Contacts of the helix formed by residues 187 - 201 (chain A) in PDB entry 1G1F
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 SER 187 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185A PRO* 3.3 2.0 - - - +
186A GLU* 1.3 80.8 - - - +
188A PRO* 1.4 74.0 - - - +
189A ALA* 3.6 9.5 + - - +
190A SER* 2.9 37.9 + - - -
191A PHE 3.3 5.4 + - - -
269A PHE* 3.5 13.1 - - - -
294A LEU* 4.5 8.1 + - - -
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Residues in contact with PRO 188 (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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187A SER* 1.4 85.2 - - - +
189A ALA* 1.3 56.1 + - + +
191A PHE* 3.3 2.1 + - + +
192A LEU* 2.9 38.2 + - + +
269A PHE* 3.7 19.3 - - + -
272A LEU* 4.0 45.3 - - + +
273A ALA* 4.4 6.7 - - - -
276A GLU* 4.2 16.4 - - + -
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Residues in contact with ALA 189 (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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187A SER* 3.1 9.8 - - - +
188A PRO* 1.3 79.8 - - - +
190A SER* 1.3 56.0 + - - +
192A LEU 3.9 0.2 - - - -
193A ASN* 3.0 31.4 + - - +
276A GLU* 5.2 2.3 - - + +
291A TRP* 3.8 36.4 - - + +
294A LEU* 3.9 34.3 - - + -
295A SER* 4.5 0.2 - - - -
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Residues in contact with SER 190 (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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152A TYR* 2.8 44.8 + - - -
176A TYR* 3.1 18.0 + - - -
186A GLU* 3.8 12.8 + - - -
187A SER* 2.9 39.8 + - - -
189A ALA* 1.3 73.6 - - - +
191A PHE* 1.3 62.8 + - - +
194A PHE* 3.4 8.5 + - - +
295A SER* 3.9 15.0 - - - -
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Residues in contact with PHE 191 (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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176A TYR* 4.2 10.8 - + - -
179A TRP* 3.9 32.8 - + - -
185A PRO* 4.1 8.1 - - + -
187A SER 3.3 3.3 + - - +
188A PRO 3.3 6.8 + - - +
190A SER* 1.3 82.0 + - - +
192A LEU* 1.3 63.7 + - + +
194A PHE* 3.2 6.9 + + - +
195A LEU* 2.9 44.2 + - + +
224A THR* 4.3 2.9 - - + -
225A PHE* 3.8 39.5 - + - -
228A ALA* 3.5 33.7 - - + -
269A PHE* 3.8 21.1 - + + -
273A ALA* 3.8 21.1 - - + -
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Residues in contact with LEU 192 (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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188A PRO 2.9 20.7 + - - +
189A ALA 4.1 0.9 - - - +
191A PHE* 1.3 85.1 - - + +
193A ASN* 1.3 60.2 + - - +
195A LEU* 4.2 10.8 - - + -
196A PHE* 2.9 56.2 + - + +
232A LEU* 4.0 15.5 - - + -
273A ALA* 3.5 28.7 - - + +
276A GLU* 3.8 15.3 - - + -
277A GLY* 3.7 15.5 - - - +
291A TRP* 3.8 30.7 - - + -
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Residues in contact with ASN 193 (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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152A TYR* 3.0 21.8 + - - +
153A TYR* 4.0 4.2 + - - -
189A ALA 3.0 19.1 + - - +
192A LEU* 1.3 74.9 - - - +
194A PHE* 1.3 61.5 + - - +
196A PHE* 4.0 3.3 - - - +
197A LYS* 3.2 22.3 + - - +
288A GLN* 4.8 5.8 + - - +
291A TRP* 4.1 16.3 - - + +
292A LYS* 3.7 27.1 - - - +
295A SER* 3.6 10.8 + - - -
297A GLU* 2.8 25.7 + - - +
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Residues in contact with PHE 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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108A VAL* 3.9 20.4 - - + -
110A LEU* 3.9 11.7 - - + -
152A TYR* 3.9 4.9 + - + +
153A TYR* 3.8 37.7 - + + -
174A PHE* 3.6 41.1 - + + -
