Contacts of the helix formed by residues 164 - 180 (chain D) in PDB entry 3U1K
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 GLU 164 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D THR* 4.5 0.9 - - - -
126D LYS* 4.6 6.2 + - - -
162D VAL 4.7 0.5 - - - +
163D ASN* 1.3 69.5 - - - +
165D PRO* 1.3 77.4 - - - +
166D ASP* 3.4 24.5 + - - +
167D VAL* 4.0 5.0 + - + +
168D LEU* 3.6 19.2 + - - +
192D ARG* 3.7 7.8 + - - +
204D PRO 4.1 12.2 + - - +
206D ARG* 3.5 35.9 - - - +
209D MET* 3.7 29.2 - - - +
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Residues in contact with PRO 165 (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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78D THR* 4.0 14.6 - - + -
80D VAL* 3.8 17.4 - - + +
102D TYR* 3.4 20.9 - - - +
126D LYS* 5.6 3.4 - - - +
156D LEU* 3.8 20.6 - - + -
159D VAL* 4.3 16.8 - - + -
163D ASN 3.5 8.3 - - - +
164D GLU* 1.3 90.1 - - + +
166D ASP* 1.3 64.5 + - - +
168D LEU* 3.1 5.3 + - + +
169D ALA* 2.9 22.2 + - - +
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Residues in contact with ASP 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D TYR* 3.8 5.8 + - - +
126D LYS* 3.0 34.5 + - - +
130D THR* 3.7 23.6 - - + +
133D ILE* 6.0 4.0 - - + +
164D GLU* 3.6 10.0 - - - +
165D PRO* 1.3 80.5 - - - +
167D VAL* 1.3 76.5 + - - +
169D ALA* 3.0 14.6 + - - +
170D ILE* 3.1 17.8 + - + +
192D ARG* 2.9 44.5 + - - -
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Residues in contact with VAL 167 (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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56D LEU* 6.5 0.2 - - + -
164D GLU* 4.0 5.1 + - + +
165D PRO 3.4 0.4 - - - -
166D ASP* 1.3 88.1 + - - +
168D LEU* 1.3 70.2 + - + +
169D ALA 3.2 0.2 + - - -
170D ILE* 3.3 9.5 + - + +
171D ASN* 3.0 30.7 + - - +
190D ALA* 3.4 27.6 - - + +
191D VAL* 3.8 4.5 - - - -
192D ARG* 3.9 37.7 - - + +
203D ASN* 3.8 20.2 - - - +
217D VAL* 4.6 11.9 - - + -
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Residues in contact with LEU 168 (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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56D LEU* 3.3 33.7 - - + -
73D VAL* 3.8 22.8 - - + +
75D SER* 3.7 20.0 - - - +
78D THR* 3.4 47.6 - - + +
80D VAL* 3.9 14.0 - - + +
163D ASN* 5.4 1.3 - - + -
164D GLU 3.6 12.5 + - - +
165D PRO 3.1 8.1 + - - +
167D VAL* 1.3 83.7 - - + +
169D ALA* 1.3 59.2 + - - +
171D ASN* 3.3 4.1 + - - +
172D GLY* 2.8 25.5 + - - -
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Residues in contact with ALA 169 (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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80D VAL* 3.8 19.3 - - + +
82D VAL* 3.6 5.1 - - - +
102D TYR* 3.6 34.5 - - + -
134D ILE* 3.8 11.1 - - + +
154D CYS* 4.0 6.2 - - - -
165D PRO 2.9 7.5 + - - +
166D ASP 3.0 9.6 + - - +
168D LEU* 1.3 75.1 - - - +
170D ILE* 1.3 66.6 + - - +
172D GLY* 3.0 1.6 + - - -
173D ALA* 2.9 22.7 + - - +
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Residues in contact with ILE 170 (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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130D THR* 5.8 1.1 - - + -
133D ILE* 3.7 26.7 - - + -
134D ILE* 3.7 25.8 - - + +
137D SER* 3.7 28.0 - - - +
138D ILE* 5.0 2.2 - - + +
166D ASP* 3.1 16.6 + - + +
167D VAL* 3.3 12.3 + - + +
169D ALA* 1.3 76.2 - - - +
171D ASN* 1.3 63.7 + - - +
173D ALA* 3.2 11.6 + - - +
174D SER* 3.3 11.8 + - - -
188D VAL* 5.1 5.3 - - + +
190D ALA* 3.6 24.2 - - + -
217D VAL* 3.8 21.3 - - + -
219D ALA* 5.0 0.9 - - + -
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Residues in contact with ASN 171 (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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56D LEU* 4.4 10.9 - - + +
58D ILE* 5.8 1.6 - - + -
73D VAL* 4.1 13.2 - - + -
167D VAL* 3.0 24.5 + - - +
168D LEU* 3.7 7.2 - - - +
169D ALA 3.2 0.2 - - - -
170D ILE* 1.3 77.6 - - - +
172D GLY* 1.3 59.6 + - - +
174D SER* 3.3 6.9 + - - -
175D VAL* 2.9 38.3 + - + +
188D VAL* 4.2 1.1 - - - +
189D GLY* 3.5 3.6 - - - -
190D ALA* 2.8 47.9 + - - +
255D ILE* 3.5 25.5 - - + +
259D ILE* 5.1 0.6 - - + +
