Contacts of the helix formed by residues 193 - 207 (chain A) in PDB entry 1F7U
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 193 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192A TRP* 1.3 76.5 - - - +
194A LYS* 1.3 66.9 - - - -
195A GLN* 2.9 4.0 - - - -
196A PHE* 2.8 14.4 + - - +
197A GLY 3.2 7.1 + - - -
252A PHE* 3.0 36.5 - - - -
350A ARG* 4.5 1.3 - - - +
976B A 3.9 18.2 - - - -
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Residues in contact with LYS 194 (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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193A GLY* 1.3 70.1 - - - -
195A GLN* 1.3 64.9 + - - +
197A GLY* 2.8 17.0 + - - +
198A LEU* 2.8 15.9 + - - +
245A ASN* 4.9 11.7 + - - +
248A ALA* 5.1 4.0 - - + +
249A ARG* 3.6 43.2 - - + +
252A PHE* 4.1 15.8 - - + -
340A LYS* 2.8 34.5 - - - +
342A ASP* 5.2 2.2 - - - -
975B C 4.1 15.1 + - - +
976B A 4.7 3.4 + - - -
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Residues in contact with GLN 195 (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 ASN* 2.9 28.0 + - - +
154A ILE* 5.9 0.7 - - - -
155A ALA* 3.7 10.5 + - + +
156A LYS* 2.7 33.1 + - - +
190A GLY 3.8 15.5 + - - +
192A TRP 3.8 13.9 + - - +
193A GLY* 4.1 0.4 - - - -
194A LYS* 1.3 80.6 - - - +
196A PHE* 1.3 59.9 + - - +
198A LEU* 3.5 9.6 - - - +
199A LEU* 3.0 22.7 - - - +
224A TYR* 3.8 10.9 - - - +
975B C 5.4 4.3 + - - +
976B A 3.8 33.0 + - - -
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Residues in contact with PHE 196 (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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154A ILE* 3.8 33.7 - - + -
155A ALA* 6.2 0.2 - - + -
191A ASP* 4.4 4.7 - - - -
192A TRP* 4.2 18.4 - + - +
193A GLY 2.8 8.9 + - - +
195A GLN* 1.3 79.3 - - + +
197A GLY* 1.3 62.9 + - - +
198A LEU 2.9 5.6 - - - -
199A LEU* 3.0 24.7 + - + +
200A ALA* 3.3 12.5 + - + +
255A MET* 3.5 23.6 - - + -
262A ALA 5.1 1.1 - - - -
265A ILE* 4.6 3.1 - - + -
266A TRP* 3.2 55.4 - + + -
269A PHE* 3.6 33.7 - + + -
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Residues in contact with GLY 197 (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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193A GLY 3.2 7.2 + - - -
194A LYS* 2.8 9.4 + - - -
196A PHE* 1.3 76.8 - - - +
198A LEU* 1.3 58.3 + - - +
199A LEU 3.4 0.2 - - - -
200A ALA* 3.6 12.7 - - - +
201A VAL* 3.6 13.5 + - - +
248A ALA* 3.7 27.4 - - - +
251A TYR* 4.3 2.4 - - - +
252A PHE 4.7 1.3 - - - -
255A MET* 3.5 21.7 - - - +
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Residues in contact with LEU 198 (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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194A LYS 2.8 9.5 + - - +
195A GLN* 3.5 12.3 - - - +
196A PHE 2.9 0.2 - - - -
197A GLY* 1.3 77.9 - - - +
199A LEU* 1.3 59.7 + - - +
200A ALA 3.3 0.4 - - - -
201A VAL* 3.1 6.5 - - + +
202A GLY* 2.9 25.8 + - - -
224A TYR* 3.3 20.4 - - + +
227A ILE* 3.6 30.4 - - + +
228A ASN* 2.9 32.8 - - - +
231A ILE* 4.1 25.6 - - + -
244A THR* 5.6 0.4 - - + -
245A ASN* 5.2 2.5 - - - +
248A ALA* 4.2 17.7 - - + +
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Residues in contact with LEU 199 (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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155A ALA* 3.9 19.7 - - + -
195A GLN 3.0 29.4 - - - +
196A PHE* 3.0 18.8 + - + +
198A LEU* 1.3 76.4 - - - +
200A ALA* 1.3 56.7 + - - +
202A GLY* 4.8 1.1 - - - -
203A PHE* 2.7 38.4 + - - +
220A LEU* 3.3 39.7 - - + +
223A VAL* 4.3 7.3 - - + +
224A TYR* 3.4 33.0 - - + +
227A ILE* 5.4 0.2 - - - -
269A PHE* 4.2 17.9 - - + -
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Residues in contact with ALA 200 (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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196A PHE* 3.3 12.1 + - + +
