Contacts of the helix formed by residues 152 - 159 (chain B) in PDB entry 3OFN
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 152 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150B THR* 2.9 15.1 + - - +
151B GLY* 1.3 79.9 - - - +
153B LYS* 1.3 60.7 + - - +
154B ALA 4.6 1.1 - - - +
155B VAL* 3.1 27.5 + - + +
156B ASP* 2.8 35.2 + - - +
179B ALA 6.1 0.4 - - - -
180B VAL* 3.8 39.7 - - + +
183B ASP* 3.7 31.0 - - + +
365B PRO* 4.4 16.8 - - + -
432B GLN* 3.4 20.4 - - + +
433B ASN 5.5 0.4 - - - +
437B PRO* 5.7 0.4 - - + -
443B GLN* 4.7 0.2 - - - -
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Residues in contact with LYS 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 GLY 3.7 1.0 + - - -
152B LEU* 1.3 69.9 - - - +
154B ALA* 1.3 61.8 + - - +
156B ASP 4.0 0.2 - - - -
157B ALA* 3.0 30.5 + - - +
429B LEU* 2.7 25.6 + - + +
430B LEU* 3.7 16.4 - - + +
431B LYS 2.6 28.8 + - - -
432B GLN* 2.7 33.7 + - - +
438B LEU* 3.8 17.5 - - + -
443B GLN* 4.1 21.3 + - + +
446B LEU* 4.5 8.5 - - + -
447B ILE* 4.7 9.1 - - + +
467B GLU* 3.1 35.3 + - - +
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Residues in contact with ALA 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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152B LEU 3.2 0.8 - - - -
153B LYS* 1.3 80.0 - - - +
155B VAL* 1.3 56.6 + - - +
158B LEU* 3.1 38.4 + - + +
159B VAL 3.9 0.5 + - - -
365B PRO* 4.3 21.5 - - + +
367B ILE* 3.7 25.0 - - + +
430B LEU* 3.8 29.4 + - + +
432B GLN* 4.2 1.6 + - - -
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Residues in contact with VAL 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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150B THR* 3.6 30.5 - - + +
152B LEU* 3.1 28.5 + - + +
154B ALA* 1.3 73.1 - - + +
156B ASP* 1.3 59.2 + - - +
157B ALA 3.0 7.6 + - - -
159B VAL* 2.9 55.5 + - - +
160B PRO* 5.0 0.9 - - + -
161B ILE* 4.0 5.6 - - + +
180B VAL* 4.3 13.5 - - + -
352B ILE* 3.9 17.5 - - + -
365B PRO* 5.4 1.3 - - + -
367B ILE* 3.8 18.2 - - + -
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Residues in contact with ASP 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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148B VAL 3.8 6.9 - - - +
149B GLN* 2.7 28.0 + - - +
150B THR* 2.8 34.9 + - - +
151B GLY 2.9 14.4 + - - -
152B LEU 2.8 11.3 + - - +
155B VAL* 1.3 72.1 - - - +
157B ALA* 1.3 56.2 + - - +
160B PRO* 4.1 9.3 - - - +
161B ILE 5.7 0.2 + - - -
381B GLN* 3.2 14.6 + - - +
385B LEU* 3.1 25.5 - - + +
443B GLN* 2.9 33.7 + - - +
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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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153B LYS 3.0 20.3 + - - +
155B VAL 3.8 0.2 - - - -
156B ASP* 1.3 78.4 - - - +
158B LEU* 1.3 75.8 + - + +
160B PRO* 4.1 1.3 - - - +
381B GLN* 2.9 22.0 + - - +
385B LEU* 4.7 3.4 - - + -
389B ALA* 4.8 11.0 - - + +
392B LEU* 4.7 5.8 - - + -
393B LYS* 5.7 0.7 - - - +
430B LEU* 4.6 4.9 - - + -
447B ILE* 3.7 24.9 - - + -
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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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154B ALA* 3.1 23.1 + - + +
157B ALA* 1.3 82.7 - - + +
159B VAL* 1.3 69.3 + - + +
160B PRO* 3.5 6.9 - - - +
367B ILE* 5.4 5.4 - - + -
369B VAL* 3.7 19.3 - - + -
374B SER 5.2 1.0 + - - -
389B ALA* 6.2 0.7 - - + -
392B LEU* 3.8 23.6 - - + -
393B LYS* 3.3 61.2 - - + +
396B LEU* 3.7 20.4 - - + -
430B LEU* 4.3 11.4 - - + -
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Residues in contact with VAL 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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154B ALA 4.3 0.7 - - - +
155B VAL* 2.9 31.2 + - - +
158B LEU* 1.3 84.1 - - + +
160B PRO* 1.3 66.5 - - - +
161B ILE* 3.6 6.6 + - - +
167B GLU* 4.4 4.7 - - - +
352B ILE* 3.5 31.8 - - + +
367B ILE* 4.2 16.6 - - + -
372B SER* 3.9 15.9 - - - +
373B VAL* 3.8 35.0 - - - +
374B SER* 3.8 6.4 - - - +
393B LYS* 4.6 1.8 - - - -
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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