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Residues in contact with GLY 172 (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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71D ALA* 4.1 4.4 - - - +
73D VAL* 3.6 19.4 - - - +
80D VAL 5.6 0.4 - - - -
82D VAL* 3.5 21.2 - - - +
168D LEU 2.8 11.6 + - - -
169D ALA 3.0 5.5 + - - -
171D ASN* 1.3 76.1 - - - +
173D ALA* 1.3 51.1 + - - +
175D VAL* 3.4 2.6 + - - +
176D ALA* 2.8 36.4 + - - +
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Residues in contact with ALA 173 (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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82D VAL* 3.5 11.5 - - + +
134D ILE* 3.8 26.5 - - + -
138D ILE* 4.0 14.1 - - + -
152D VAL* 3.9 17.9 - - + -
169D ALA 2.9 8.4 + - - +
170D ILE 3.2 8.7 + - - +
172D GLY* 1.3 73.3 - - - +
174D SER* 1.3 58.3 + - - +
176D ALA* 3.8 1.4 - - - +
177D LEU* 2.9 38.1 + - + +
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Residues in contact with SER 174 (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 ILE* 4.7 2.5 - - - +
170D ILE 3.3 9.3 + - - -
171D ASN* 3.5 9.6 - - - -
173D ALA* 1.3 75.7 - - - +
175D VAL* 1.3 60.5 + - - +
178D SER* 2.8 34.2 + - - -
184D TRP* 3.4 22.7 - - - -
187D PRO* 3.8 1.7 - - - +
188D VAL* 2.7 48.5 + - - -
259D ILE* 3.8 6.1 - - - +
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Residues in contact with VAL 175 (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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58D ILE* 3.5 35.7 - - + -
71D ALA* 3.3 25.1 - - + -
73D VAL* 4.5 3.6 - - + -
171D ASN* 2.9 24.7 + - - +
172D GLY 3.7 0.9 - - - +
174D SER* 1.3 72.2 + - - +
176D ALA* 1.3 66.4 + - - +
178D SER* 3.0 7.0 + - - -
179D LEU* 2.9 41.3 + - + +
259D ILE* 3.8 26.0 - - + -
262D LEU* 3.8 5.6 - - + -
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Residues in contact with ALA 176 (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 GLY* 3.6 18.2 - - - +
70D SER* 4.2 7.0 - - - +
71D ALA* 3.8 7.1 - - - +
82D VAL* 3.6 29.2 - - + +
84D ALA* 4.3 10.5 - - + +
172D GLY 2.8 21.4 + - - +
173D ALA* 3.8 4.3 - - - +
175D VAL* 1.3 74.2 - - - +
177D LEU* 1.3 63.0 + - - +
179D LEU* 3.5 1.3 + - - +
180D SER* 3.1 24.4 + - - -
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Residues in contact with LEU 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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84D ALA* 4.0 21.3 - - + -
138D ILE* 3.9 29.6 - - + -
142D PHE* 3.9 25.8 - - + -
150D THR* 5.4 2.2 - - - +
152D VAL* 4.7 6.1 - - + -
173D ALA 2.9 22.7 + - - +
174D SER 3.9 0.2 - - - +
176D ALA* 1.3 76.7 - - - +
178D SER* 1.3 59.7 + - - +
180D SER* 2.6 21.6 + - - -
182D ILE* 4.0 19.8 - - + +
184D TRP* 3.6 42.3 - - + +
270D LYS* 3.0 13.7 + - - -
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Residues in contact with SER 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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174D SER 2.8 23.9 + - - -
175D VAL 3.0 3.3 + - - -
177D LEU* 1.3 78.3 - - - +
179D LEU* 1.3 60.8 + - - +
184D TRP* 3.5 17.3 - - - -
186D GLY 4.9 0.5 - - - -
187D PRO* 3.9 17.0 - - - +
259D ILE* 4.2 7.0 - - - -
263D VAL* 3.7 25.1 - - - +
268D VAL* 3.3 21.0 - - - +
270D LYS* 3.4 10.1 + - - +
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Residues in contact with LEU 179 (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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60D SER* 3.6 32.8 - - - +
68D ASP 4.9 0.6 - - - +
69D GLY* 5.2 1.1 - - - -
70D SER 4.1 8.5 - - - +
175D VAL* 2.9 34.8 + - + +
176D ALA 4.2 2.9 - - - +
178D SER* 1.3 73.2 - - - +
180D SER* 1.3 66.5 + - - +
259D ILE* 6.4 0.2 - - + -
262D LEU* 3.8 14.4 - - + -
263D VAL* 3.9 28.5 - - + -
266D THR* 3.9 27.2 - - + +
267D GLY 5.2 0.9 - - - +
268D VAL* 3.6 21.2 - - + +
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Residues in contact with SER 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D ASP 3.4 25.6 - - - -
69D GLY* 3.6 5.8 - - - -
84D ALA* 5.0 0.4 - - - -
176D ALA 3.1 16.8 + - - -
177D LEU* 2.6 21.8 + - - -
179D LEU* 1.3 83.1 - - - +
181D ASP* 1.3 58.3 + - - +
182D ILE* 3.1 29.5 + - - +
268D VAL* 3.4 7.6 - - - +
269D THR 5.0 0.2 - - - -
270D LYS* 2.8 19.9 + - - -
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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