Contacts of the helix formed by residues 221 - 237 (chain A) in PDB entry 3FCL
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 221 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A TYR* 3.3 27.5 - - - -
105A LEU* 3.7 11.7 - - - +
219A GLU 3.5 2.0 - - - -
220A ARG* 1.3 79.7 - - - +
222A TRP* 1.3 64.4 + - - +
223A GLU* 3.2 4.9 + - - -
224A GLN* 3.3 13.6 + - - -
225A PHE 3.3 8.3 + - - -
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Residues in contact with TRP 222 (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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2A SCN 4.1 9.0 - - - -
102A PHE* 5.0 0.9 - + - -
105A LEU* 3.6 32.9 - - + +
106A MET* 3.8 13.5 - - + -
108A PHE* 6.4 0.2 - + - -
109A VAL* 3.9 7.6 - - + +
125A VAL* 3.7 11.7 - - + -
126A PHE* 3.7 29.8 - + - -
205A ALA 3.5 14.2 - - - +
206A VAL* 3.7 18.4 - - + -
207A LEU* 3.5 43.3 - - + -
208A THR* 2.8 41.4 + - + +
217A HIS* 4.3 9.9 - - + +
220A ARG* 3.8 0.6 - - + +
221A GLY* 1.3 76.8 - - - +
223A GLU* 1.3 59.5 + - - +
225A PHE* 3.0 18.0 + + - +
226A THR* 2.8 35.0 + - - +
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Residues in contact with GLU 223 (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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205A ALA* 3.9 2.0 - - + +
206A VAL* 3.4 21.7 - - + +
217A HIS 4.8 0.3 - - - +
218A LYS* 3.7 9.4 - - - +
219A GLU* 2.7 62.4 + - - +
220A ARG 3.8 0.9 + - - -
221A GLY* 3.9 1.4 + - - -
222A TRP* 1.3 83.5 + - - +
224A GLN* 1.3 57.3 + - - +
226A THR* 3.4 8.2 + - - -
227A ASP* 2.9 40.9 + - - +
248A TYR* 3.7 20.6 + - - +
252A LYS* 4.3 3.6 - - - +
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Residues in contact with GLN 224 (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 GLU* 4.7 4.6 + - - +
99A LYS* 4.8 7.3 - - - +
101A TYR* 3.4 54.3 - - + +
221A GLY* 3.3 5.1 + - - +
222A TRP 3.3 0.6 - - - -
223A GLU* 1.3 78.0 - - - +
225A PHE* 1.3 62.9 + - - +
227A ASP* 3.5 9.5 + - + +
228A ALA* 3.0 22.2 + - - +
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Residues in contact with PHE 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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85A PHE* 4.1 16.8 - + - -
93A LEU* 4.3 17.0 - - + -
96A GLU* 4.0 13.9 - - + -
97A PHE* 3.7 29.6 - + - -
101A TYR* 3.2 27.9 - - + +
102A PHE* 3.7 18.2 - + + -
105A LEU* 4.8 0.2 - - + -
126A PHE* 4.1 9.9 - + - -
128A TRP* 3.8 26.7 - + - -
207A LEU* 4.5 0.4 - - + -
221A GLY 3.3 5.5 + - - +
222A TRP* 3.0 29.2 + + + +
224A GLN* 1.3 78.4 - - - +
226A THR* 1.3 69.2 + - + +
228A ALA* 3.1 14.5 + - - +
229A VAL* 3.1 16.2 + - + +
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Residues in contact with THR 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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203A LEU* 4.1 13.9 - - + -
204A ASN 3.4 18.2 - - - +
205A ALA 2.7 29.5 + - - +
207A LEU* 4.0 22.0 - - + -
222A TRP 2.8 15.6 + - - +
223A GLU* 3.4 0.3 + - - -
225A PHE* 1.3 74.2 - - + +
227A ASP* 1.3 64.3 + - - +
229A VAL* 3.2 8.3 + - + +
230A VAL* 3.1 27.2 + - - +
252A LYS* 2.8 29.8 + - - -
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Residues in contact with ASP 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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223A GLU* 2.9 29.8 + - - +
224A GLN* 3.5 9.0 - - + +
226A THR* 1.3 76.2 + - - +
228A ALA* 1.3 51.3 + - - +
230A VAL* 3.3 7.3 + - - +
231A SER* 2.8 36.9 + - - -
252A LYS* 2.7 37.3 + - - +
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Residues in contact with ALA 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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93A LEU* 4.2 7.0 - - + +
96A GLU* 3.7 36.6 - - + +
224A GLN 3.0 13.1 + - - +
225A PHE 3.1 13.0 + - - +
227A ASP* 1.3 76.9 - - - +
229A VAL* 1.3 55.1 + - - +
231A SER* 3.8 6.6 - - - -
232A TRP* 3.0 28.4 + - - +
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Residues in contact with VAL 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A TRP* 4.2 15.7 - - + -
