Contacts of the helix formed by residues 214 - 232 (chain A) in PDB entry 4LOU
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 214 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A THR* 2.7 42.7 + - - +
35A ILE* 5.3 0.2 - - - -
172A GLU* 4.4 6.5 - - - -
176A THR* 3.1 10.9 + - - +
212A LEU 2.8 10.7 + - - -
213A ILE* 1.3 69.4 - - - +
215A ILE* 1.3 58.4 + - - +
216A LYS* 3.6 2.9 + - - +
217A ALA* 3.2 22.4 + - - +
218A VAL* 3.1 26.2 + - - +
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Residues in contact with ILE 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A ILE* 4.6 7.1 - - + +
200A ILE* 6.3 0.9 - - + -
201A ILE* 3.5 42.4 - - + -
213A ILE* 3.1 13.4 + - + +
214A SER* 1.3 68.7 - - - +
216A LYS* 1.3 68.0 + - - +
217A ALA 3.0 1.8 - - - -
218A VAL* 3.4 9.1 + - + +
219A PHE* 3.1 35.7 + - + +
201B ILE* 5.9 1.6 - - + +
202B GLU* 4.8 23.8 - - + +
207B GLN* 5.9 4.9 - - - +
405B PRO* 6.4 0.9 - - + -
406B LEU* 5.3 2.5 - - + -
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Residues in contact with LYS 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ASP* 3.0 29.2 + - - +
31A THR* 4.7 1.3 - - - +
36A LEU* 4.4 9.4 - - + -
214A SER* 3.4 7.3 + - - +
215A ILE* 1.3 78.9 - - - +
217A ALA* 1.3 57.9 + - - +
219A PHE* 3.1 24.7 - - - +
220A ILE* 3.2 12.8 + - + +
405B PRO* 6.1 3.6 - - + -
430B LEU* 5.0 3.6 - - + -
433B THR* 2.6 52.8 + - + -
434B LEU* 3.5 29.2 - - + -
437B GLN* 2.7 32.2 + - - +
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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
----------------------------------------------------------
31A THR* 4.5 2.2 - - + -
35A ILE* 4.5 3.4 - - + -
36A LEU* 4.0 20.0 - - + -
39A ALA* 3.4 22.8 - - + +
176A THR* 3.9 16.4 - - + -
180A THR* 4.2 0.4 + - - -
214A SER* 3.2 24.3 + - - +
215A ILE 3.0 0.6 - - - -
216A LYS* 1.3 77.5 - - - +
218A VAL* 1.3 66.0 + - - +
219A PHE 3.0 1.6 - - - -
220A ILE* 3.0 13.2 + - - -
221A GLY 3.2 10.0 + - - -
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Residues in contact with VAL 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A THR* 4.9 1.3 - - + +
179A ALA* 4.5 1.6 - - + -
180A THR* 3.5 28.0 + - + +
183A ALA* 3.5 29.2 - - + -
197A ILE* 4.5 17.0 - - + -
200A ILE* 4.3 12.8 - - + -
213A ILE* 3.7 22.4 - - + -
214A SER 3.1 17.7 - - - +
215A ILE* 3.8 9.9 - - + +
217A ALA* 1.3 76.1 - - - +
219A PHE* 1.3 61.0 + - - +
221A GLY* 3.5 1.2 + - - -
222A VAL* 3.1 23.9 + - + +
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Residues in contact with PHE 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A LEU* 4.9 0.7 - - + -
197A ILE* 3.3 37.0 - - + +
215A ILE* 3.1 24.5 + - + +
216A LYS* 3.1 14.8 - - - +
217A ALA 3.0 0.2 - - - -
218A VAL* 1.3 74.0 - - - +
220A ILE* 1.3 60.8 + - - +
222A VAL* 3.2 4.7 + - + +
223A ILE* 2.9 31.9 + - + +
405B PRO* 4.9 4.9 - - + -
406B LEU* 3.6 42.2 - - + -
409B ILE* 4.3 14.1 - - + -
426B ILE* 3.4 38.8 - - + -
430B LEU* 3.4 31.0 - - + -
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Residues in contact with ILE 220 (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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36A LEU* 3.9 42.0 - - + +
