Contacts of the helix formed by residues 220 - 237 (chain A) in PDB entry 3FIE
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 ASP 220 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A ARG* 3.1 30.7 + - - -
200A GLU* 4.2 1.6 - - - -
219A ALA* 1.3 74.2 - - - +
221A PRO* 1.3 60.0 - - - +
222A ALA* 2.9 9.3 + - - +
223A ILE* 2.9 27.4 + - + +
224A SER* 3.2 10.0 + - - -
362A VAL* 3.6 30.7 - - + +
386A TYR* 2.5 36.8 + - - -
391A GLY* 3.9 2.6 - - - -
392A PHE* 4.4 6.9 + - + -
393A ASN* 5.7 1.0 + - - -
404A GLN* 3.9 7.6 + - - +
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Residues in contact with PRO 221 (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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94A LEU* 3.8 20.9 - - + -
195A PHE* 3.6 12.9 - - + -
197A PRO* 4.7 5.4 - - + +
200A GLU* 3.3 27.3 - - + +
219A ALA 3.5 6.7 - - - +
220A ASP* 1.3 88.0 - - - +
222A ALA* 1.3 54.8 + - - +
224A SER* 3.8 1.5 - - - +
225A LEU* 3.0 27.2 + - - +
377A VAL* 4.1 26.9 - - + -
380A LEU* 4.2 9.9 - - + -
386A TYR* 4.2 5.8 - - + -
392A PHE* 3.9 13.0 - - + -
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Residues in contact with ALA 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A LEU* 4.1 16.1 - - + +
97A ARG* 3.8 25.8 - - + +
98A ILE* 3.5 13.9 - - + +
220A ASP* 2.9 7.5 + - - +
221A PRO* 1.3 78.6 - - - +
223A ILE* 1.3 62.4 + - + +
225A LEU* 3.2 7.8 + - - +
226A ALA* 2.8 24.6 + - - +
360A PHE* 5.8 1.8 - - + -
386A TYR* 3.2 20.1 + - - +
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Residues in contact with ILE 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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98A ILE* 6.5 0.4 - - + -
219A ALA* 6.3 0.4 - - + -
220A ASP* 2.9 16.0 + - + +
222A ALA* 1.3 77.2 - - + +
224A SER* 1.3 60.5 + - - +
226A ALA* 3.0 8.4 + - + +
227A HIS* 2.7 28.4 + - - +
353A GLU* 3.4 42.1 - - + +
356A LEU* 4.2 12.3 - - + +
357A ALA* 4.0 26.5 - - + +
360A PHE* 4.3 21.3 - - + -
362A VAL* 3.7 27.4 - - + -
364A CYS* 5.3 2.9 - - + -
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Residues in contact with SER 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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165A ASN* 4.1 16.1 + - - -
195A PHE* 4.6 2.5 - - - -
200A GLU* 2.8 40.6 + - - -
201A TYR* 4.5 5.5 - - - -
219A ALA* 4.5 3.8 - - - +
220A ASP 3.2 5.1 + - - -
221A PRO 3.9 4.5 - - - -
223A ILE* 1.3 78.6 - - - +
225A LEU* 1.3 61.1 + - - +
227A HIS* 3.2 21.2 - - - +
228A GLU* 3.2 16.4 + - - +
353A GLU* 4.7 4.6 + - - -
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Residues in contact with LEU 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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91A THR* 4.5 1.3 - - + +
94A LEU* 3.9 21.8 - - + -
95A PHE* 3.8 35.7 - - + -
98A ILE* 3.7 20.9 - - + -
155A VAL* 5.8 2.0 - - + -
193A VAL* 4.8 11.7 - - + -
195A PHE* 3.8 34.3 - - + -
221A PRO 3.0 15.6 + - - +
222A ALA 3.3 7.6 - - - +
223A ILE 3.1 0.2 - - - -
224A SER* 1.3 74.1 - - - +
226A ALA* 1.3 67.6 + - - +
228A GLU* 3.1 4.9 + - - +
229A LEU* 3.0 33.1 + - + +
