Contacts of the helix formed by residues 170 - 179 (chain B) in PDB entry 1AHF
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 PHE 170 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168B LEU* 3.0 24.4 + - + +
169B ASP* 1.3 69.8 + - - +
171B ASP* 1.3 62.6 + - - +
173B LEU* 3.0 24.9 + - + +
174B ILE* 2.7 58.4 + - + +
204B GLN* 3.6 43.7 - - + +
207B THR* 3.4 18.2 - - + -
208B LEU* 3.6 41.5 - - + -
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Residues in contact with ASP 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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169B ASP* 3.6 8.1 - - - +
170B PHE* 1.3 76.6 + - - +
172B ALA* 1.3 57.1 + - - +
174B ILE* 4.1 9.2 - - + -
175B ASN* 2.6 54.6 + - - +
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Residues in contact with ALA 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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159B ALA* 3.8 15.2 - - + +
169B ASP* 3.2 38.2 + - + +
170B PHE 3.2 0.6 - - - -
171B ASP* 1.3 77.6 + - - +
173B LEU* 1.3 64.7 + - - +
175B ASN* 3.9 6.2 + - - +
176B SER* 3.0 25.6 + - - -
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Residues in contact with LEU 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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158B TYR* 3.0 45.1 - - + -
159B ALA 3.0 21.5 + - - +
160B TYR* 3.6 21.1 - - + -
168B LEU* 5.0 2.9 - - + -
169B ASP 2.8 14.1 + - - +
170B PHE* 3.1 39.5 - - + +
172B ALA* 1.3 74.0 - - - +
174B ILE* 1.3 55.8 + - - +
176B SER* 2.8 29.6 + - - -
177B LEU* 3.2 15.0 + - + +
188B PHE* 6.0 2.0 - - + -
208B LEU* 3.8 22.7 - - + -
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Residues in contact with ILE 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 PHE* 2.7 64.5 + - + +
171B ASP* 3.6 7.6 - - + +
173B LEU* 1.3 72.5 - - + +
175B ASN* 1.3 70.5 + - - +
176B SER 3.4 0.2 + - - -
177B LEU* 3.5 7.7 + - - +
178B ASN* 3.2 29.1 + - - +
207B THR* 4.4 8.7 - - + -
208B LEU* 4.6 12.1 - - + -
211B LEU* 4.6 20.2 - - + +
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Residues in contact with ASN 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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171B ASP* 2.6 38.9 + - - +
172B ALA* 4.0 5.3 + - - +
174B ILE* 1.3 83.6 + - - +
176B SER* 1.3 61.4 + - - +
177B LEU 3.7 0.2 + - - -
178B ASN* 3.8 22.4 + - - +
179B GLU* 4.4 2.6 + - - +
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Residues in contact with SER 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* 4.1 9.5 - - - -
157B GLU 5.0 1.9 + - - -
158B TYR* 3.8 10.3 - - - -
159B ALA* 3.2 32.3 + - - +
172B ALA 3.0 16.3 + - - -
173B LEU 2.8 14.6 + - - -
175B ASN* 1.3 78.2 - - - +
177B LEU* 1.3 59.5 + - - -
179B GLU* 3.4 21.1 - - - +
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Residues in contact with LEU 177 (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* 4.2 20.4 - - + -
158B TYR* 3.4 43.5 - - + -
173B LEU* 3.2 21.5 + - + +
174B ILE* 3.5 8.5 + - - +
175B ASN 3.4 0.2 - - - -
176B SER* 1.3 69.9 - - - +
178B ASN* 1.3 54.3 + - - +
179B GLU 2.8 6.3 - - - -
180B ALA* 2.5 36.6 + - + +
186B VAL* 4.2 17.9 - - + -
188B PHE* 4.9 9.0 - - + -
208B LEU* 5.0 7.2 - - + -
211B LEU* 5.9 0.9 - - + -
217B TRP* 3.3 37.7 - - + -
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Residues in contact with ASN 178 (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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174B ILE* 3.2 22.3 + - - +
175B ASN* 3.8 19.4 - - - +
176B SER 3.3 0.4 - - - -
177B LEU* 1.3 78.0 - - - +
179B GLU* 1.3 61.0 + - - +
180B ALA 3.2 7.4 + - - +
211B LEU* 4.9 7.3 - - - +
215B LYS* 3.6 33.8 + - - +
217B TRP* 4.9 0.7 - - - -
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Residues in contact with GLU 179 (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* 3.7 21.7 - - + -
175B ASN 4.4 2.1 + - - +
176B SER 3.4 16.5 + - - +
177B LEU 2.8 0.6 - - - -
178B ASN* 1.3 80.0 - - - +
180B ALA* 1.3 59.0 + - - +
181B GLN* 3.6 10.6 + - - +
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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