Contacts of the helix formed by residues 152 - 170 (chain B) in PDB entry 4U1D
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 THR 152 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B ILE* 1.3 78.5 - - - +
153B SER* 1.3 58.9 + - - +
155B LEU* 3.0 12.1 + - - +
156B ARG* 2.8 29.2 + - + +
195B ARG* 5.2 10.5 - - - +
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Residues in contact with SER 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B LYS* 2.7 31.4 + - - -
151B ILE 3.3 3.6 - - - +
152B THR* 1.3 79.8 - - - +
154B TRP* 1.3 58.1 + - - +
156B ARG* 4.1 7.5 - - - +
157B PHE* 2.9 27.6 + - - +
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Residues in contact with TRP 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B VAL 3.7 15.0 - - - -
61B GLU 4.4 8.5 - - - -
63B LYS* 3.4 43.5 - - + +
100B VAL 5.9 0.2 - - - -
103B LYS* 3.5 49.1 - - + -
104B ILE* 3.7 13.9 - - + +
107B GLU* 3.7 36.0 + - + -
151B ILE* 3.3 25.6 + - - +
152B THR 3.0 0.6 - - - -
153B SER* 1.3 78.1 - - - +
155B LEU* 1.3 59.8 + - - +
157B PHE* 3.5 19.0 - + - +
158B THR* 2.8 33.4 + - - -
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Residues in contact with LEU 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B ILE* 3.7 22.4 - - + -
108B GLN* 4.7 8.5 - - - +
151B ILE* 3.2 15.4 + - + +
152B THR* 3.0 12.4 + - - +
154B TRP* 1.3 73.1 - - - +
156B ARG* 1.3 61.1 + - - +
158B THR* 3.1 5.0 + - - -
159B TRP* 2.9 27.7 + - - +
189B PHE* 3.8 14.9 - - + -
193B TYR* 3.6 38.8 - - + +
195B ARG* 3.2 39.9 - - - +
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Residues in contact with ARG 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B THR* 2.8 21.2 + - + +
153B SER* 4.1 8.3 - - - +
155B LEU* 1.3 73.5 - - - +
157B PHE* 1.3 56.8 + - - +
159B TRP* 3.3 7.7 + - - +
160B GLU* 2.9 57.2 + - + +
195B ARG* 3.7 11.2 - - - +
198B GLU* 2.8 31.3 + - - -
201B ARG* 3.4 22.8 - - - +
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Residues in contact with PHE 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B VAL* 4.3 21.1 - - + -
63B LYS* 3.6 51.6 - - + -
65B GLY* 3.8 16.8 - - - -
68B LEU* 4.1 19.7 - - + -
96B PHE* 4.7 0.4 - + - -
100B VAL* 3.9 21.3 - - + -
153B SER 2.9 21.9 + - - +
154B TRP* 3.5 20.6 - + + +
156B ARG* 1.3 76.2 - - - +
158B THR* 1.3 57.4 + - - +
160B GLU* 3.4 7.3 + - + +
161B SER* 2.8 47.5 + - - -
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Residues in contact with THR 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B VAL* 3.3 27.8 - - + +
101B GLU* 5.5 1.6 - - + +
104B ILE* 3.0 26.7 - - + +
154B TRP* 2.8 16.3 + - - -
155B LEU 3.1 8.7 + - - -
157B PHE* 1.3 75.0 - - - +
159B TRP* 1.3 65.6 + - - +
161B SER* 3.1 3.3 + - - -
162B TYR* 2.9 51.8 + - + +
189B PHE* 3.9 13.7 - - + -
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Residues in contact with TRP 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B LEU 2.9 12.4 + - - +
156B ARG* 3.7 13.7 - - - +
158B THR* 1.3 75.5 - - - +
160B GLU* 1.3 81.0 + - + +
161B SER 3.1 0.3 + - - -
162B TYR* 3.2 6.8 + - + +
163B ARG* 2.9 50.5 + - + +
186B THR* 3.7 28.0 - - + -
189B PHE* 4.1 16.8 - + + -
190B CYS* 4.1 6.1 - - - -
198B GLU* 3.2 70.7 - - + +
201B ARG* 4.0 19.6 - - + +
202B LEU* 3.6 25.6 - - + -
205B MET* 5.0 5.2 - - + -
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Residues in contact with GLU 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B LYS* 3.0 34.6 + - - +
156B ARG* 2.9 53.7 + - + +
157B PHE* 3.7 8.3 - - + +
159B TRP* 1.3 86.8 + - + +
161B SER* 1.3 57.3 + - - +
163B ARG* 3.5 19.8 + - - +
164B ALA* 3.0 29.5 + - - +
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Residues in contact with SER 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B GLY* 6.1 0.2 - - - -
69B LYS* 5.5 1.1 - - - +
96B PHE* 3.3 31.2 - - - -
97B ILE* 4.3 3.1 - - - -
100B VAL* 4.1 17.7 - - - -
157B PHE* 2.8 33.5 + - - -
158B THR 3.3 9.6 - - - -
159B TRP 3.1 0.2 - - - -
160B GLU* 1.3 74.7 - - - +
162B TYR* 1.3 65.3 + - - +
164B ALA* 3.2 4.0 + - - +
165B VAL* 3.0 28.8 + - - +
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Residues in contact with TYR 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B ILE* 3.4 37.5 - - + -
