Contacts of the helix formed by residues 208 - 217 (chain A) in PDB entry 1FS6
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 LYS 208 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A THR* 5.3 8.9 + - - -
138A VAL* 2.7 35.3 + - + +
139A GLY* 4.0 6.0 - - - +
140A ASN* 2.9 27.4 + - - +
203A VAL* 3.5 26.0 - - + -
204A LEU 3.2 28.0 - - - +
205A GLY 3.0 5.5 + - - +
207A GLN* 1.3 93.1 - - + +
209A ALA* 1.3 64.4 + - - +
210A LEU 3.3 2.7 - - - -
211A ALA* 3.0 9.3 + - - +
212A LEU* 2.8 22.1 + - - +
243A SER 4.4 1.1 - - - -
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Residues in contact with ALA 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A GLY 3.9 0.8 + - - -
206A SER 3.1 20.7 + - - +
207A GLN 3.3 0.2 - - - -
208A LYS* 1.3 77.6 - - - +
210A LEU* 1.3 63.3 + - + +
212A LEU* 3.3 2.4 + - - +
213A GLN* 3.0 24.1 + - - +
243A SER 3.1 23.4 + - - +
245A MET* 4.1 11.0 - - + -
246A GLU* 3.4 30.3 + - + +
247A LEU* 5.6 0.3 - - - +
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Residues in contact with LEU 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A ASN 4.7 4.9 - - - +
207A GLN 4.9 3.0 + - - +
208A LYS 3.3 1.0 - - - -
209A ALA* 1.3 77.4 - - + +
211A ALA* 1.3 57.9 + - - +
213A GLN* 3.3 14.0 + - - +
214A ALA* 2.9 28.2 + - - +
224A TRP* 3.8 23.7 - - + -
246A GLU* 3.5 35.0 - - + +
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Residues in contact with ALA 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A VAL* 4.2 15.3 - - + -
139A GLY 3.5 24.2 - - - +
140A ASN 4.2 3.9 + - - +
142A GLY* 3.9 17.0 - - - +
208A LYS* 3.0 11.0 + - - +
210A LEU* 1.3 76.9 - - - +
212A LEU* 1.3 58.7 + - - +
214A ALA 3.2 0.2 + - - -
215A ALA* 2.9 30.0 + - - +
224A TRP* 3.6 13.6 - - + -
226A ILE* 3.6 6.5 - - - +
237A MET* 5.8 0.2 - - - -
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Residues in contact with LEU 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A LEU* 4.0 13.0 - - + -
138A VAL* 5.7 0.4 - - - +
203A VAL* 4.0 22.6 - - + +
208A LYS 2.8 12.3 + - - +
209A ALA 3.6 7.0 - - - +
211A ALA* 1.3 75.6 - - - +
213A GLN* 1.3 58.1 + - - +
215A ALA* 3.2 2.7 + - - +
216A VAL* 2.8 53.0 + - + +
237A MET* 4.0 21.5 - - + -
239A CYS* 4.2 18.2 - - + -
243A SER* 3.6 21.1 - - - +
244A THR* 4.2 0.7 - - - -
247A LEU* 3.6 32.5 - - + -
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Residues in contact with GLN 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A ALA 3.0 17.3 + - - +
210A LEU* 3.4 14.1 - - - +
212A LEU* 1.3 78.6 - - - +
214A ALA* 1.3 60.4 + - - +
217A GLU* 2.8 55.4 + - - +
218A GLY* 2.9 15.4 + - - +
246A GLU* 3.3 33.2 - - + +
247A LEU* 3.7 13.6 - - + +
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Residues in contact with ALA 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A LEU 2.9 16.3 + - - +
211A ALA 3.2 5.4 + - - +
213A GLN* 1.3 82.3 + - - +
215A ALA* 1.3 61.8 + - - +
218A GLY* 3.6 18.8 + - - +
219A CYS 4.5 0.2 - - - +
221A ASN* 5.7 1.1 - - - +
224A TRP* 3.7 41.1 - - + -
226A ILE* 4.4 1.3 - - + -
227A SER* 3.5 18.1 - - - -
230A GLN* 3.7 3.6 + - - -
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Residues in contact with ALA 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 3.9 9.3 - - + +
211A ALA 2.9 16.7 + - - +
212A LEU 3.5 2.5 - - - +
213A GLN 3.2 0.2 - - - -
214A ALA* 1.3 78.7 - - - +
216A VAL* 1.3 60.1 + - + +
226A ILE* 3.5 28.0 - - + +
227A SER* 4.1 10.3 - - - +
230A GLN* 3.0 29.6 + - - +
237A MET* 3.5 22.9 - - + -
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Residues in contact with VAL 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 4.4 16.6 - - - -
3A LEU* 4.3 18.2 - - + -
212A LEU* 2.8 42.0 + - + +
215A ALA* 1.3 77.3 - - + +
217A GLU* 1.3 59.3 + - - +
230A GLN* 4.3 6.6 + - - +
237A MET* 4.5 2.5 - - + -
247A LEU* 4.3 6.7 - - + -
251A THR* 4.0 13.7 - - + -
255A PHE* 3.6 36.3 - - + -
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Residues in contact with GLU 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A GLN* 2.8 36.0 + - - +
216A VAL* 1.3 74.8 - - + +
218A GLY* 1.3 65.6 + - - +
219A CYS* 5.5 1.2 - - - -
246A GLU 4.2 2.1 - - - +
247A LEU* 3.6 13.3 - - + -
248A LYS* 2.8 40.9 + - - +
251A THR* 2.5 41.4 + - + +
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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