Contacts of the helix formed by residues 176 - 190 (chain D) in PDB entry 3LEE
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 ALA 176 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172D CYS 3.2 9.2 + - - +
174D TYR 3.2 1.0 - - - -
175D VAL* 1.3 78.2 - - - +
177D GLY* 1.3 69.7 + - - +
178D LEU 3.3 1.3 - - - -
179D VAL* 3.2 12.3 + - - +
180D GLY 3.2 13.9 + - - -
208D GLY* 3.7 15.0 - - - +
212D GLN* 3.2 43.7 - - + +
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Residues in contact with GLY 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172D CYS 2.5 19.6 + - - -
173D HIS* 3.1 6.4 + - - -
176D ALA* 1.3 71.8 - - - +
178D LEU* 1.3 62.0 + - - +
180D GLY* 2.9 14.4 + - - -
181D ILE* 3.2 12.5 + - - +
205D ASN* 3.7 31.9 - - - -
208D GLY* 4.2 0.4 - - - -
209D LEU* 3.8 9.8 - - - +
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Residues in contact with LEU 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D ILE* 3.8 26.2 - - + +
149D ARG* 3.6 57.9 - - + +
150D MET* 3.8 14.8 - - + +
173D HIS* 2.7 31.8 + - + +
174D TYR* 3.5 35.7 - - + +
176D ALA 3.3 0.2 - - - -
177D GLY* 1.3 72.0 - - - +
179D VAL* 1.3 51.9 + - - +
181D ILE* 2.7 30.5 + - + +
182D GLY* 2.8 17.3 + - - -
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Residues in contact with VAL 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D PHE* 4.0 12.1 - - + -
76D LEU* 3.4 33.0 - - + -
146D ILE* 4.4 0.4 - - - +
150D MET* 4.0 15.5 - - + -
175D VAL 4.1 14.4 - - - +
176D ALA* 3.4 9.2 - - - +
177D GLY 3.2 0.6 - - - -
178D LEU* 1.3 75.8 - - - +
180D GLY* 1.3 64.8 + - - +
182D GLY* 3.8 0.3 - - - -
183D LEU* 3.0 42.0 + - + +
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Residues in contact with GLY 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176D ALA 3.2 5.3 + - - -
177D GLY 2.9 11.3 + - - -
179D VAL* 1.3 80.3 - - - +
181D ILE* 1.3 52.8 + - - +
183D LEU* 3.4 7.4 + - - +
184D SER* 2.7 36.9 + - - -
204D ALA* 3.9 16.6 - - - -
207D MET* 5.3 4.5 - - - -
208D GLY* 4.9 5.6 - - - -
276D TYR* 4.7 0.5 + - - -
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Residues in contact with ILE 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D ILE* 4.6 3.6 - - + -
149D ARG* 5.0 7.2 - - - +
173D HIS* 4.3 12.8 - - + -
177D GLY 3.5 12.3 - - - +
178D LEU* 2.7 21.5 + - + +
180D GLY* 1.3 68.8 - - - -
182D GLY* 1.3 52.9 + - - +
184D SER* 3.1 1.7 + - - -
185D ARG* 2.5 65.3 + - + +
198D GLY 4.8 2.0 - - - +
201D THR* 3.4 44.2 - - + +
204D ALA* 3.8 19.1 - - + -
205D ASN* 4.2 16.2 - - + +
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Residues in contact with GLY 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D PHE* 4.1 9.6 - - - -
142D VAL* 3.5 14.3 - - - +
146D ILE* 3.9 23.0 - - - +
178D LEU 2.8 16.3 + - - -
179D VAL 3.8 2.5 - - - -
181D ILE* 1.3 73.1 - - - +
183D LEU* 1.3 50.5 + - - +
185D ARG* 3.3 2.4 + - - -
186D LEU* 2.7 35.8 + - - +
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Residues in contact with LEU 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D VAL* 3.3 41.3 - - + -
72D PHE* 3.9 18.4 - - + -
179D VAL* 3.0 35.6 + - + +
180D GLY* 3.8 5.2 - - - +
182D GLY* 1.3 71.7 - - - +
184D SER* 1.3 57.1 + - - +
186D LEU* 2.8 5.5 + - + +
187D PHE* 2.6 55.6 + - + -