175A HIS 4.0 1.6 - - - -
176A TYR* 3.6 40.8 - + + -
190A SER 3.4 11.1 + - - +
191A PHE* 3.2 10.9 + + - +
193A ASN* 1.3 78.0 - - - +
195A LEU* 1.3 67.2 + - - +
197A LYS* 3.1 17.2 + - + +
198A VAL* 3.2 20.9 + - + +
225A PHE* 3.9 15.9 - + - -
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Residues in contact with LEU 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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191A PHE* 2.9 41.9 + - + +
192A LEU* 3.3 10.1 + - + +
194A PHE* 1.3 72.0 - - - +
196A PHE* 1.3 61.8 + - + +
198A VAL* 3.2 7.0 + - - +
199A ARG* 3.0 33.0 + - + +
204A LEU* 5.1 2.0 - - + -
225A PHE* 3.8 36.8 - - + +
228A ALA 4.6 0.2 - - - -
229A ASP* 3.5 42.0 - - + +
232A LEU* 4.1 25.4 - - + -
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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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192A LEU* 2.9 46.1 + - + +
193A ASN* 4.3 4.3 - - - +
195A LEU* 1.3 81.9 - - + +
197A LYS* 1.3 59.2 + - - +
199A ARG* 3.6 39.8 - - + +
200A GLU* 2.9 40.2 + - + +
232A LEU* 4.3 11.4 - - + -
277A GLY 5.1 1.1 - - - -
280A PHE* 3.6 38.6 - + + -
281A ILE* 4.3 9.9 - - + -
288A GLN* 4.1 19.7 - - + +
291A TRP* 3.6 25.8 - + + -
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Residues in contact with LYS 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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148A ASP* 5.1 8.9 + - - -
150A LYS* 6.3 1.2 - - - +
153A TYR* 4.1 30.8 + - + +
155A VAL* 4.5 21.3 - - + -
174A PHE* 4.0 8.0 - - + -
193A ASN 3.2 13.6 + - - +
194A PHE* 3.1 14.3 + - + +
196A PHE* 1.3 75.3 - - - +
198A VAL* 1.3 63.6 + - + +
200A GLU* 3.6 12.5 + - + +
201A SER* 3.4 23.0 + - - -
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Residues in contact with VAL 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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108A VAL* 4.0 19.7 - - + -
174A PHE* 3.8 40.6 - - + -
194A PHE* 3.2 29.5 + - + +
195A LEU 3.4 7.2 - - - +
197A LYS* 1.3 77.2 - - - +
199A ARG* 1.3 58.7 + - - +
201A SER* 2.7 23.7 + - - -
202A GLY 4.0 1.2 + - - -
203A SER* 4.0 9.9 + - - -
204A LEU* 4.0 22.1 + - + +
211A VAL* 4.9 2.5 - - + -
225A PHE* 4.4 12.1 - - + -
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Residues in contact with ARG 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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79A ARG* 3.7 10.0 - - - +
195A LEU* 3.0 21.8 + - + +
196A PHE* 3.6 49.6 - - + +
197A LYS 3.3 0.2 - - - -
198A VAL* 1.3 77.1 - - - +
200A GLU* 1.3 61.9 + - + +
201A SER 3.3 1.0 + - - -
202A GLY* 3.4 13.0 + - - -
204A LEU* 3.8 25.2 + - + +
229A ASP* 2.9 44.5 + - - +
232A LEU* 3.6 16.5 - - - +
233A LEU* 3.8 17.5 - - - +
281A ILE* 4.3 11.9 - - - +
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Residues in contact with GLU 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* 2.9 26.4 + - + +
197A LYS* 4.2 12.7 - - + +
199A ARG* 1.3 75.0 - - + +
201A SER* 1.3 62.4 + - - +
202A GLY* 3.3 1.0 + - - -
280A PHE* 5.9 0.3 - - - -
288A GLN* 2.9 34.2 + - - +
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Residues in contact with SER 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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105A ARG* 3.0 22.7 + - - -
172A LEU* 3.8 13.0 - - - +
174A PHE* 3.3 23.7 - - - -
197A LYS 3.4 9.4 + - - -
198A VAL 2.7 19.6 + - - -
200A GLU* 1.3 77.7 - - - +
202A GLY* 1.3 57.5 + - - +
203A SER* 3.0 18.1 + - - -
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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