39A ALA* 4.6 0.2 - - + -
40A ALA* 3.8 30.3 - - + +
216A LYS* 3.2 11.0 + - + +
217A ALA* 3.0 7.4 + - - +
219A PHE* 1.3 74.4 - - - +
221A GLY* 1.3 65.5 + - - +
223A ILE* 3.6 5.0 - - + +
224A MET* 3.2 24.9 + - + +
430B LEU* 3.6 19.1 - - + -
434B LEU* 3.8 28.9 - - + -
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Residues in contact with GLY 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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39A ALA 3.5 22.0 + - - -
43A GLY* 3.6 7.9 - - - -
180A THR* 3.6 15.3 - - - -
184A ALA* 4.0 7.2 - - - -
217A ALA 3.2 10.7 + - - -
218A VAL 3.9 0.2 - - - -
219A PHE 3.2 0.2 - - - -
220A ILE* 1.3 73.6 - - - +
222A VAL* 1.3 64.0 + - - +
224A MET* 2.8 17.1 + - - +
225A SER* 3.0 10.6 + - - -
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Residues in contact with VAL 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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183A ALA* 3.9 14.1 - - + +
184A ALA* 3.9 30.2 - - - +
187A ALA* 4.1 4.9 - - + -
193A PRO* 3.5 40.6 - - + +
197A ILE* 3.8 24.5 - - + +
218A VAL 3.1 16.5 + - - +
219A PHE* 3.5 8.7 - - + +
221A GLY* 1.3 72.0 - - - +
223A ILE* 1.3 68.1 + - + +
225A SER* 3.7 0.5 - - - -
226A THR* 2.9 30.0 + - - +
426B ILE* 5.4 0.9 - - + -
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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
----------------------------------------------------------
193A PRO* 6.1 0.4 - - - -
219A PHE* 2.9 18.7 + - + +
220A ILE* 3.6 11.7 - - + +
222A VAL* 1.3 74.9 - - + +
224A MET* 1.3 67.4 + - - +
226A THR* 3.8 4.1 - - - -
227A ILE* 3.0 48.2 + - + +
423B LEU* 5.7 3.4 - - + +
426B ILE* 3.5 38.1 - - + +
427B ILE* 3.9 22.7 - - + -
430B LEU* 3.4 27.8 - - + -
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Residues in contact with MET 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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40A ALA* 3.9 22.7 - - + +
43A GLY 4.5 0.2 - - - -
44A THR* 3.4 31.2 - - + +
220A ILE* 3.2 18.2 - - + +
221A GLY 2.8 11.3 + - - +
223A ILE* 1.3 79.3 - - + +
225A SER* 1.3 60.2 + - - +
227A ILE* 3.4 13.7 + - + +
228A MET* 2.9 53.2 + - + +
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Residues in contact with SER 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A GLY 3.6 17.8 + - - -
47A GLY* 3.7 11.9 + - - -
184A ALA* 2.7 47.9 + - - -
187A ALA* 5.2 0.2 - - - -
188A ALA* 3.2 15.9 + - - +
221A GLY 3.0 4.2 + - - -
222A VAL 3.7 4.9 - - - -
224A MET* 1.3 77.4 - - - +
226A THR* 1.3 56.9 + - - +
228A MET* 3.4 2.5 + - - +
229A TYR* 3.0 30.1 + - - +
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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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187A ALA* 3.8 20.6 - - - +
188A ALA* 5.1 3.4 - - - +
191A ASN* 3.8 9.9 - - - +
193A PRO* 4.0 17.2 - - + +
222A VAL 2.9 19.0 + - - -
223A ILE* 3.8 3.8 - - - -
225A SER* 1.3 74.0 - - - +
227A ILE* 1.3 58.4 + - - +
229A TYR* 3.5 5.2 + - - +
