Contacts of the helix formed by residues 203 - 217 (chain A) in PDB entry 1FX8
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 ASN 203 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A THR* 5.2 1.8 - - - +
21A LEU* 5.3 3.0 - - - +
67A LEU 2.7 27.7 + - - -
68A ASN* 3.2 13.6 - - - +
69A PRO* 3.3 9.4 - - - +
201A ALA 2.7 14.6 + - - +
202A MET* 1.3 78.2 - - - +
204A PRO* 1.3 68.2 - - - +
205A ALA* 3.0 8.2 + - - +
206A ARG* 2.9 38.4 + - + +
207A ASP* 3.2 14.4 + - - +
236A PRO 4.2 2.7 - - - -
240A PRO* 3.9 2.6 - - - +
662A GOL 6.0 0.2 - - - +
663A GOL 3.0 21.1 + - - +
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Residues in contact with PRO 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ASN* 3.4 14.6 - - - +
69A PRO* 3.9 15.5 - - + -
70A ALA 3.9 7.0 - - - +
94A VAL* 5.5 0.4 - - - -
203A ASN* 1.3 83.7 - - - +
205A ALA* 1.3 57.9 + - - +
207A ASP* 3.3 0.9 + - - +
208A PHE* 2.9 35.1 + - - +
236A PRO 3.5 13.9 - - - +
237A LEU* 3.4 38.0 - - + +
240A PRO* 3.9 9.9 - - + -
241A ILE* 3.9 18.2 - - + -
474A BOG 6.2 2.0 - - + -
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Residues in contact with ALA 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A THR* 4.4 4.5 - - + -
68A ASN* 5.3 0.2 - - - -
69A PRO* 3.5 21.3 - - + +
93A GLN* 3.7 11.2 - - + +
94A VAL* 3.7 36.7 - - + +
97A ALA* 3.3 13.3 - - - +
203A ASN* 3.0 8.7 + - - +
204A PRO* 1.3 76.2 - - - +
206A ARG* 1.3 66.4 + - - +
207A ASP 3.1 0.9 + - - -
209A GLY* 3.3 19.4 + - - +
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Residues in contact with ARG 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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18A THR* 5.1 1.0 - - + +
21A LEU* 4.8 2.7 - - + -
22A ILE* 3.9 28.6 - - + +
26A VAL* 4.9 1.0 - - - +
29A VAL* 6.0 1.0 - - - +
48A TRP* 3.5 31.3 - - + -
133A GLY 5.5 1.2 + - - -
134A THR 5.4 1.4 + - - -
135A PHE 2.9 26.9 + - - -
136A SER* 3.6 10.9 + - - +
137A THR* 3.8 17.4 - - - +
201A ALA* 4.0 12.3 - - - +
203A ASN* 2.9 32.2 + - + +
205A ALA* 1.3 76.8 - - - +
207A ASP* 1.3 62.9 + - - +
210A PRO* 3.1 16.4 - - - +
662A GOL 2.6 47.6 + - - +
663A GOL 5.9 0.2 - - - +
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Residues in contact with ASP 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A SER* 3.4 3.9 - - - -
137A THR* 2.7 41.9 + - - +
201A ALA* 4.5 1.3 - - + -
203A ASN 3.2 12.9 + - - +
204A PRO 4.0 2.0 - - - +
205A ALA 3.1 0.6 - - - -
206A ARG* 1.3 84.6 - - - +
208A PHE* 1.3 65.6 + - - +
210A PRO* 3.6 1.9 - - - +
211A LYS* 2.8 54.8 + - - +
233A PHE* 4.8 2.1 - - - +
236A PRO* 3.3 32.3 - - + +
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Residues in contact with PHE 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A VAL* 4.4 12.8 - - + -
204A PRO 2.9 20.8 + - - +
205A ALA* 5.1 1.1 - - - -
207A ASP* 1.3 72.7 + - - +
209A GLY* 1.3 67.7 - - - +
211A LYS* 3.1 5.0 + - + +
212A VAL* 2.8 48.4 + - + +
224A PHE* 4.0 22.0 - + - -
233A PHE* 4.2 22.2 - + + -
237A LEU* 4.3 13.5 - - + -
474A BOG 3.5 66.2 - - + -
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Residues in contact with GLY 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A VAL* 4.1 26.5 - - - +
98A PHE* 3.4 23.3 - - - -
205A ALA 3.3 9.5 + - - -
208A PHE* 1.3 81.9 - - - +
210A PRO* 1.3 67.8 - - - +
212A VAL* 3.2 4.2 + - - +
213A PHE 3.1 14.7 + - - -
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Residues in contact with PRO 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ILE* 4.3 12.8 - - + -
26A VAL* 5.1 0.2 - - + -
97A ALA* 3.9 18.8 - - + +
