Contacts of the helix formed by residues 156 - 170 (chain D) in PDB entry 5U03
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 156 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41D PRO* 4.7 6.7 - - - -
147D LEU* 4.9 11.0 - - - -
148D GLY 4.2 18.2 - - - -
149D GLY* 5.1 0.7 - - - -
150D THR 3.8 15.1 + - - -
151D VAL* 5.3 1.0 - - - -
152D GLY 5.1 0.9 + - - -
153D ASP* 2.9 21.6 + - - -
154D ILE 3.0 0.2 - - - -
155D GLU* 1.3 79.4 - - - +
157D MET* 1.3 63.2 + - - +
158D PRO* 3.3 3.6 - - - -
159D PHE* 2.9 25.6 + - - +
160D ILE* 3.1 18.4 + - - +
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Residues in contact with MET 157 (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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154B ILE* 4.3 16.8 - - + -
157B MET* 5.7 5.2 - - - +
152D GLY* 3.7 28.3 - - - +
153D ASP 3.5 9.4 - - - +
154D ILE* 3.1 30.9 + - + +
156D SER* 1.3 76.6 + - - +
158D PRO* 1.3 71.4 - - + +
160D ILE* 2.9 23.9 + - + +
161D GLU* 3.2 11.4 + - - +
207D LEU* 5.7 13.2 - - + -
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Residues in contact with PRO 158 (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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154B ILE* 5.1 7.6 - - + -
90D THR* 6.4 0.7 - - + -
113D VAL* 4.1 32.1 - - + -
117D ILE* 4.8 6.5 - - + -
118D THR* 3.5 12.9 - - + +
121D ILE* 3.7 14.8 - - + +
154D ILE 3.4 11.2 - - - +
155D GLU 4.0 7.9 - - - +
156D SER 3.3 4.3 - - - -
157D MET* 1.3 97.7 - - + +
159D PHE* 1.3 60.4 + - + +
161D GLU* 3.5 2.7 + - + +
162D ALA* 3.1 21.1 + - - +
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Residues in contact with PHE 159 (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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39D ILE* 3.5 38.6 - - + -
40D ASP 5.4 0.4 - - - -
41D PRO* 5.0 4.3 - - + -
88D LEU* 6.3 2.2 - - + -
89D THR 5.7 0.7 - - - -
90D THR* 3.8 31.0 - - + -
93D ILE* 3.9 17.3 - - + -
121D ILE* 3.6 38.1 - - + -
147D LEU* 4.0 14.4 - - + -
155D GLU 3.9 8.1 - - - -
156D SER* 2.9 23.2 + - - +
158D PRO* 1.3 80.2 - - + +
160D ILE* 1.3 66.9 + - - +
161D GLU 3.1 0.7 - - - -
162D ALA* 3.6 4.4 - - - +
163D PHE* 2.8 44.4 + + + -
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Residues in contact with ILE 160 (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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7D THR* 5.4 3.4 - - + -
147D LEU* 4.4 19.7 - - + -
151D VAL* 5.5 6.7 - - + -
156D SER* 3.1 19.8 + - - +
157D MET* 2.9 16.7 + - + +
159D PHE* 1.3 77.5 - - - +
161D GLU* 1.3 57.7 + - - +
163D PHE* 3.8 2.1 - - - +
164D ARG* 2.8 28.0 + - + +
204D LEU* 4.7 5.4 - - + -
207D LEU* 3.8 50.9 - - + +
209D LEU* 3.8 29.3 - - + +
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Residues in contact with GLU 161 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205A ARG* 5.8 0.3 + - - -
235A HIS* 4.1 11.3 + - - -
113D VAL* 5.8 0.9 - - + -
114D VAL* 3.8 30.5 - - + +
118D THR* 3.8 9.2 - - + +
157D MET 3.2 7.7 + - - +
158D PRO* 3.8 8.7 - - + +
159D PHE 3.1 0.2 - - - -
160D ILE* 1.3 77.0 - - - +
162D ALA* 1.3 69.2 + - - +
164D ARG* 2.7 54.2 + - - +
165D GLN* 3.1 13.9 + - + +
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Residues in contact with ALA 162 (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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118D THR* 3.8 25.1 - - - +
121D ILE* 3.6 32.8 - - + -
122D GLN* 3.0 17.9 + - + +
158D PRO 3.1 13.3 + - - +
159D PHE 3.2 7.2 + - - +
161D GLU* 1.3 80.5 - - - +
163D PHE* 1.3 59.4 + - + +
165D GLN* 3.5 0.6 + - - -
166D PHE* 2.9 24.6 + - - +