276D TYR* 5.6 0.7 - - - +
288D PHE* 3.7 26.5 - - + -
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Residues in contact with SER 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180D GLY 2.7 19.6 + - - -
181D ILE* 3.3 7.6 - - - -
183D LEU* 1.3 74.9 - - - +
185D ARG* 1.3 64.3 + - - +
186D LEU 3.0 0.3 + - - -
187D PHE* 3.0 5.5 + - - +
188D SER* 2.9 24.6 + - - -
197D VAL* 3.8 29.3 - - - +
198D GLY* 3.8 7.1 + - - -
204D ALA* 3.4 17.4 - - - +
276D TYR* 2.9 24.1 + - - -
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Residues in contact with ARG 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D THR* 6.1 1.0 - - - +
142D VAL* 3.9 30.0 + - + +
145D ASP* 2.9 37.8 + - - +
146D ILE* 4.1 11.8 - - - +
149D ARG* 3.5 18.0 - - - +
181D ILE* 2.5 47.0 + - + +
182D GLY* 3.5 6.7 - - - +
184D SER* 1.3 71.3 - - - +
186D LEU* 1.3 56.6 + - - +
188D SER* 3.7 2.5 + - - -
189D ALA* 3.1 26.5 + - - +
198D GLY* 4.0 18.2 - - - +
201D THR* 5.3 3.6 - - - +
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Residues in contact with LEU 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D MET* 5.3 2.1 - - - +
68D ALA* 4.1 32.5 - - + +
69D VAL* 4.2 11.2 - - + -
72D PHE* 4.1 22.4 - - + -
139D TYR* 3.9 35.0 - - + +
142D VAL* 3.2 37.0 - - + -
143D ILE* 4.5 2.7 - - + -
182D GLY 2.7 17.5 + - - +
183D LEU* 2.8 7.8 + - + +
185D ARG* 1.3 73.9 - - - +
187D PHE* 1.3 68.4 + - + +
189D ALA* 3.2 5.8 + - - +
190D SER* 3.1 22.0 + - - -
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Residues in contact with PHE 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D LEU* 5.0 3.1 - - + -
65D MET* 3.2 27.8 - - + -
69D VAL* 4.5 10.3 - - + -
183D LEU* 2.6 49.0 + - + -
184D SER* 3.4 6.3 - - - +
186D LEU* 1.3 74.3 - - + +
188D SER* 1.3 62.6 + - - +
190D SER* 2.7 23.7 + - - -
191D GLU 3.5 4.9 + - - -
193D GLU* 3.5 29.2 + - + -
197D VAL* 4.6 4.3 - - + -
276D TYR* 4.0 15.5 - - - -
280D LEU* 5.2 0.7 - - + -
285D VAL* 3.5 23.1 - - + -
288D PHE* 3.9 26.2 - + + -
289D CYS* 3.6 17.3 - - - -
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Residues in contact with SER 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184D SER 2.9 14.2 + - - -
185D ARG* 4.1 3.6 - - - -
187D PHE* 1.3 77.0 - - - +
189D ALA* 1.3 62.2 + - - +
191D GLU* 3.5 10.8 + - - +
193D GLU 4.0 5.0 - - - +
194D ASP 2.1 36.3 + - - -
195D PRO* 3.3 13.1 - - - +
197D VAL* 3.6 1.2 - - - +
198D GLY* 3.2 23.1 + - - -
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Residues in contact with ALA 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D LYS* 3.4 35.2 + - + +
139D TYR* 3.6 19.3 - - + -
142D VAL* 5.3 2.9 - - + -
185D ARG 3.1 19.0 + - - +
186D LEU* 3.4 7.4 - - - +
187D PHE 3.1 0.2 - - - -
188D SER* 1.3 79.1 - - - +
190D SER* 1.3 60.0 + - - +
191D GLU* 3.1 10.0 + - - +
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Residues in contact with SER 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D GLU* 3.9 13.2 - - - +
65D MET* 3.4 15.5 - - - +
138D LYS* 4.1 1.1 - - - +
139D TYR* 3.2 23.6 - - - -
186D LEU 3.1 7.7 + - - -
187D PHE 2.7 21.9 + - - -
189D ALA* 1.3 76.2 - - - +
191D GLU* 1.3 68.1 + - - +
192D PHE* 2.9 39.4 + - - +
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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