Contacts of the helix formed by residues 196 - 209 (chain A) in PDB entry 1GRF
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 196 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194A GLY 3.7 1.2 - - - -
195A ALA* 1.4 80.0 - - - +
197A TYR* 1.3 66.4 + - - -
198A ILE* 3.3 2.5 - - - -
199A ALA* 3.2 5.2 + - - +
200A VAL* 3.0 19.9 + - - +
223A LEU* 3.6 7.9 - - - -
288A ALA 4.9 3.7 + - - -
480A PO4 5.3 0.8 + - - -
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Residues in contact with TYR 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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66A LYS* 4.5 0.2 - - - -
196A GLY* 1.3 72.1 - - - -
198A ILE* 1.3 83.4 + - + +
200A VAL* 3.3 4.4 + - - +
201A GLU* 2.8 61.2 + - - +
223A LEU* 3.5 13.4 - - + +
226A PHE* 5.1 4.5 - + + -
337A LEU* 4.2 10.3 + - + -
338A LEU* 5.3 7.6 - - + -
370A VAL 5.4 2.2 - - - -
371A VAL* 3.8 30.1 - - + -
479A FAD 3.1 53.8 + + - -
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Residues in contact with ILE 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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177A SER* 4.3 20.0 - - - +
196A GLY 3.3 0.8 - - - -
197A TYR* 1.3 112.5 - - + +
199A ALA* 1.3 59.2 + - - +
201A GLU* 3.2 5.7 + - - +
202A MET* 2.9 47.4 + - + +
286A LEU* 5.7 0.2 - - + -
288A ALA* 4.2 15.7 - - + +
291A ARG* 4.4 19.3 - - + -
479A FAD 4.1 32.5 - - + -
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Residues in contact with ALA 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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192A ILE* 3.9 9.0 - - + +
194A GLY* 3.1 37.7 - - - +
195A ALA* 4.3 0.4 - - - -
196A GLY 3.2 11.4 + - - +
198A ILE* 1.3 76.6 - - - +
200A VAL* 1.3 66.5 + - + +
202A MET* 3.4 1.5 + - - -
203A ALA* 3.0 25.8 + - - +
215A LEU* 4.0 7.6 - - + -
288A ALA* 3.7 22.2 + - + +
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Residues in contact with VAL 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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195A ALA 4.5 1.1 - - - +
196A GLY 3.0 17.0 + - - +
197A TYR* 3.6 9.4 - - - +
199A ALA* 1.3 79.2 - - - +
201A GLU* 1.3 63.0 + - - +
203A ALA* 3.9 4.6 - - - +
204A GLY* 3.1 19.4 + - - -
215A LEU* 4.8 4.9 - - + +
222A VAL* 3.8 38.8 - - + -
223A LEU* 4.1 9.6 - - + -
234A CYS* 4.1 12.1 - - - -
238A LEU* 4.5 14.4 - - + +
371A VAL* 4.5 7.2 - - + -
373A SER* 4.0 27.3 - - - -
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Residues in contact with GLU 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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66A LYS* 2.7 46.8 + - + +
197A TYR* 2.8 45.0 + - - +
198A ILE* 3.8 5.0 - - - +
200A VAL* 1.3 71.3 - - - +
202A MET* 1.3 69.7 + - + +
204A GLY* 3.2 2.9 + - - -
205A ILE* 3.1 29.0 + - + +
370A VAL 4.4 1.0 - - - +
371A VAL* 3.8 7.7 - - + -
372A PHE* 2.9 53.3 + - - +
373A SER* 5.4 0.2 - - - +
374A HIS* 5.5 0.3 + - - -
479A FAD 4.8 2.3 - - - -
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Residues in contact with MET 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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66A LYS* 4.9 8.7 - - + -
177A SER* 4.6 13.5 - - - -
180A PHE* 3.7 50.9 - - + -
181A PHE* 5.0 4.3 - - + -
192A ILE* 4.4 7.6 - - + -
198A ILE* 2.9 29.4 + - + +
199A ALA* 4.0 4.0 - - - +
201A GLU* 1.3 82.1 - - + +
203A ALA* 1.3 64.8 + - - +
205A ILE* 3.8 18.1 - - + +
206A LEU* 3.1 29.4 + - + +
286A LEU* 4.3 22.9 - - + -
479A FAD 5.6 3.4 - - + -