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Residues in contact with PHE 163 (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 LEU* 3.6 42.0 - - + -
39D ILE* 3.7 26.7 - - + -
121D ILE* 5.1 5.4 - - + -
125D VAL* 4.3 16.8 - - + -
145D ILE* 3.9 21.3 - - + -
147D LEU* 4.3 7.4 - - + -
159D PHE* 2.8 42.6 + + + +
160D ILE* 4.0 4.5 - - - +
162D ALA* 1.3 76.5 - - + +
164D ARG* 1.3 66.6 + - - +
166D PHE* 3.7 13.5 - + + -
167D GLN* 2.9 27.4 + - - +
175D PHE* 4.1 21.1 - + + -
209D LEU* 4.5 5.4 - - + -
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Residues in contact with ARG 164 (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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205A ARG* 4.0 29.6 - - - +
235A HIS* 3.7 12.7 + - - -
160D ILE* 2.8 20.9 + - + +
161D GLU* 2.7 44.8 + - - +
163D PHE* 1.3 77.0 - - - +
165D GLN* 1.3 89.7 + - - +
167D GLN* 3.1 8.7 + - - +
168D PHE* 3.0 47.0 - - + -
207D LEU 4.1 17.3 - - - +
208D GLY* 4.0 21.8 - - - +
209D LEU* 3.6 14.6 - - + -
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Residues in contact with GLN 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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205A ARG* 4.8 0.2 + - - -
235A HIS* 3.3 41.6 - - + +
122D GLN* 4.0 5.4 - - - +
161D GLU* 3.1 11.8 + - + +
162D ALA* 4.0 3.1 - - - +
164D ARG* 1.3 114.8 + - - +
166D PHE* 1.3 55.7 + - - +
168D PHE* 2.8 41.5 + - - +
169D LYS* 3.1 34.1 + - - +
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Residues in contact with PHE 166 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3D TYR* 3.7 47.6 - + + -
122D GLN* 3.5 36.3 - - + +
125D VAL* 3.8 20.6 - - + -
126D MET* 4.8 9.4 - - + -
162D ALA 2.9 20.1 + - - +
163D PHE* 3.2 17.7 + + + +
165D GLN* 1.3 76.7 - - - +
167D GLN* 1.3 58.8 + - - +
169D LYS* 2.8 29.0 + - + +
170D VAL* 2.9 33.2 + - + +
175D PHE* 4.1 15.9 - + - -
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Residues in contact with GLN 167 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163D PHE 2.9 11.4 + - - +
164D ARG* 3.1 22.4 + - - +
166D PHE* 1.3 75.9 - - - +
168D PHE* 1.3 84.0 + - + +
170D VAL* 2.9 27.8 - - - +
171D LYS 4.0 6.2 - - - +
172D ARG* 4.6 2.9 + - - -
175D PHE* 3.5 40.3 - - + +
177D ASN* 5.4 4.0 + - - +
208D GLY 4.0 7.1 + - - -
209D LEU* 3.5 28.2 - - - +
210D SER 5.5 3.5 + - - +
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Residues in contact with PHE 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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164D ARG* 3.0 47.6 - - + -
165D GLN* 2.8 24.2 + - - +
167D GLN* 1.3 101.4 - - + +
169D LYS* 1.3 62.7 + - - +
170D VAL 3.2 8.3 - - - +
208D GLY 5.5 2.5 - - - -
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Residues in contact with LYS 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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235A HIS* 6.2 0.9 - - - -
119D ASP* 4.1 12.1 + - - -
122D GLN* 2.7 40.4 + - - +
165D GLN* 3.1 27.3 + - - +
166D PHE* 2.8 13.1 + - + +
168D PHE* 1.3 78.0 - - - +
170D VAL* 1.3 63.8 + - + +
171D LYS* 5.5 3.3 + - - +
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Residues in contact with VAL 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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3D TYR* 3.9 11.9 - - + -
126D MET* 6.2 0.9 - - - -
166D PHE* 2.9 51.8 + - + +
167D GLN* 2.9 29.3 - - - +
168D PHE* 3.2 11.1 - - - +
169D LYS* 1.3 80.0 - - + +
171D LYS* 1.3 72.6 + - - +
172D ARG 3.9 0.2 + - - -
174D ASN* 4.2 15.0 - - + +
175D PHE* 3.9 12.6 - - + -
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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