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Residues in contact with ALA 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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98A ILE* 4.0 20.0 - - + -
107A LEU* 3.9 10.7 - - + +
222A ALA 2.8 14.2 + - - +
223A ILE* 3.0 15.5 + - + +
225A LEU* 1.3 75.9 - - - +
227A HIS* 1.3 62.7 + - - +
229A LEU* 3.0 6.2 + - - +
230A ILE* 3.0 28.9 + - - +
353A GLU* 6.4 0.4 - - - -
356A LEU* 4.0 24.5 - - + -
360A PHE* 6.5 0.9 - - + -
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Residues in contact with HIS 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 ILE 2.7 13.1 + - - +
224A SER* 3.2 14.4 - - - +
226A ALA* 1.3 76.9 - - - +
228A GLU* 1.3 68.9 + - - +
230A ILE* 3.3 25.1 + - - +
231A HIS* 3.3 10.3 + - - -
266A GLU* 4.5 1.6 - - - -
269A THR* 3.6 17.5 - - + +
270A PHE* 4.1 17.3 - - + -
353A GLU* 2.7 39.8 + - + +
365A ARG* 5.5 0.2 - - - -
368A TYR* 4.5 6.9 - + - -
428A ZN 2.2 36.6 - - - -
58C DCY 3.4 12.7 - - - -
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Residues in contact with GLU 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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165A ASN* 3.7 24.5 - - + +
166A SER* 3.2 36.4 - - - +
167A SER* 3.5 9.0 + - - -
193A VAL* 3.8 26.0 - - + +
195A PHE* 5.3 2.2 - - + -
224A SER* 3.2 13.1 + - - +
225A LEU* 3.1 9.0 + - - +
227A HIS* 1.3 84.2 - - - +
229A LEU* 1.3 63.9 + - - +
231A HIS* 3.2 15.2 + - - +
232A ALA* 3.1 20.3 + - - +
57C ASP 4.1 1.7 - - - +
58C DCY 3.7 18.8 - - - -
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Residues in contact with LEU 229 (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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95A PHE* 4.1 17.9 - - + -
98A ILE* 4.1 22.0 - - + -
107A LEU* 4.2 13.2 - - + -
108A LEU* 3.7 29.4 - - + -
111A ILE* 3.2 22.4 - - + +
153A LEU* 3.4 32.8 - - + -
155A VAL* 5.9 0.4 - - + -
193A VAL* 4.9 4.7 - - + -
225A LEU* 3.0 23.3 + - + +
226A ALA* 3.0 8.5 + - - +
228A GLU* 1.3 77.1 - - - +
230A ILE* 1.3 57.1 + - - +
232A ALA* 3.1 6.3 + - - +
233A LEU* 2.8 25.5 + - - +
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Residues in contact with ILE 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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107A LEU* 4.2 10.5 - - + -
226A ALA 3.0 15.2 + - - +
227A HIS* 3.5 13.0 - - - +
229A LEU* 1.3 77.6 - - - +
231A HIS* 1.3 62.1 + - - +
233A LEU* 3.2 7.6 + - + +
234A HIS* 3.0 43.9 + - + +
269A THR* 3.5 19.5 - - + +
348A LEU 5.0 0.2 - - - +
351A PHE* 3.6 50.0 - - + +
352A THR* 3.8 12.3 - - - +
353A GLU* 4.1 2.9 - - - +
356A LEU* 3.9 15.3 - - + -
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Residues in contact with HIS 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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167A SER* 3.5 15.7 - - - +
191A ASN* 4.3 1.1 + - - -
227A HIS* 3.3 18.5 + + - -
228A GLU* 3.2 19.4 + - - +
230A ILE* 1.3 77.4 - - - +
232A ALA* 1.3 58.3 + - - +
234A HIS* 3.1 4.7 + - - +
235A GLY* 2.8 25.6 + - - -
240A ARG* 4.3 5.2 - - - -
265A GLU* 2.8 32.0 + - + -
266A GLU* 3.7 8.7 - - - -
269A THR* 3.2 21.6 + - - -
428A ZN 2.1 37.9 - - - -
57C ASP* 3.4 33.1 - - + +
58C DCY 4.5 0.2 - - - -
