Contacts of the helix formed by residues 168 - 176 (chain B) in PDB entry 4F5G
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 ASP 168 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B ALA* 6.1 0.2 - - + -
159B TYR 2.8 17.4 + - - +
160B TYR 5.1 0.4 - - - -
161B ASP* 4.1 27.0 - - + +
166B THR* 3.4 6.2 + - - -
167B LEU* 1.3 70.1 - - - +
169B PHE* 1.3 63.1 + - - +
170B ASP* 3.7 6.8 + - - +
171B ALA* 3.2 30.3 + - + +
172B LEU* 3.0 20.3 + - - +
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Residues in contact with PHE 169 (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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167B LEU* 2.9 18.6 + - + +
168B ASP* 1.3 72.8 + - - +
170B ASP* 1.3 65.5 + - - +
172B LEU* 3.1 22.2 + - + +
173B ILE* 3.0 52.7 + - + +
199B PRO* 5.3 0.9 - - + -
203B GLN* 3.3 74.3 - - + +
206B THR* 3.9 17.3 - - + -
207B LEU* 3.8 14.6 - - + -
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Residues in contact with ASP 170 (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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168B ASP* 3.3 6.5 + - - +
169B PHE* 1.3 81.0 - - - +
171B ALA* 1.3 63.4 + - - +
173B ILE* 3.8 6.3 - - - +
174B ASN* 3.1 53.8 + - - +
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Residues in contact with ALA 171 (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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158B ALA* 3.5 16.8 - - + +
168B ASP* 3.2 34.3 + - + +
170B ASP* 1.3 77.7 + - - +
172B LEU* 1.3 64.5 + - - +
174B ASN* 3.8 5.4 - - - +
175B SER* 2.9 27.2 + - - -
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Residues in contact with LEU 172 (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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157B TYR* 3.2 39.5 - - + -
158B ALA* 3.2 15.8 - - - +
159B TYR* 4.4 10.5 - - + -
167B LEU* 4.2 13.5 - - + -
168B ASP 3.0 12.9 + - - +
169B PHE* 3.3 36.6 - - + +
171B ALA* 1.3 76.5 - - - +
173B ILE* 1.3 65.2 + - - +
175B SER* 2.8 17.9 + - - -
176B LEU* 3.0 21.9 + - + +
187B PHE* 4.7 2.7 - - + -
199B PRO* 5.6 0.7 - - + -
207B LEU* 3.9 20.0 - - + -
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Residues in contact with ILE 173 (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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169B PHE* 3.0 54.0 + - + +
170B ASP* 3.8 6.7 - - - +
172B LEU* 1.3 74.1 - - - +
174B ASN* 1.3 73.5 + - - +
176B LEU* 3.2 14.9 + - - +
177B ASN* 3.5 13.9 + - - +
206B THR* 4.3 9.9 - - + -
207B LEU* 3.7 20.2 - - + -
210B LEU* 3.8 27.3 - - + +
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Residues in contact with ASN 174 (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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170B ASP* 3.1 38.9 + - - +
171B ALA* 4.0 5.0 - - - +
173B ILE* 1.3 87.3 - - - +
175B SER* 1.3 62.7 + - - +
177B ASN* 3.1 34.1 + - - +
178B GLU 4.5 0.2 + - - -
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Residues in contact with SER 175 (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 TRP* 4.6 7.4 - - - -
156B GLU 5.6 0.2 - - - -
157B TYR* 3.4 9.4 - - - +
158B ALA* 2.9 34.1 + - - -
171B ALA 2.9 14.2 + - - -
172B LEU 2.8 16.7 + - - -
174B ASN* 1.3 76.5 - - - +
176B LEU* 1.3 61.4 + - - +
177B ASN 3.1 0.9 + - - -
178B GLU* 3.3 21.1 + - - +
179B ALA 4.6 0.2 + - - -
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Residues in contact with LEU 176 (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 TRP* 4.6 5.6 - - + -
157B TYR* 3.8 32.5 - - + -
172B LEU* 3.0 32.3 + - + +
173B ILE* 3.6 9.6 - - - +
174B ASN 3.2 0.8 - - - -
175B SER* 1.3 73.9 + - - +
177B ASN* 1.3 61.6 + - - +
178B GLU 2.9 6.1 - - - -
179B ALA* 2.9 35.6 + - + +
185B VAL* 4.0 13.0 - - + -
187B PHE* 4.1 15.7 - - + -
207B LEU* 4.4 7.6 - - + -
210B LEU* 4.7 1.8 - - + -
214B LYS* 5.4 0.5 - - - -
216B TRP* 3.5 41.5 - - + -
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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