Contacts of the helix formed by residues 150 - 154 (chain B) in PDB entry 2F37
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 PRO 150 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A ASN* 4.0 20.2 - - - +
234A GLN* 4.3 10.1 - - - +
106B THR* 4.5 1.0 - - - +
142B ASP* 3.6 9.9 - - - +
147B ASN 4.1 9.9 - - - +
148B PRO 3.5 10.7 - - - +
149B GLN* 1.3 85.4 - - - +
151B LEU* 1.3 66.2 + - - +
152B VAL* 4.2 18.8 - - + -
153B ASN* 3.1 21.6 + - + +
154B ALA* 3.6 6.2 + - - -
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Residues in contact with LEU 151 (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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105B LEU* 4.0 36.6 - - + +
106B THR* 3.6 21.3 - - + -
118B THR* 3.8 30.8 + - + +
119B CYS* 4.0 10.1 - - - -
120B LEU* 3.8 27.7 - - + +
138B LEU* 4.3 13.0 - - + +
139B LEU* 5.1 3.6 - - + +
142B ASP* 2.8 31.9 + - + +
149B GLN 3.3 3.2 + - - -
150B PRO* 1.3 71.2 - - - +
152B VAL* 1.3 63.8 + - - +
153B ASN 3.0 1.0 + - - -
154B ALA* 3.1 15.8 + - - +
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Residues in contact with VAL 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B LEU* 3.6 13.1 - - - +
139B LEU* 3.8 24.5 - - + +
142B ASP* 4.6 0.6 + - - -
150B PRO* 4.2 12.6 - - + -
151B LEU* 1.3 79.0 - - - +
153B ASN* 1.3 80.9 + - - +
154B ALA 3.8 2.6 + - - +
165B SER* 5.1 2.3 - - - -
166B ALA* 4.3 12.6 + - - +
167B LEU 5.2 1.0 + - - -
182B LEU* 3.8 35.4 - - + +
185B ASN 3.4 20.6 - - - +
186B GLY 3.9 4.0 - - - -
187B ALA* 3.8 14.4 - - + +
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Residues in contact with ASN 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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150B PRO* 3.1 17.2 + - + +
151B LEU 3.1 0.6 - - - -
152B VAL* 1.3 86.4 - - + +
154B ALA* 1.3 66.4 + - - +
155B GLN* 3.4 17.8 + - - +
165B SER* 5.4 4.0 - - - -
186B GLY 3.0 23.1 + - - -
187B ALA* 3.3 6.6 - - - +
188B ASN* 2.6 39.3 + - + +
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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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106B THR* 4.5 13.0 - - + -
118B THR* 3.5 31.0 - - + +
121B MSE 3.0 15.9 - - + +
150B PRO 3.6 3.2 + - - -
151B LEU 3.1 17.9 + - - +
152B VAL 3.5 0.9 - - - +
153B ASN* 1.3 80.8 - - - +
155B GLN* 1.3 63.4 + - - +
165B SER* 3.8 9.0 - - - -
166B ALA* 4.5 1.4 + - - +
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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