Contacts of the helix formed by residues 167 - 186 (chain D) in PDB entry 1JT6
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 ASN 167 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166D GLN* 1.3 73.6 - - + +
168D ILE* 1.3 69.7 + - - +
169D ASN* 2.8 52.2 + - - +
170D GLU* 2.8 29.7 + - + +
171D ARG* 3.0 9.7 + - - +
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Residues in contact with ILE 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D LEU* 4.0 29.4 - - + +
88D THR* 4.4 11.7 - - + -
166D GLN 3.2 4.8 + - - +
167D ASN* 1.3 74.7 - - - +
169D ASN* 1.3 72.0 + - - +
171D ARG* 3.7 30.3 - - + +
172D ILE* 3.1 36.7 + - + +
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Residues in contact with ASN 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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167D ASN* 2.8 25.6 + - - +
168D ILE* 1.3 89.1 - - - +
170D GLU* 1.3 65.3 + - - +
172D ILE* 3.5 10.6 + - - +
173D LYS* 3.0 21.8 + - - +
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Residues in contact with GLU 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166D GLN* 4.1 13.2 + - + +
167D ASN* 2.8 21.8 + - + +
169D ASN* 1.3 76.1 - - - +
171D ARG* 1.3 67.3 + - - +
173D LYS* 3.1 22.9 + - + +
174D LEU* 2.9 54.8 + - - +
639D SO4 4.6 2.8 + - - -
147E ALA* 5.8 0.3 - - - +
150E LYS* 3.5 24.0 + - - -
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Residues in contact with ARG 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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87D LEU* 3.3 45.5 + - + +
159D ILE* 5.1 2.8 - - - +
160D VAL* 3.2 22.6 + - - +
163D THR* 2.4 57.0 + - - +
164D HIS* 3.9 18.2 + - - +
166D GLN* 3.2 35.2 - - + -
167D ASN 3.0 9.9 + - - +
168D ILE* 3.6 23.7 - - + +
169D ASN 3.1 0.2 - - - -
170D GLU* 1.3 78.1 - - - +
172D ILE* 1.3 56.8 + - - +
174D LEU* 3.3 8.0 + - - +
175D MET* 2.8 30.1 + - - +
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Residues in contact with ILE 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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84D GLU* 3.7 27.1 - - + +
87D LEU* 3.8 20.2 - - + -
88D THR* 4.5 12.3 - - + -
168D ILE* 3.1 32.9 + - + +
169D ASN* 4.0 9.9 - - - +
170D GLU 3.3 0.2 - - - -
171D ARG* 1.3 75.3 - - - +
173D LYS* 1.3 63.0 - - - +
175D MET* 3.7 0.8 - - - +
176D ASN* 3.0 37.8 + - - +
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Residues in contact with LYS 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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169D ASN 3.0 15.2 + - - +
170D GLU* 3.1 26.9 + - + +
172D ILE* 1.3 78.4 - - - +
174D LEU* 1.3 62.9 + - - +
176D ASN* 3.2 8.0 + - - +
177D LYS* 3.0 20.6 + - - +
639D SO4 3.0 42.9 + - - +
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Residues in contact with LEU 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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159D ILE* 5.3 8.1 - - + -
163D THR* 5.2 9.9 - - + -
166D GLN* 3.9 17.9 - - - +
170D GLU* 2.9 47.5 + - - +
171D ARG* 3.7 5.8 - - - +
173D LYS* 1.3 71.5 - - - +
175D MET* 1.3 67.0 + - - +
177D LYS* 3.1 1.9 + - - -
178D PHE* 2.9 21.3 + - - +
639D SO4 4.1 3.1 - - - +
147E ALA* 3.8 40.2 - - + +
150E LYS* 4.4 17.7 - - + +
151E ILE* 3.0 23.0 - - + +
154E ASN* 5.7 1.3 - - - +
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Residues in contact with MET 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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83D ASN* 3.4 47.3 - - + +
84D GLU* 4.1 4.0 - - - +
87D LEU* 3.5 18.8 - - + -
156D VAL* 3.6 15.7 - - + -
159D ILE* 3.8 33.6 - - + +
160D VAL* 3.5 27.4 - - + -
171D ARG 2.8 17.6 + - - +
172D ILE* 3.7 4.3 - - - +
174D LEU* 1.3 77.7 - - - +
176D ASN* 1.3 60.0 + - - +
178D PHE* 3.4 13.2 + - - +
179D SER* 2.9 31.2 + - - -
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Residues in contact with ASN 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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80D TYR* 3.8 27.7 + - + -
84D GLU* 3.1 45.6 + - - +
172D ILE* 3.0 25.1 + - - +
173D LYS* 3.7 4.8 - - - +
175D MET* 1.3 79.1 + - - +
177D LYS* 1.3 66.6 + - - +
179D SER* 4.3 3.7 + - - +
180D GLN* 2.9 23.7 + - - +
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Residues in contact with LYS 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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173D LYS 3.0 12.6 + - - +
174D LEU 3.1 1.7 + - - +
176D ASN* 1.3 76.5 - - - +
178D PHE* 1.3 58.9 + - - +
180D GLN* 3.2 29.5 + - - +
