Contacts of the helix formed by residues 183 - 188 (chain B) in PDB entry 4TTB
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 GLU 183 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150B ARG* 3.7 25.5 + - - +
181B ILE* 3.6 14.6 + - + +
182B LYS* 1.3 70.2 - - - +
184B TYR* 1.3 62.8 + - - +
185B LEU 3.1 2.9 - - - -
186B ASP* 2.9 22.5 + - + +
187B THR* 3.2 27.9 + - + +
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Residues in contact with TYR 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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104B ARG* 3.1 49.8 - - + +
106B ILE* 4.4 15.7 - - + +
181B ILE 5.1 0.7 - - - -
182B LYS* 3.3 38.1 + - + +
183B GLU* 1.3 83.1 - - + +
185B LEU* 1.3 82.4 + - + +
186B ASP 3.2 0.2 - - - -
187B THR* 3.4 13.7 - - - +
188B ALA* 2.9 35.9 + - - +
236B VAL* 3.9 22.1 - - + +
238B THR* 4.4 13.2 - - + +
264B PRO* 3.7 15.2 - - + +
301B FMN 4.6 9.7 + - - -
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Residues in contact with LEU 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B LYS* 3.4 23.1 + - - +
149B ILE* 4.9 0.7 - - + -
150B ARG* 3.8 26.7 - - + +
153B ILE* 3.5 37.5 - - + -
154B GLU* 5.7 0.2 - - + -
182B LYS* 3.7 28.5 - - + +
183B GLU 3.1 0.6 - - - -
184B TYR* 1.3 99.9 - - + +
186B ASP* 1.3 61.3 + - - +
191B LEU* 3.9 23.9 - - + +
238B THR* 6.0 1.6 - - + +
262B LEU* 4.0 26.9 - - + -
264B PRO* 4.4 2.0 - - + -
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Residues in contact with ASP 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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143B PRO 4.8 1.7 - - - +
146B LYS* 3.1 22.1 + - - +
147B HIS* 3.0 52.4 + - - +
150B ARG* 2.8 34.0 + - - +
183B GLU* 2.9 11.1 + - + +
185B LEU* 1.3 81.7 - - - +
187B THR* 1.3 62.4 + - + +
188B ALA 3.5 0.2 - - - -
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Residues in contact with THR 187 (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 ILE 2.9 25.7 + - - -
108B ASN* 3.0 37.3 - - + +
146B LYS* 4.6 0.3 + - - -
183B GLU* 3.2 29.9 + - + +
184B TYR* 3.4 17.0 + - - +
186B ASP* 1.3 77.3 - - + +
188B ALA* 1.3 68.5 + - - +
189B PRO* 3.2 0.9 - - - +
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Residues in contact with ALA 188 (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 ILE* 3.7 23.3 + - + -
146B LYS* 2.3 37.1 + - - -
184B TYR 2.9 20.2 + - - +
187B THR* 1.3 75.9 + - - +
189B PRO* 1.3 62.8 - - + +
190B ILE 3.3 5.1 + - - +
191B LEU* 4.8 2.7 - - + -
264B PRO* 4.0 7.6 - - + -
265B VAL 3.9 20.2 - - - +
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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