Contacts of the helix formed by residues 224 - 232 (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 TRP 224 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A ASN 3.5 16.8 - - - -
141A ASP* 3.3 41.7 - - + -
142A GLY* 3.6 6.1 - - - -
210A LEU* 3.8 25.1 - - + -
211A ALA* 3.6 19.7 - - - -
214A ALA* 3.7 30.1 - - + -
221A ASN* 3.1 27.9 + - - +
223A MET* 1.3 83.4 - - + +
225A THR* 1.3 66.7 + - - +
226A ILE* 3.1 4.3 - - + -
227A SER* 2.8 22.1 + - - -
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Residues in contact with THR 225 (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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142A GLY 3.5 12.1 + - - -
143A HIS* 4.1 12.2 - - - -
144A ILE* 3.8 22.5 + - + +
147A ASN* 5.7 0.7 - - - +
148A GLU 4.2 13.2 + - - -
149A PRO* 4.4 2.8 - - - +
150A ALA 4.5 0.7 + - - -
151A SER* 4.8 4.1 + - - -
153A LEU* 4.5 10.5 - - + -
190A VAL* 3.8 33.2 - - + +
221A ASN 4.6 1.8 - - - -
222A HIS 3.8 12.9 + - - -
223A MET 3.6 2.8 + - - -
224A TRP* 1.3 72.0 - - - +
226A ILE* 1.3 63.3 + - - +
228A CYS* 2.9 24.1 + - + +
229A LEU* 4.2 1.2 + - - +
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Residues in contact with ILE 226 (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* 5.0 0.5 - - - +
138A VAL* 3.8 24.5 - - + -
142A GLY* 2.8 33.6 + - - +
144A ILE* 4.4 13.7 - - + +
201A ILE* 3.9 28.0 - - + -
211A ALA 3.6 21.3 - - - +
214A ALA* 4.4 7.2 - - + -
215A ALA* 3.5 24.7 - - + +
224A TRP 3.0 3.1 + - - +
225A THR* 1.3 73.7 - - - +
227A SER* 1.3 64.9 + - - +
229A LEU* 3.1 31.1 + - + +
230A GLN 4.6 0.2 + - - -
237A MET* 3.9 10.8 - - + -
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Residues in contact with SER 227 (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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214A ALA* 3.5 26.9 - - - -
215A ALA* 4.1 3.6 - - - +
219A CYS 3.7 13.9 - - - -
220A VAL* 3.9 3.9 - - - +
221A ASN* 2.8 43.0 + - - -
224A TRP* 2.8 11.0 + - - -
226A ILE* 1.3 79.8 - - - +
228A CYS* 1.3 59.7 + - - +
229A LEU 3.1 1.1 - - - -
230A GLN* 3.2 28.3 + - - +
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Residues in contact with CYS 228 (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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153A LEU* 3.4 48.7 - - + -
194A LEU* 4.8 11.0 - - + +
220A VAL* 3.9 21.8 - - + -
221A ASN 3.7 24.2 - - - -
222A HIS* 4.5 1.6 - - - -
225A THR* 2.9 13.6 + - + +
227A SER* 1.3 76.2 + - - +
229A LEU* 1.3 56.5 + - - +
230A GLN 2.9 6.1 - - - -
231A LEU* 3.0 26.9 + - + +
232A HIS* 3.7 2.8 + - - +
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Residues in contact with LEU 229 (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* 3.7 18.7 - - + +
144A ILE* 5.1 3.6 - - + -
193A LEU* 4.4 8.1 - - + -
194A LEU* 3.5 28.5 - - + -
199A VAL* 3.8 25.4 - - + +
201A ILE* 3.6 30.5 - - + -
225A THR 4.2 0.8 + - - +
226A ILE* 3.1 29.0 + - + +
227A SER 3.1 1.6 - - - -
228A CYS* 1.3 77.2 - - - +
230A GLN* 1.3 60.2 + - - +
231A LEU 3.0 0.4 - - - -
232A HIS* 3.1 29.6 + - + +
235A ALA* 3.7 17.2 - - + +
236A ILE 5.6 0.2 - - - +
237A MET* 4.5 6.3 - - - -
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Residues in contact with GLN 230 (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 15.0 + - + -
214A ALA 3.7 7.9 + - - -
215A ALA 3.0 28.3 + - - +
216A VAL 4.3 6.8 + - - -
218A GLY 2.9 29.6 + - - +
219A CYS* 4.5 2.8 - - - -
220A VAL* 3.6 22.3 + - + +
227A SER 3.2 20.1 + - - +
228A CYS 2.9 0.4 - - - -
229A LEU* 1.3 80.3 - - - +
231A LEU* 1.3 62.6 + - + +
232A HIS 3.7 4.0 + - - +
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Residues in contact with LEU 231 (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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153A LEU* 5.6 6.5 - - + -
220A VAL* 4.0 37.2 - - + -
228A CYS* 3.0 15.7 + - + +
230A GLN* 1.3 84.2 - - + +
232A HIS* 1.3 60.7 + - - +
233A PRO* 3.7 4.0 - - - +
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Residues in contact with HIS 232 (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* 5.7 2.6 + - - -
194A LEU* 3.2 39.8 + - + -
196A ALA 2.8 29.1 + - - -
197A GLU 3.4 18.6 - - - -
199A VAL* 3.7 13.5 - - + +
228A CYS 3.7 1.4 + - - -
229A LEU* 3.1 36.5 + - + +
230A GLN 4.2 4.3 - - - +
231A LEU* 1.3 79.7 - - - +
233A PRO* 1.3 78.8 - - + +
234A LYS* 2.9 38.3 + - - -
235A ALA* 4.4 5.0 + - + +
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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