181D ILE* 2.9 55.4 + - + +
639D SO4 4.1 25.8 + - - +
143E ASN* 2.9 43.4 + - - +
147E ALA* 5.6 0.4 - - + -
148E VAL* 4.7 7.6 - - + +
151E ILE* 3.5 17.5 - - + -
186E LEU* 6.4 0.2 - - - -
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Residues in contact with PHE 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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79D PHE* 4.8 2.9 - + - -
83D ASN* 4.4 4.0 - - - -
152D ALA* 5.1 1.3 - - - -
155D ALA* 3.6 29.2 - - + -
156D VAL* 3.7 24.2 - - + -
159D ILE* 4.6 9.6 - - + -
174D LEU 2.9 15.3 + - - +
175D MET* 3.6 17.5 - - - +
177D LYS* 1.3 75.3 - - - +
179D SER* 1.3 74.9 + - - +
180D GLN 3.1 0.3 + - - -
181D ILE* 3.2 4.9 + - - +
182D PHE* 3.0 56.1 + + + +
151E ILE* 3.5 32.9 - - + +
155E ALA* 4.3 6.1 - - + -
178E PHE* 4.3 12.1 - + - -
182E PHE* 4.3 9.4 - + - -
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Residues in contact with SER 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D PHE* 4.1 11.7 - - - -
80D TYR* 3.9 26.6 + - - -
83D ASN* 2.7 33.4 + - - +
175D MET 2.9 19.6 + - - -
176D ASN* 3.8 5.3 + - - -
178D PHE* 1.3 81.2 - - - +
180D GLN* 1.3 62.5 + - - +
182D PHE* 3.9 0.3 - - - +
183D LEU* 3.2 29.5 + - - +
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Residues in contact with GLN 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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76D ARG* 4.5 6.7 + - - +
80D TYR* 3.2 24.2 + - + +
176D ASN 2.9 15.9 + - - +
177D LYS* 3.2 31.5 - - - +
178D PHE 3.1 0.2 - - - -
179D SER* 1.3 75.2 - - - +
181D ILE* 1.3 67.0 + - - +
183D LEU* 3.2 3.7 + - - +
184D ASN* 2.9 43.7 + - - +
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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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177D LYS* 2.9 42.0 + - + +
178D PHE* 3.7 6.1 - - - +
180D GLN* 1.3 75.8 - - - +
182D PHE* 1.3 66.9 + - - +
184D ASN* 3.1 3.0 + - - +
185D GLY* 2.8 19.9 + - - -
148E VAL* 4.2 12.3 - - + -
151E ILE* 5.0 3.4 - - + -
181E ILE 4.3 0.3 - - - +
182E PHE* 3.4 58.3 - - + +
185E GLY* 3.2 20.2 - - - +
186E LEU* 3.8 26.5 - - + -
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Residues in contact with PHE 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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79D PHE* 3.4 30.1 - + + -
131D PHE* 3.9 20.2 - + - -
148D VAL* 4.3 8.3 - - + -
151D ILE* 4.1 19.5 - - + -
152D ALA* 4.1 15.0 - - + -
178D PHE* 3.0 42.5 + + + +
179D SER 3.9 3.6 - - - +
181D ILE* 1.3 79.6 - - - +
183D LEU* 1.3 66.1 + - + +
185D GLY* 3.0 12.3 + - - -
186D LEU* 3.4 14.0 + - + +
178E PHE* 4.5 10.3 - + - -
181E ILE* 3.5 47.4 - - + +
182E PHE* 5.5 4.0 - + - +
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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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76D ARG* 3.7 34.1 - - + +
79D PHE* 3.5 34.3 - - + -
80D TYR* 3.5 30.7 - - + +
131D PHE* 4.7 2.5 - - + -
140D TRP* 3.9 25.8 - - + -
179D SER 3.2 12.2 + - - +
180D GLN* 3.9 2.9 - - - +
182D PHE* 1.3 76.2 - - + +
184D ASN* 1.3 65.1 + - - +
186D LEU* 3.0 33.9 + - + +
187D SER 4.7 0.2 + - - -
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Residues in contact with ASN 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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76D ARG* 5.0 8.7 + - - +
180D GLN* 2.9 42.6 + - - +
181D ILE 3.6 6.1 - - - +
183D LEU* 1.3 79.0 - - - +
185D GLY* 1.3 62.0 + - - +
186D LEU 3.1 1.4 + - - -
187D SER* 3.8 8.7 + - - -
184E ASN* 4.3 7.0 - - - +
185E GLY* 3.8 21.1 + - - +
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Residues in contact with GLY 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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181D ILE 2.8 10.1 + - - -
182D PHE 3.0 5.1 + - - -
184D ASN* 1.3 76.7 - - - +
186D LEU* 1.3 59.0 + - - +
187D SER 3.4 1.0 + - - -
181E ILE* 3.0 38.9 - - - +
184E ASN* 3.4 19.0 - - - +
185E GLY* 3.5 10.0 - - - -
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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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131D PHE* 3.6 20.2 - - + -
140D TRP* 4.4 16.6 - - + -
141D SER 4.0 14.4 + - - +
142D ILE* 3.5 36.3 - - + -
148D VAL* 4.5 10.8 - - + -
182D PHE* 3.7 13.0 - - + +
183D LEU* 3.0 28.4 + - + +
185D GLY* 1.3 77.4 - - - +
187D SER* 1.3 67.0 + - - +
177E LYS* 6.3 0.4 - - - -
181E ILE* 4.1 30.5 - - + -
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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