100B VAL* 6.0 0.9 - - + -
101B GLU* 3.1 33.7 + - + +
158B THR* 2.9 43.3 + - + +
159B TRP* 3.5 7.2 - - + +
161B SER* 1.3 74.9 - - - +
163B ARG* 1.3 63.8 + - - +
165B VAL* 3.3 2.3 + - - +
166B LEU* 2.9 30.2 + - - +
182B VAL* 4.0 4.9 - - + +
185B LYS* 3.9 24.5 + - + -
186B THR* 3.4 33.2 - - + +
189B PHE* 3.7 32.2 - + + +
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Residues in contact with ARG 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B LYS* 5.0 5.9 - - - +
159B TRP* 2.9 42.1 + - + +
160B GLU* 3.5 25.7 + - - +
162B TYR* 1.3 76.7 - - - +
164B ALA* 1.3 58.0 + - - +
166B LEU* 3.2 4.2 + - - +
167B ASP* 3.0 40.9 + - - +
201B ARG* 6.2 0.2 - - - +
205B MET* 4.1 27.2 - - + -
463C TRP* 6.1 1.2 - - - +
464C ASP* 4.6 16.6 + - - -
467C LYS* 4.0 16.9 - - - +
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Residues in contact with ALA 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B LYS* 3.6 39.9 - - + +
72B LEU* 6.6 0.2 - - + -
73B HIS* 4.4 7.3 - - + -
96B PHE* 5.0 6.3 - - + -
160B GLU 3.0 18.1 + - - +
161B SER* 3.2 5.8 + - - +
163B ARG* 1.3 79.2 - - - +
165B VAL* 1.3 56.9 + - - +
167B ASP* 3.4 8.4 + - - +
168B LEU* 2.9 28.7 + - - +
463C TRP* 6.2 0.9 - - - +
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Residues in contact with VAL 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B LEU* 5.1 3.4 - - + -
93B ALA* 4.1 18.4 - - + +
96B PHE* 3.5 29.2 - - + -
97B ILE* 3.9 18.2 - - + -
161B SER 3.0 19.0 + - - +
162B TYR 3.7 3.4 - - - +
164B ALA* 1.3 75.7 - - - +
166B LEU* 1.3 57.6 + - - +
168B LEU* 3.1 8.6 + - + +
169B LEU* 2.9 41.0 + - + +
182B VAL* 3.9 29.8 - - + -
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Residues in contact with LEU 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B TYR 2.9 16.8 + - - +
163B ARG 3.2 8.0 + - - +
165B VAL* 1.3 77.4 - - - +
167B ASP* 1.3 56.9 + - - +
168B LEU 3.1 0.2 - - - -
169B LEU* 5.9 0.4 - - + -
170B ARG* 3.1 25.3 + - - +
179B TYR* 3.4 27.4 - - + +
182B VAL* 3.9 23.1 - - + -
183B VAL* 3.6 30.1 - - + -
186B THR* 3.7 18.2 - - + +
202B LEU* 3.7 17.9 - - + -
205B MET* 3.5 29.6 - - + -
206B LEU* 4.7 2.2 - - + -
209B HIS* 3.6 4.4 - - + -
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Residues in contact with ASP 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B HIS* 4.1 7.7 + - + -
163B ARG* 3.0 30.2 + - - +
164B ALA* 3.7 6.7 - - - +
166B LEU* 1.3 75.0 - - - +
168B LEU* 1.3 57.7 + - - +
170B ARG* 3.1 36.6 + - - +
205B MET* 3.7 11.6 - - - +
209B HIS* 2.8 30.5 + - - -
463C TRP* 5.3 12.6 - - + +
464C ASP* 4.4 4.3 - - - +
467C LYS* 2.7 34.4 + - - +
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Residues in contact with LEU 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B LEU* 3.8 33.9 - - + +
73B HIS* 3.6 48.2 - - + +
76B LYS* 3.7 44.4 + - + -
89B VAL* 4.9 8.1 - - + +
92B VAL* 6.1 0.9 - - + -
93B ALA* 4.9 7.0 - - + -
164B ALA 2.9 15.3 + - - +
165B VAL* 3.4 10.1 - - - +
166B LEU 3.1 0.2 - - - -
167B ASP* 1.3 80.3 - - - +
169B LEU* 1.3 73.9 + - + +
170B ARG* 3.3 5.8 + - - +
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Residues in contact with LEU 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B VAL* 4.7 11.4 - - + -
90B GLY* 5.2 0.7 - - - -
93B ALA* 3.7 21.5 - - + -
165B VAL* 2.9 33.3 + - + +
168B LEU* 1.3 91.4 - - + +
170B ARG* 1.3 66.1 + - - +
171B ASN 3.4 1.6 + - - -
172B ASN* 3.8 8.5 + - - +
175B LEU* 4.0 30.5 - - + +
178B THR* 3.6 22.2 - - + +
179B TYR* 3.6 47.8 - - + +
182B VAL* 4.3 1.8 - - + -
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Residues in contact with ARG 170 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B HIS* 5.5 0.4 + - - -
166B LEU 3.1 15.3 + - - +
167B ASP* 3.1 28.2 + - - +
168B LEU 3.3 3.1 - - - +
169B LEU* 1.3 79.4 - - - +
171B ASN* 1.3 74.9 + - - +
172B ASN* 3.4 2.8 + - - +
179B TYR* 3.8 8.5 - - - -
209B HIS* 3.6 36.4 + - + +
463C TRP* 3.3 31.2 + - - +
466C GLU* 4.5 13.7 + - - +
467C LYS* 3.1 49.7 - - - +
470C LEU* 6.4 2.0 - - - -
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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
------------------------------------------------------------
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