93A LEU* 3.9 24.5 - - + -
128A TRP* 3.8 34.8 - - + -
134A ILE* 6.1 1.1 - - + +
201A LEU* 4.4 0.9 - - + -
203A LEU* 3.9 19.7 - - + -
225A PHE* 3.1 20.1 + - + +
226A THR* 3.2 12.5 + - - +
228A ALA* 1.3 75.0 - - - +
230A VAL* 1.3 63.0 + - - +
232A TRP* 3.3 3.3 + - - +
233A LEU* 3.1 33.9 + - + +
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Residues in contact with VAL 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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140A VAL* 5.5 1.3 - - + -
142A LEU* 4.0 29.8 - - + -
203A LEU* 4.3 8.1 - - + -
226A THR 3.1 15.5 + - - +
227A ASP* 3.6 9.2 - - - +
229A VAL* 1.3 74.8 - - - +
231A SER* 1.3 58.0 + - - +
233A LEU* 3.3 9.5 + - + +
234A ASN* 2.8 29.4 + - + +
242A PHE* 4.4 12.1 - - + -
252A LYS* 4.3 22.2 - - + +
256A ILE* 4.3 25.6 - - + -
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Residues in contact with SER 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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227A ASP 2.8 21.2 + - - -
228A ALA* 3.8 7.9 - - - -
230A VAL* 1.3 74.4 - - - +
232A TRP* 1.3 61.3 + - - +
234A ASN* 3.3 8.8 + - - +
235A GLN* 3.1 25.5 + - - +
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Residues in contact with TRP 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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92A HIS* 3.4 66.7 + + + +
93A LEU* 4.7 7.2 - - + -
134A ILE* 3.7 31.4 - - + -
135A LYS* 3.8 25.6 - - + -
228A ALA 3.0 18.6 + - - +
229A VAL* 3.7 6.1 - - - +
230A VAL 3.3 0.2 - - - -
231A SER* 1.3 77.6 - - - +
233A LEU* 1.3 74.8 + - + +
235A GLN* 3.3 0.9 + - - -
236A ASN* 2.9 80.3 + - + +
237A SER* 5.3 1.6 - - - -
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Residues in contact with LEU 233 (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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89A TRP* 4.9 2.0 - - + -
134A ILE* 4.3 16.2 - - + +
137A VAL* 4.3 14.8 - - + -
140A VAL* 4.2 14.8 - - + -
201A LEU* 3.5 31.6 - - + -
229A VAL* 3.1 27.6 + - + +
230A VAL* 3.8 6.7 - - + +
232A TRP* 1.3 100.2 - - + +
234A ASN* 1.3 63.6 + - - +
237A SER* 2.5 34.9 + - - +
240A LEU* 3.8 20.9 - - + -
242A PHE* 4.6 4.7 - - + -
261A HIS* 3.5 2.1 + - - -
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Residues in contact with ASN 234 (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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230A VAL* 2.8 18.6 + - + +
231A SER* 3.5 10.3 + - - +
232A TRP 3.2 0.2 - - - -
233A LEU* 1.3 76.3 - - - +
235A GLN* 1.3 62.3 + - - +
242A PHE* 4.8 3.1 - - + -
255A ALA 4.1 8.5 + - - -
256A ILE* 3.6 14.4 - - + +
257A ASP* 2.8 39.9 + - - +
260A ARG* 3.9 10.4 - - - -
261A HIS* 2.9 36.9 + - - -
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Residues in contact with GLN 235 (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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231A SER* 3.1 16.6 + - - +
232A TRP* 5.0 0.2 - - - -
234A ASN* 1.3 79.1 - - - +
236A ASN* 1.3 78.8 + - - +
237A SER 3.7 0.9 - - - -
260A ARG* 3.1 27.8 + - - +
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Residues in contact with ASN 236 (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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135A LYS* 3.8 19.7 + - - +
232A TRP* 2.9 69.2 + - + +
233A LEU 4.0 0.4 - - - -
235A GLN* 1.3 99.7 + - - +
237A SER* 1.3 60.2 + - - +
260A ARG* 4.1 4.9 - - - +
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Residues in contact with SER 237 (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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134A ILE 6.2 0.2 - - - -
137A VAL 5.6 0.7 - - - -
232A TRP* 5.3 1.8 - - - -
233A LEU* 2.5 30.4 + - - -
236A ASN* 1.3 79.6 - - - +
238A ASN* 1.3 58.4 + - - +
240A LEU* 3.0 34.2 - - - +
260A ARG* 2.7 31.3 + - - -
261A HIS* 3.2 8.9 + - - -
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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