Contacts of the helix formed by residues 185 - 195 (chain F) in PDB entry 3IFS
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 GLY 185 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145F LYS 5.1 0.4 - - - -
146F SER* 3.9 13.2 - - - -
184F ARG* 1.3 76.5 - - - +
186F ALA* 1.3 61.6 + - - -
187F LEU 3.4 2.2 - - - -
188F LYS 3.6 1.0 + - - -
189F THR* 2.8 36.7 + - - -
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Residues in contact with ALA 186 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348E LEU* 3.3 45.1 - - + +
349E ASP* 4.1 2.0 - - + -
146F SER 3.0 14.5 + - - +
147F GLY 4.0 14.4 - - - +
148F THR* 4.0 9.5 - - + +
185F GLY* 1.3 72.0 - - - +
187F LEU* 1.3 56.6 + - - +
189F THR* 3.9 2.2 - - - -
190F LEU* 3.1 27.7 + - - +
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Residues in contact with LEU 187 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142F VAL* 4.0 40.2 - - + +
144F SER* 3.5 35.4 - - - +
146F SER 3.6 2.6 + - - -
147F GLY* 3.8 15.2 - - - +
156F PHE* 4.3 17.9 - - + -
178F ALA* 4.2 8.7 - - + -
179F THR 4.0 2.9 - - - +
180F THR* 3.6 22.2 - - + +
185F GLY 3.4 0.4 - - - -
186F ALA* 1.3 76.5 - - - +
188F LYS* 1.3 61.2 + - - +
190F LEU* 3.2 10.1 + - + -
191F ALA* 2.8 29.8 + - - +
196F TYR* 5.4 1.8 - - + -
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Residues in contact with LYS 188 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180F THR* 3.9 9.7 + - + +
181F ASP 3.4 22.2 - - - +
182F LYS* 3.4 23.6 + - - +
183F ALA* 3.8 20.3 + - - +
184F ARG 3.6 18.4 - - - +
185F GLY 3.6 2.0 + - - -
186F ALA 3.5 0.2 - - - -
187F LEU* 1.3 76.9 - - - +
189F THR* 1.3 57.2 + - - +
191F ALA* 3.3 3.1 + - + +
192F ASP* 2.6 66.3 + - - +
198F THR* 4.1 26.2 - - + -
200F VAL* 6.4 0.4 - - - -
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Residues in contact with THR 189 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348E LEU* 4.2 19.5 - - + -
184F ARG* 5.2 0.9 - - - -
185F GLY 2.8 26.3 + - - -
186F ALA* 3.9 4.3 - - - -
188F LYS* 1.3 74.4 - - - +
190F LEU* 1.3 59.9 + - - +
192F ASP* 3.3 9.5 + - + +
193F ASN* 2.9 53.6 + - - +
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Residues in contact with LEU 190 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348E LEU* 3.8 18.8 - - + +
156F PHE* 3.5 32.1 - - + -
160F ARG* 4.2 19.7 - - - +
186F ALA 3.1 16.6 + - - +
187F LEU* 3.5 9.9 - - + +
189F THR* 1.3 78.1 - - - +
191F ALA* 1.3 58.0 + - - +
193F ASN* 3.1 5.6 + - + -
194F GLU* 2.9 55.4 + - + +
196F TYR* 4.0 17.5 - - + +
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Residues in contact with ALA 191 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178F ALA* 4.1 11.0 - - + -
187F LEU 2.8 17.1 + - - +
188F LYS* 3.6 8.3 - - - +
190F LEU* 1.3 77.8 - - - +
192F ASP* 1.3 54.9 + - - +
195F GLY* 2.7 30.1 + - - -
196F TYR* 3.2 32.9 + - + +
198F THR* 3.5 26.5 - - + +
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Residues in contact with ASP 192 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183F ALA 5.1 1.9 - - - +
188F LYS* 2.6 56.9 + - - +
189F THR* 3.6 8.9 - - - +
191F ALA* 1.3 78.2 - - - +
193F ASN* 1.3 66.5 + - - +
194F GLU 3.5 0.2 + - - -
195F GLY* 3.7 6.3 + - - -
198F THR* 5.2 1.6 + - - -
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Residues in contact with ASN 193 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346E ASN* 5.9 3.6 - - - +
348E LEU* 4.5 10.5 - - - +
189F THR* 2.9 39.5 + - - +
190F LEU* 3.1 7.4 + - + +
192F ASP* 1.3 83.7 - - - +
194F GLU* 1.3 66.3 + - + +
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Residues in contact with GLU 194 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160F ARG* 5.1 2.1 + - - -
164F GLU* 5.0 0.3 - - - +
169F LYS* 3.6 30.3 + - - -
173F ARG* 3.2 40.8 + - - +
190F LEU* 2.9 39.3 + - + +
193F ASN* 1.3 83.6 - - + +
195F GLY* 1.3 61.6 + - - +
196F TYR* 3.6 31.7 + - + +
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Residues in contact with GLY 195 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173F ARG* 4.2 14.6 + - - +
191F ALA 2.7 17.4 + - - -
192F ASP 3.7 5.2 + - - -
193F ASN 3.5 2.4 - - - -
194F GLU* 1.3 76.4 - - - +
196F TYR* 1.3 63.9 + - - -
197F GLU 3.8 0.9 + - - -
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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