Contacts of the helix formed by residues 165 - 178 (chain D) in PDB entry 1J0B
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 LEU 165 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9D LEU* 3.9 11.7 - - + +
12D PHE* 4.1 25.1 - - + -
60D TYR* 3.4 22.0 + - + -
161D PRO 4.0 11.7 - - - +
162D ILE* 3.6 26.2 - - + +
163D GLY 2.9 0.4 - - - -
164D THR* 1.3 81.6 - - + +
166D GLY* 1.3 63.7 + - - +
167D TYR 3.2 1.1 - - - -
168D VAL* 3.5 21.8 - - + +
169D ARG* 3.2 17.5 + - - +
200D LEU* 4.3 6.5 - - + -
234D ALA 4.4 6.1 - - - +
237D LEU* 5.1 3.4 - - + -
238D LEU* 3.9 37.5 - - + -
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Residues in contact with GLY 166 (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 ARG* 3.4 38.6 + - - +
57D LYS* 4.4 0.2 - - - -
60D TYR* 3.9 8.2 - - - -
163D GLY 3.0 13.2 + - - -
165D LEU* 1.3 80.6 - - - +
167D TYR* 1.3 62.4 + - - +
168D VAL 3.2 0.2 - - - -
169D ARG* 3.6 5.2 + - - +
170D ALA* 3.3 19.6 + - - +
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Residues in contact with TYR 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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41D LYS* 6.3 0.2 - - - -
43D ASP* 2.4 36.5 + - - +
53D ASN* 3.1 52.4 - - + +
56D ARG* 3.2 18.3 - - + +
57D LYS* 4.9 6.7 - - + -
163D GLY 4.7 0.2 + - - -
164D THR 3.7 3.6 + - - +
166D GLY* 1.3 76.8 - - - +
168D VAL* 1.3 59.5 + - - +
169D ARG 3.3 0.4 - - - -
170D ALA* 3.4 16.6 - - + -
171D VAL* 3.3 21.9 + - + +
194D THR* 3.6 46.0 - - + +
197D GLY* 3.1 16.2 - - - +
198D LEU* 3.8 5.6 + - + +
306D ILE* 4.0 27.4 - - + -
308D THR* 4.0 0.4 - - + +
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Residues in contact with VAL 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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5D ILE* 3.2 14.6 - - + +
9D LEU* 4.1 22.0 - - + -
164D THR* 3.2 19.7 - - + +
165D LEU* 3.2 24.1 + - + +
167D TYR* 1.3 78.4 - - - +
169D ARG* 1.3 63.8 + - - +
171D VAL* 2.9 24.0 - - - +
197D GLY* 3.1 22.4 - - - +
200D LEU* 3.9 11.9 - - + -
201D GLY* 4.3 13.2 - - - -
204D ILE* 4.6 3.8 - - + -
238D LEU* 4.1 12.8 - - + -
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Residues in contact with ARG 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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1D MET* 4.1 29.5 - - - +
5D ILE* 4.2 3.6 - - - -
6D PHE* 5.3 11.9 + - - +
9D LEU* 4.0 23.6 + - + +
14D ARG* 2.9 49.3 - - - +
56D ARG* 5.6 5.6 - - - +
59D GLU* 4.3 7.9 - - - -
60D TYR* 3.6 23.0 + - + +
165D LEU 3.2 15.6 + - - +
166D GLY 3.7 5.4 - - - +
168D VAL* 1.3 77.3 - - - +
170D ALA* 1.3 58.0 - - - +
172D GLY* 3.3 2.6 + - - -
173D GLU* 2.9 28.1 + - + +
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Residues in contact with ALA 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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41D LYS* 4.9 2.6 - - - -
43D ASP* 4.9 0.4 - - - +
56D ARG* 3.9 17.9 - - - +
166D GLY 3.3 6.2 + - - +
167D TYR* 3.4 44.9 - - + -
169D ARG* 1.3 77.4 - - - +
171D VAL* 1.3 62.9 + - + +
173D GLU* 2.9 9.6 + - - +
174D ILE* 2.7 35.5 + - + +
306D ILE* 6.0 0.2 - - + -
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Residues in contact with VAL 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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5D ILE* 4.1 3.8 - - + -
167D TYR* 3.3 12.5 + - + +
168D VAL 2.9 22.0 - - - +
170D ALA* 1.3 76.1 - - + +
172D GLY* 1.3 65.5 + - - +
174D ILE* 2.9 16.6 + - + +