230A ARG* 2.9 52.9 + - - +
423B LEU* 3.5 31.0 - - + -
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Residues in contact with ILE 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* 3.0 40.2 + - + +
224A MET* 3.6 15.9 - - + +
226A THR* 1.3 77.1 - - - +
228A MET* 1.3 78.6 + - + +
230A ARG* 3.0 9.1 + - - +
231A ILE* 3.0 32.9 + - + +
249B LEU* 5.1 4.2 - - + +
252B LEU* 4.3 21.3 - - + -
423B LEU* 4.3 9.9 - - + -
427B ILE* 4.2 14.1 - - + -
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Residues in contact with MET 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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44A THR* 3.8 39.3 - - + +
47A GLY* 4.2 11.0 - - - -
48A LEU* 4.2 23.1 - - + -
51A VAL* 4.4 0.7 - - - -
224A MET* 2.9 38.4 + - + +
225A SER* 3.7 4.5 - - - +
227A ILE* 1.3 87.3 - - + +
229A TYR* 1.3 64.3 + - - +
231A ILE* 3.0 29.7 + - + +
232A PHE* 3.2 21.0 - - - -
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Residues in contact with TYR 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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47A GLY* 4.9 0.9 - - - +
50A ALA 5.5 1.8 - - - -
51A VAL* 3.5 24.6 - - + +
54A ASP* 4.3 13.5 + - + -
188A ALA* 3.5 37.7 - - + -
189A ALA* 5.2 4.0 - - - -
191A ASN* 3.7 40.2 + - + +
225A SER 3.0 17.8 + - - +
226A THR* 4.0 4.7 - - - +
228A MET* 1.3 76.6 - - - +
230A ARG* 1.3 61.3 + - + +
232A PHE 3.6 1.8 + - - -
233A ASN* 3.1 63.9 + - + +
236A VAL 5.1 4.7 + - - -
238A LEU* 4.0 25.1 + - - +
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Residues in contact with ARG 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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191A ASN* 2.4 53.8 + - - +
193A PRO* 5.2 1.2 - - - +
226A THR* 2.9 36.1 + - - +
227A ILE* 3.4 7.9 - - - +
228A MET 3.0 0.4 - - - -
229A TYR* 1.3 77.8 - - + +
231A ILE* 1.3 65.0 + - - +
232A PHE 3.1 2.7 - - - -
233A ASN 3.2 17.2 + - - +
234A HIS* 3.3 26.6 + - - +
249B LEU* 3.9 22.3 - - + +
420B GLN 5.4 4.6 + - - -
422B ILE* 4.3 11.7 - - - +
423B LEU* 3.2 43.1 - - + +
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Residues in contact with ILE 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 ILE* 3.0 23.7 + - + +
228A MET* 3.0 31.9 + - + +
230A ARG* 1.3 77.1 - - - +
232A PHE* 1.3 83.9 + - + +
233A ASN 3.6 0.2 - - - -
234A HIS* 4.0 3.3 + - - -
249B LEU* 4.2 19.3 - - + -
103E TYR* 3.0 37.7 + - + +
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Residues in contact with PHE 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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48A LEU* 3.7 28.3 - - + -
51A VAL* 3.7 35.2 - - + -
55A LYS* 3.6 16.4 - - - -
228A MET* 3.2 18.1 + - - -
229A TYR 3.6 0.2 + - - -
230A ARG 3.1 0.8 - - - -
231A ILE* 1.3 99.6 - - + +
233A ASN* 1.3 73.6 + - - +
234A HIS* 5.4 0.7 - - - -
103E TYR* 5.6 1.3 - - - -
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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
------------------------------------------------------------
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