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Residues in contact with ALA 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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192A ILE* 3.5 24.1 - - + +
199A ALA 3.0 17.4 + - - +
200A VAL 3.9 3.6 - - - +
202A MET* 1.3 77.7 - - - +
204A GLY* 1.3 56.6 + - - +
207A SER* 3.0 33.3 + - - -
213A THR* 4.0 9.5 - - + +
215A LEU* 4.2 18.4 - - + -
238A LEU* 4.7 2.9 - - + -
243A VAL* 4.4 14.8 - - + -
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Residues in contact with GLY 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 VAL 3.1 14.0 + - - -
201A GLU* 3.7 3.4 - - - -
202A MET 3.1 0.4 - - - -
203A ALA* 1.3 75.6 - - - +
205A ILE* 1.3 59.0 + - - +
207A SER* 4.1 3.4 - - - -
208A ALA* 3.1 29.8 + - - +
238A LEU* 4.8 9.4 - - - +
243A VAL* 5.0 1.3 - - - -
373A SER* 6.1 0.9 - - - -
374A HIS* 3.6 24.6 + - - -
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Residues in contact with ILE 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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66A LYS* 4.2 13.2 - - + +
69A MET* 4.0 38.4 - - + +
70A TRP* 4.2 17.5 - - + +
73A ALA* 4.1 8.3 - - + -
96A TRP* 5.4 0.7 - - + -
180A PHE* 4.1 17.5 - - + -
201A GLU* 3.1 23.3 + - + +
202A MET* 3.8 23.3 - - + +
204A GLY* 1.3 74.1 - - - +
206A LEU* 1.4 67.3 + - - +
208A ALA* 3.3 1.4 + - - +
209A LEU* 3.1 50.8 + - + +
374A HIS* 4.2 3.1 + - - +
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Residues in contact with LEU 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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96A TRP* 4.1 7.0 - - + -
180A PHE* 3.8 31.6 - - + -
186A LEU* 4.1 11.8 - - + +
187A PRO* 4.0 32.1 - - + -
190A SER* 4.0 13.9 - - - +
192A ILE* 4.0 21.3 - - + -
202A MET 3.1 18.3 + - - +
203A ALA 4.2 1.8 - - - +
205A ILE* 1.4 76.9 - - - +
207A SER* 1.3 61.8 + - - +
209A LEU* 3.3 6.2 + - - +
210A GLY 3.2 5.4 + - - -
211A SER* 2.9 27.1 + - - -
213A THR* 3.8 12.8 - - + +
284A CYS* 5.0 3.1 - - - -
286A LEU* 4.6 7.4 - - + -
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Residues in contact with SER 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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203A ALA 3.0 20.0 + - - -
204A GLY 4.1 2.7 - - - -
206A LEU* 1.3 77.5 - - - +
208A ALA* 1.3 62.1 + - - +
210A GLY* 3.1 12.6 + - - -
211A SER 3.8 7.1 + - - +
213A THR* 3.5 15.9 + - - -
241A ALA* 3.9 15.5 + - - -
242A GLY 4.1 8.5 + - - -
243A VAL* 3.6 24.4 - - - +
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Residues in contact with ALA 208 (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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73A ALA* 3.5 34.5 - - + +
76A SER* 2.7 28.4 + - - -
77A GLU* 4.4 14.1 - - + +
80A HIS* 5.1 4.8 + - - -
204A GLY 3.1 20.6 + - - +
205A ILE 3.3 0.4 + - - +
207A SER* 1.3 75.6 - - - +
209A LEU* 1.3 58.0 + - - +
210A GLY 3.5 0.9 + - - -
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Residues in contact with LEU 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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69A MET* 4.1 11.4 - - + +
72A THR* 4.0 20.6 - - + +
73A ALA* 4.0 21.3 - - - -
76A SER* 4.4 7.4 - - - -
94A PHE* 4.0 39.9 - - + +
96A TRP* 4.0 18.8 - - + -
186A LEU* 3.2 26.6 - - + +
205A ILE* 3.1 38.9 + - + +
206A LEU 3.7 4.9 - - - +
207A SER 3.2 0.4 - - - -
208A ALA* 1.3 78.6 - - - +
210A GLY* 1.3 57.0 + - - +
211A SER 3.7 0.7 - - - -
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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