN* 3.1 8.8 + - + +
156B GLU* 2.6 49.7 + - + +
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Residues in contact with GLY 153 (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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151B LEU* 3.2 3.7 - - - +
152B PRO* 1.3 80.5 - - - +
154B ASP* 1.3 59.2 + - - +
156B GLU* 3.8 11.5 + - - +
157B ALA* 3.0 26.9 + - - +
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Residues in contact with ASP 154 (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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141B GLN* 5.1 8.0 + - - +
150B LEU* 3.8 23.0 - - + +
151B LEU* 2.6 52.7 + - - +
153B GLY* 1.3 71.4 - - - +
155B ASN* 1.3 62.2 + - - -
157B ALA* 3.4 7.2 + - - +
158B LEU* 3.1 27.8 + - - +
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Residues in contact with ASN 155 (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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13B ALA 4.6 0.2 - - - +
14B ILE* 3.8 13.9 - - - +
15B VAL* 2.8 52.5 + - - +
17B PHE* 4.1 10.5 - - - -
150B LEU* 3.8 16.7 - - + +
151B LEU 2.7 14.1 + - - +
152B PRO* 3.4 12.8 - - + +
154B ASP* 1.3 73.2 - - - +
156B GLU* 1.3 67.2 + - + +
158B LEU* 3.0 15.3 + - - +
159B ALA* 3.0 10.0 + - - +
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Residues in contact with GLU 156 (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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3B LEU* 5.7 0.2 - - - +
11B PRO* 3.5 35.4 - - + +
12B SER 4.7 2.1 + - - -
13B ALA 4.6 9.3 - - - +
152B PRO* 2.6 40.4 + - + +
153B GLY* 3.8 9.7 + - - +
155B ASN* 1.3 75.8 - - + +
157B ALA* 1.3 63.0 + - - +
159B ALA* 3.4 1.9 + - - +
160B ALA* 3.0 25.2 + - - +
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Residues in contact with ALA 157 (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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1B ALA 5.2 5.2 - - - -
153B GLY 3.0 18.9 + - - +
154B ASP* 3.6 10.1 - - - +
156B GLU* 1.3 77.6 - - - +
158B LEU* 1.3 64.8 + - + +
160B ALA* 3.1 5.2 + - - +
161B GLU* 3.0 25.4 + - - +
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Residues in contact with LEU 158 (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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15B VAL* 3.6 12.8 - - + -
17B PHE* 4.5 9.2 - - + -
133B ILE* 4.7 3.8 - - + -
134B THR* 3.9 10.0 - - + +
136B SER* 5.0 1.3 - - - -
137B MET* 4.1 34.1 - - + +
141B GLN* 3.9 34.8 - - + +
150B LEU* 3.9 22.9 - - + -
154B ASP 3.1 15.0 + - - +
155B ASN 3.0 7.0 + - - +
157B ALA* 1.3 82.2 - - + +
159B ALA* 1.3 64.0 + - - +
161B GLU* 3.3 10.5 + - - +
162B THR* 3.0 26.3 + - - -
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Residues in contact with ALA 159 (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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13B ALA* 3.4 40.4 - - + +
14B ILE 3.8 1.3 - - - +
15B VAL* 3.6 11.1 - - + +
34B VAL* 3.7 17.4 - - + +
155B ASN 3.0 14.1 + - - +
156B GLU 3.8 2.2 - - - +
158B LEU* 1.3 76.6 - - - +
160B ALA* 1.3 59.3 + - - +
162B THR* 3.3 1.7 + - - -
163B VAL* 2.8 33.6 + - - +
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Residues in contact with ALA 160 (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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1B ALA 3.7 26.2 - - - +
2B ALA* 4.6 1.8 - - - -
3B LEU* 3.8 32.5 - - + +
156B GLU 3.0 17.2 + - - +
157B ALA 3.1 3.1 + - - +
159B ALA* 1.3 74.6 - - - +
161B GLU* 1.3 62.0 + - - +
164B LEU* 2.9 39.5 + - + +
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Residues in contact with GLU 161 (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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1B ALA 6.0 1.0 - - - +
134B THR* 3.4 18.7 + - + +
136B SER* 2.6 36.8 + - - -
157B ALA 3.0 15.7 + - - +
158B LEU* 3.7 9.4 - - - +
160B ALA* 1.3 78.2 - - - +
162B THR* 1.3 56.3 + - - +
164B LEU* 3.6 5.5 + - - +
165B ALA* 2.9 30.8 + - + +
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Residues in contact with THR 162 (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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34B VAL* 3.6 27.4 - - + +
132B ASN* 3.2 27.1 - - - +
133B ILE* 4.0 1.0 - - - +
134B THR* 3.1 27.7 + - - +
158B LEU 3.0 13.6 + - - -
159B ALA 3.5 7.6 - - - -
161B GLU* 1.3 75.5 - - - +
163B VAL* 1.3 67.3 + - - +
165B ALA* 3.0 5.2 + - - +
166B GLN* 3.0 40.5 + - + +
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Residues in contact with VAL 163 (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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3B LEU* 4.0 21.1 - - + -
13B ALA* 3.9 22.7 - - + -
34B VAL* 4.0 10.8 - - + -
36B ASN* 4.3 24.0 - - + +
159B ALA 2.8 23.2 + - - +
160B ALA 4.0 2.7 - - - +
162B THR* 1.3 74.0 - - - +
164B LEU* 1.3 65.9 + - + +
166B GLN* 3.2 37.4 + - - +
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Residues in contact with LEU 164 (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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1B ALA* 4.1 28.5 - - + +
2B ALA 5.2 2.0 - - - +
3B LEU* 3.6 25.4 - - + -
160B ALA* 2.9 26.0 + - + +
161B GLU* 4.1 4.7 - - - +
163B VAL* 1.3 80.5 - - + +
165B ALA* 1.3 58.4 + - - +
166B GLN 3.3 2.7 - - - +
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Residues in contact with ALA 165 (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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134B THR* 5.9 3.4 - - - +
161B GLU* 2.9 21.4 + - + +
162B THR* 3.0 5.5 + - - +
164B LEU* 1.3 76.6 - - - +
166B GLN* 1.3 66.9 + - - +
167B LYS* 3.6 4.9 + - - +
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Residues in contact with GLN 166 (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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34B VAL* 5.0 3.6 + - - +
36B ASN* 5.5 1.6 + - - -
132B ASN* 3.4 28.1 - - + +
162B THR* 3.0 25.9 + - + +
163B VAL* 3.2 42.0 + - - +
164B LEU 4.4 2.6 - - - +
165B ALA* 1.3 80.5 - - - +
167B LYS* 1.3 63.2 + - - +
1295B HEC 4.0 21.1 + - - +
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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