Contacts of the helix formed by residues 181 - 186 (chain B) in PDB entry 5V8V
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 181 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B TYR* 4.6 13.2 - - + -
153B THR 3.6 28.3 - - - +
179B GLU* 3.7 5.6 - - + +
180B MET* 1.3 89.1 - - - +
182B ALA* 1.3 65.4 + - - +
183B LEU 3.5 18.7 + - - +
184B PRO* 4.9 1.6 - - + -
185B PHE* 3.2 31.8 + - + +
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Residues in contact with ALA 182 (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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81A TYR* 6.0 2.0 - - - +
186A MET 5.8 0.2 - - - +
187A LEU* 3.4 15.6 - - + +
121B TYR* 5.5 1.2 - - - -
122B THR* 5.3 9.8 - - - +
123B ALA* 5.1 0.9 - - - +
180B MET 3.5 2.3 + - - -
181B PRO* 1.3 72.0 - - - +
183B LEU* 1.3 57.9 + - - +
184B PRO 3.1 2.1 - - - -
185B PHE 3.1 1.9 + - - -
186B MET* 2.8 53.7 + - + +
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Residues in contact with LEU 183 (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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183A LEU* 5.3 1.6 - - + -
187A LEU* 4.0 23.7 - - + +
319A PHE* 3.6 45.1 - - + -
502A 90D 4.0 56.5 - - + -
151B THR 4.6 6.2 - - - +
181B PRO* 3.5 16.4 - - - +
182B ALA* 1.3 77.2 - - - +
184B PRO* 1.3 69.0 - - + +
187B LEU* 4.3 10.8 - - + -
502B 90D 4.9 2.2 - - + -
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Residues in contact with PRO 184 (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 THR* 3.4 43.1 - - + +
152B GLY* 6.1 0.7 - - - -
181B PRO* 5.0 1.8 - - + -
182B ALA 3.1 7.4 - - - -
183B LEU* 1.3 91.9 - - + +
185B PHE* 1.3 78.8 - - + +
187B LEU* 2.8 31.8 + - + +
502B 90D 4.6 8.5 - - + -
503B 90D 3.6 32.1 - - + -
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Residues in contact with PHE 185 (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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111B TRP* 3.7 23.8 - + - -
123B ALA* 4.0 6.5 - - + -
127B HIS* 3.0 25.8 - - - -
149B TYR* 4.6 8.3 - + - -
151B THR* 5.1 1.3 - - - -
152B GLY 6.4 0.7 - - - -
153B THR 5.3 1.6 - - - -
154B VAL* 3.5 32.8 - - + -
180B MET* 3.6 30.5 - - + -
181B PRO* 3.2 25.4 + - + +
182B ALA 3.1 3.0 + - - -
184B PRO* 1.3 95.3 - - + +
186B MET* 1.3 58.3 + - - +
187B LEU 3.1 2.5 + - - -
188B ALA* 3.5 8.1 + - + +
190B PHE* 4.2 13.7 - + - -
503B 90D 3.4 37.5 - + - -
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Residues in contact with MET 186 (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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122A THR* 5.9 0.2 - - - +
126A TYR* 5.8 2.5 - - + -
182A ALA* 5.1 0.3 - - - +
186A MET* 3.6 62.7 - - + +
187A LEU* 4.1 11.0 - - + -
122B THR* 3.6 28.5 - - + +
123B ALA* 3.8 27.4 - - - +
126B TYR* 4.7 14.1 - - + -
127B HIS* 5.0 1.8 - - - -
182B ALA* 2.8 43.2 + - + +
185B PHE* 1.3 71.5 - - - +
187B LEU* 1.3 59.0 + - - +
188B ALA 3.4 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