Contacts of the helix formed by residues 179 - 186 (chain B) in PDB entry 5FHK
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 HIS 179 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177B PRO* 3.8 7.3 - - - +
178B THR* 1.3 108.4 + - - +
180B ALA* 1.3 67.4 + - - +
181B GLU* 3.0 12.4 + - + +
182B ASP* 3.1 26.7 + - - +
254B LEU* 3.7 7.2 - - - -
257B TRP* 5.1 3.4 - - + +
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Residues in contact with ALA 180 (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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164B LEU* 6.3 0.2 - - + -
179B HIS* 1.3 73.4 - - - +
181B GLU* 1.3 63.0 + - - +
182B ASP 3.3 0.2 - - - -
183B LEU* 3.5 26.2 + - + +
184B HIS* 5.2 0.9 - - - -
199B LEU* 5.6 2.9 - - + -
207B VAL* 4.0 21.3 - - + +
209B ASN* 5.2 1.0 + - - -
254B LEU* 4.0 16.1 - - + +
257B TRP* 3.6 48.4 - - + +
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Residues in contact with GLU 181 (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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179B HIS* 3.0 7.5 + - + -
180B ALA* 1.3 75.5 - - - +
182B ASP* 1.3 62.8 + - - +
183B LEU 3.0 11.0 + - - -
184B HIS* 3.2 36.2 + - + +
185B ASP* 5.1 0.3 - - - +
207B VAL* 3.6 32.0 - - - +
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Residues in contact with ASP 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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177B PRO* 3.5 19.4 - - + +
178B THR* 3.1 35.2 + - - +
179B HIS* 3.1 15.4 + - - +
181B GLU* 1.3 78.1 - - - +
183B LEU* 1.3 65.0 + - - +
184B HIS 3.0 2.7 - - - -
185B ASP* 2.9 27.0 + - + +
186B HIS* 3.0 17.3 - - + +
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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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164B LEU* 4.1 16.4 - - + -
177B PRO* 4.0 22.8 - - + +
180B ALA* 3.5 21.1 - - + +
181B GLU 3.0 1.2 + - - +
182B ASP* 1.3 77.4 - - - +
184B HIS* 1.3 62.7 + - - +
186B HIS* 3.1 23.7 + - - +
188B LEU* 3.8 16.3 - - + +
197B TRP* 4.1 22.7 - - + -
199B LEU* 5.2 5.6 - - + -
207B VAL* 6.2 0.9 - - + -
209B ASN* 3.6 21.5 - - + +
233B ILE* 4.1 23.3 - - + -
253B ILE* 4.1 5.2 - - + -
254B LEU* 4.1 13.7 - - + -
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Residues in contact with HIS 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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180B ALA 5.2 0.4 - - - -
181B GLU* 3.2 36.4 + - + +
182B ASP 3.0 0.8 - - - -
183B LEU* 1.3 76.8 - - - +
185B ASP* 1.3 66.1 + - - +
186B HIS 3.3 3.6 + - - +
207B VAL* 5.7 2.8 - - - +
208B VAL 4.8 9.8 + - - -
209B ASN* 4.1 12.4 + - - -
210B VAL* 5.6 0.4 - - + -
211B ASP* 2.9 42.7 + - - +
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Residues in contact with ASP 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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181B GLU 5.1 0.2 - - - +
182B ASP* 2.9 24.4 + - + +
184B HIS* 1.3 85.2 - - - +
186B HIS* 1.3 67.8 + - + +
187B PHE* 6.0 0.3 - - - -
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Residues in contact with HIS 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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170B TYR* 3.0 24.4 + - - +
174B HIS* 4.2 7.7 - - + +
175B PRO* 2.9 30.3 + - + -
176B MET* 4.0 8.7 - - + -
177B PRO* 3.3 30.6 - - + +
182B ASP* 3.0 29.1 + - - +
183B LEU* 3.1 15.9 + - - +
184B HIS 4.4 3.1 - - - +
185B ASP* 1.3 87.5 + - + +
187B PHE* 1.3 65.9 + - - +
188B LEU* 3.5 8.3 + - + +
233B ILE* 3.6 18.6 - - + +
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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