197A GLY* 3.6 14.6 - - - +
199A LEU* 1.3 82.5 - - - +
201A VAL* 1.3 62.7 + - - +
203A PHE* 3.1 3.5 + - - +
204A GLU* 3.0 26.3 + - - +
251A TYR* 3.8 22.9 - - + -
255A MET* 5.3 5.4 - - + -
262A ALA* 6.3 1.3 - - + -
265A ILE* 3.9 26.4 - - + +
269A PHE* 4.7 0.4 - - - -
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Residues in contact with VAL 201 (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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197A GLY 3.6 11.2 - - - +
198A LEU* 3.1 18.2 - - + +
200A ALA* 1.3 76.9 - - - +
202A GLY* 1.3 65.2 + - - +
204A GLU* 3.0 21.2 + - + +
205A ARG* 2.8 55.2 + - - +
227A ILE* 4.3 11.2 - - + -
244A THR* 4.6 3.8 - - + -
247A LYS* 4.3 25.4 - - + +
248A ALA* 4.0 12.8 - - + -
251A TYR* 4.6 4.0 - - + -
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Residues in contact with GLY 202 (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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198A LEU 2.9 19.8 + - - -
199A LEU 3.7 0.9 - - - -
201A VAL* 1.3 76.9 - - - +
203A PHE* 1.3 52.3 + - - +
205A ARG* 3.2 2.2 + - - +
206A TYR* 2.7 33.3 + - - -
223A VAL* 3.2 20.5 - - - +
227A ILE* 3.7 23.3 - - - -
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Residues in contact with PHE 203 (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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199A LEU 2.7 21.3 + - - +
200A ALA 3.5 3.8 - - - +
202A GLY* 1.3 68.9 - - - +
204A GLU* 1.3 66.9 + - + +
205A ARG 3.0 2.0 - - - -
207A GLY* 2.5 52.1 + - - +
208A ASN 4.0 7.6 - - - -
209A GLU* 5.0 5.4 - - - -
212A LEU* 3.6 33.0 - - + -
219A HIS* 3.9 17.9 - + - -
220A LEU* 4.4 6.5 - - + -
223A VAL* 3.4 8.9 - - + +
265A ILE* 4.3 9.2 - - + -
268A ARG* 4.7 12.8 - - - -
269A PHE* 3.5 29.6 - + + -
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Residues in contact with GLU 204 (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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200A ALA* 3.0 14.4 - - - +
201A VAL* 3.0 17.1 + - + +
203A PHE* 1.3 79.4 - - + +
205A ARG* 1.3 60.9 + - - +
207A GLY 4.7 0.3 + - - +
251A TYR* 3.0 45.8 + - - -
254A ARG* 5.1 1.2 + - - -
261A GLU* 6.0 2.6 - - - -
265A ILE* 5.5 4.5 - - + -
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Residues in contact with ARG 205 (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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201A VAL* 2.8 19.0 + - - +
202A GLY* 3.5 9.0 - - - +
203A PHE 3.0 0.2 - - - -
204A GLU* 1.3 81.6 - - - +
206A TYR* 1.3 92.5 + - + +
207A GLY 3.5 0.9 + - - +
227A ILE* 4.4 6.5 - - - +
230A ASP* 5.1 3.5 + - - +
244A THR* 3.0 44.3 + - - +
247A LYS* 3.0 31.2 - - - +
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Residues in contact with TYR 206 (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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202A GLY* 2.7 19.6 + - - +
205A ARG* 1.3 101.7 - - + +
207A GLY* 1.3 67.5 + - - +
208A ASN* 3.3 5.4 + - - +
219A HIS* 3.9 10.9 - - - -
223A VAL* 4.6 12.6 - - + -
226A ARG* 3.4 38.7 + - + -
227A ILE* 4.6 7.0 - - + -
230A ASP* 2.6 40.8 + - - -
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Residues in contact with GLY 207 (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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202A GLY 3.7 0.8 + - - -
203A PHE* 2.5 56.8 + - - +
204A GLU 5.6 0.3 - - - +
205A ARG 3.5 1.9 - - - +
206A TYR* 1.3 72.6 - - - +
208A ASN* 1.3 59.3 + - - -
209A GLU 4.0 1.4 + - - -
219A HIS* 3.9 1.8 - - - -
223A VAL* 4.7 0.4 - - - -
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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