101A ALA* 3.9 19.3 - - + -
135A PHE* 3.3 39.5 - - + +
205A ALA 3.5 5.6 - - - +
206A ARG 3.1 26.7 - - - +
207A ASP 3.6 4.0 - - - +
209A GLY* 1.3 85.9 - - - +
211A LYS* 1.3 58.5 + - - +
213A PHE* 3.2 2.6 + - + +
214A ALA* 2.9 29.3 + - - +
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Residues in contact with LYS 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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136A SER* 2.9 29.5 + - - +
137A THR 2.8 27.9 + - - -
138A TYR* 3.9 6.8 - - - +
207A ASP* 2.8 40.9 + - - +
208A PHE* 3.1 8.5 + - - +
210A PRO* 1.3 73.8 - - - +
212A VAL* 1.3 65.1 + - - +
214A ALA* 3.3 5.8 + - - +
215A TRP* 3.0 23.9 + - - +
223A ALA* 3.3 30.4 - - - +
224A PHE* 4.1 14.1 - - + -
232A TYR* 4.6 2.8 - - - -
233A PHE* 3.6 37.9 - - + +
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Residues in contact with VAL 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A VAL* 6.3 0.2 - - + -
98A PHE* 4.1 15.7 - - + -
208A PHE* 2.8 52.0 + - + +
209A GLY* 3.2 8.7 + - - +
211A LYS* 1.3 76.1 - - - +
213A PHE* 1.3 62.2 + - - +
215A TRP* 3.3 23.5 - - + +
216A LEU* 3.1 27.0 + - + +
224A PHE* 4.0 11.2 - - + -
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Residues in contact with PHE 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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98A PHE* 3.7 23.5 - + + -
101A ALA* 4.1 8.1 - - + -
102A ALA* 3.6 25.4 - - + -
105A TYR* 3.5 35.9 - + + -
135A PHE* 3.9 24.0 - + - -
209A GLY 3.1 8.2 + - - +
210A PRO* 3.5 10.3 - - + +
211A LYS 3.2 0.4 - - - -
212A VAL* 1.3 75.5 - - - +
214A ALA* 1.3 64.1 + - - +
216A LEU* 3.0 5.5 + - - +
217A ALA* 2.8 42.8 + - + +
473A BOG 3.7 25.8 - - + -
475A BOG 2.9 28.9 - - - -
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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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132A ALA* 5.0 6.1 - - + +
135A PHE* 4.0 17.5 - - + -
136A SER* 6.0 0.2 - - - +
138A TYR* 5.4 1.6 - - - +
210A PRO 2.9 16.3 + - - +
211A LYS* 3.8 5.6 - - - +
213A PHE* 1.3 82.4 - - - +
215A TRP* 1.3 59.5 + - - +
217A ALA 3.3 4.7 + - - -
219A TRP* 3.0 54.5 + - + +
223A ALA* 4.1 11.9 - - + -
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Residues in contact with TRP 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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211A LYS 3.0 14.3 + - - +
212A VAL* 3.3 27.6 - - + +
214A ALA* 1.3 79.1 - - - +
216A LEU* 1.3 91.7 + - + +
218A GLY* 3.6 3.6 + - - -
220A GLY* 3.2 55.8 + - - +
221A ASN* 4.1 5.4 - - - +
223A ALA* 3.9 1.9 - - + +
224A PHE* 3.4 31.9 - + + -
473A BOG 5.0 0.2 + - - -
474A BOG 3.8 29.4 + - - -
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Residues in contact with LEU 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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98A PHE* 3.8 34.8 - - + -
212A VAL* 3.1 13.8 + - + +
213A PHE 3.0 7.4 + - - +
215A TRP* 1.3 106.4 - - + +
217A ALA* 1.3 50.8 + - - +
218A GLY 3.2 1.3 - - - -
473A BOG 2.6 53.5 + - + +
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Residues in contact with ALA 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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105A TYR* 4.5 4.3 - - + -
123A ARG* 2.8 28.9 + - - -
213A PHE* 2.8 46.3 + - + +
214A ALA 3.3 1.4 + - - +
216A LEU* 1.3 71.8 - - - +
218A GLY* 1.3 55.5 + - - +
219A TRP* 3.7 18.2 - - + -
473A BOG 3.3 30.0 - - + +
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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