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Residues in contact with ALA 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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111A ILE* 4.4 6.3 - - + -
153A LEU* 4.0 14.4 - - + -
167A SER* 3.5 0.4 + - - +
191A ASN* 3.4 35.5 + - + +
193A VAL* 4.3 1.6 - - + -
228A GLU 3.1 10.0 + - - +
229A LEU* 3.1 13.9 + - - +
231A HIS* 1.3 79.3 - - - +
233A LEU* 1.3 52.5 + - - +
235A GLY* 3.0 2.9 + - - -
236A LEU* 2.7 41.2 + - + +
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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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107A LEU* 4.4 5.2 - - + -
110A GLU* 3.7 38.8 - - + +
111A ILE* 3.8 13.4 - - + +
114A ALA* 4.0 12.6 - - + -
229A LEU 2.8 16.1 + - - +
230A ILE* 3.2 10.5 + - - +
232A ALA* 1.3 72.0 - - - +
234A HIS* 1.3 65.0 + - + +
236A LEU* 3.3 4.2 + - - +
237A TYR* 3.2 32.6 + - + -
347A LYS* 5.4 1.6 - - - -
348A LEU* 4.3 24.2 - - + +
351A PHE* 3.6 37.9 - - + -
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Residues in contact with HIS 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 ILE* 3.0 30.7 + - + +
231A HIS 3.1 6.9 + - - +
233A LEU* 1.3 78.4 - - + +
235A GLY* 1.3 64.3 + - - +
237A TYR* 3.2 8.3 + - - -
239A ALA* 3.0 32.8 + - + +
240A ARG* 4.0 11.0 - - + -
265A GLU* 2.7 28.6 + - - +
268A LEU* 4.9 1.6 - - + -
269A THR* 3.3 24.6 + - - -
348A LEU* 2.8 37.8 + - + -
349A TYR* 3.6 29.3 - + - -
351A PHE 5.0 0.2 + - - -
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Residues in contact with GLY 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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183A SER* 3.0 27.4 + - - -
188A GLY* 3.3 5.2 - - - -
189A SER 4.9 1.1 - - - -
191A ASN* 4.4 7.9 - - - -
231A HIS 2.8 13.1 + - - -
232A ALA 3.0 3.3 + - - -
234A HIS* 1.3 77.7 - - - +
236A LEU* 1.3 52.9 + - - +
238A GLY* 2.8 21.1 + - - -
240A ARG* 3.8 19.4 - - - +
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Residues in contact with LEU 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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111A ILE* 4.4 13.2 - - + +
114A ALA* 3.6 32.5 - - + +
116A PRO* 3.7 16.9 - - + +
152A ASN* 3.4 31.4 - - + +
153A LEU* 5.1 2.0 - - + -
188A GLY* 3.6 9.3 - - - -
189A SER 3.2 23.1 - - - +
191A ASN* 4.4 4.7 - - + +
232A ALA* 2.7 36.0 + - + +
233A LEU* 3.7 8.7 - - - +
235A GLY* 1.3 72.2 - - - +
237A TYR* 1.3 59.8 + - - +
238A GLY 3.2 1.0 + - - -
323A LYS* 2.8 25.6 + - - -
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Residues in contact with TYR 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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110A GLU* 4.1 3.0 + - - -
114A ALA* 3.7 27.3 + - + -
186A GLY 3.3 12.5 - - - +
233A LEU* 3.2 29.0 + - + +
234A HIS 3.9 3.4 - - - +
235A GLY 3.1 1.2 - - - -
236A LEU* 1.3 78.3 - - - +
238A GLY* 1.3 63.1 + - - +
239A ALA 3.2 1.6 + - - +
290A LEU* 4.2 0.5 - - - +
294A TYR* 2.8 43.2 + + - +
322A TRP* 3.7 24.1 - - - -
323A LYS* 3.5 40.9 + - + +
344A ILE* 3.9 11.7 - - + -
347A LYS* 2.9 30.3 + - - -
348A LEU* 3.5 24.2 - - + -
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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