175D ALA* 2.7 35.0 + - - +
198D LEU* 3.3 43.1 - - + +
201D GLY* 3.4 30.3 - - - +
202D LEU* 4.3 7.0 - - + +
205D LEU* 4.2 9.8 - - + +
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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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1D MET* 3.5 26.2 - - - -
2D HIS 3.4 17.3 + - - -
5D ILE* 3.9 13.5 - - - -
168D VAL 3.6 0.4 + - - -
169D ARG 3.3 2.6 + - - -
170D ALA 3.1 0.8 - - - -
171D VAL* 1.3 81.8 - - - +
173D GLU* 1.3 64.6 + - - +
174D ILE 3.4 0.2 + - - -
175D ALA* 3.6 7.2 + - - +
176D THR* 3.4 14.9 + - - -
205D LEU* 4.9 0.4 - - - -
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Residues in contact with GLU 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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1D MET* 4.2 10.2 - - - +
18D ILE* 5.9 0.2 - - - +
20D TRP 4.3 3.1 - - - +
21D GLU* 3.4 46.6 - - + +
22D THR 3.3 6.4 + - - -
41D LYS* 3.1 15.1 + - - -
56D ARG* 3.0 33.2 + - - -
169D ARG* 2.9 13.7 + - + +
170D ALA* 2.9 10.8 + - - +
172D GLY* 1.3 73.7 - - - +
174D ILE* 1.3 70.1 + - - +
176D THR* 3.4 1.9 + - - -
177D GLN* 3.0 24.0 + - - +
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Residues in contact with ILE 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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24D ILE* 4.7 2.0 - - + -
41D LYS* 3.7 25.6 - - + -
170D ALA* 2.7 16.1 + - + +
171D VAL* 2.9 26.7 + - + +
173D GLU* 1.3 77.7 - - - +
175D ALA* 1.3 58.4 + - - +
176D THR 2.5 15.2 + - - -
177D GLN* 2.9 16.5 + - - +
178D SER* 2.9 15.0 + - - -
182D PHE* 4.4 16.6 - - + -
185D ILE* 4.1 17.5 - - + -
202D LEU* 6.5 0.4 - - + -
304D LEU* 3.9 29.2 - - + -
306D ILE* 4.3 14.4 - - + -
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Residues in contact with ALA 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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2D HIS* 4.2 21.5 - - + -
171D VAL 2.7 16.3 + - - +
172D GLY 3.7 7.2 - - - +
174D ILE* 1.3 75.3 - - - +
176D THR* 1.3 61.0 + - - +
178D SER* 4.0 12.6 - - - +
205D LEU* 4.1 20.4 - - + -
207D GLU* 5.8 3.6 - - - +
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Residues in contact with THR 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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1D MET 3.0 31.5 + - - +
2D HIS* 3.5 14.7 + - - -
21D GLU* 4.9 5.2 - - - +
172D GLY 3.4 0.8 + - - -
173D GLU 3.4 3.9 + - - -
174D ILE 2.5 5.5 + - - -
175D ALA* 1.3 72.5 - - - +
177D GLN* 1.3 68.5 + - - +
178D SER 3.0 10.2 + - - +
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Residues in contact with GLN 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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21D GLU* 4.3 22.9 + - - +
22D THR 2.6 25.1 - - - +
23D PRO* 4.2 3.3 - - - +
24D ILE* 3.5 21.4 + - + +
41D LYS* 2.5 36.0 + - - +
173D GLU* 3.0 17.3 + - - +
174D ILE* 2.9 25.4 + - - +
176D THR* 1.3 76.9 - - - +
178D SER* 1.3 65.1 + - - +
179D GLU* 3.7 13.9 + - - +
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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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24D ILE* 4.5 8.9 - - - +
174D ILE* 2.9 22.4 + - - -
175D ALA* 4.0 10.5 - - - +
176D THR 3.0 9.2 - - - +
177D GLN* 1.3 80.9 - - - +
179D GLU* 1.3 63.2 + - - +
180D VAL* 3.1 14.8 + - - +
182D PHE* 3.0 35.8 - - - -
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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