Contacts of the helix formed by residues 157 - 171 (chain B) in PDB entry 5UQ3
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 PHE 157 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A GLU* 3.0 37.7 - - + -
142B TYR* 5.5 7.0 - + - -
145B PHE* 3.5 40.6 - + + -
149B LEU* 3.7 8.1 - - - -
153B TRP* 2.6 24.0 + + + +
154B ARG 2.9 28.7 - - - -
155B LYS* 4.8 1.3 - - + -
156B LEU* 1.3 73.7 - - - +
158B PRO* 1.4 80.4 - - + +
160B PHE* 3.0 6.3 + - - +
161B LEU* 2.9 40.4 + - + +
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Residues in contact with PRO 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A GLU* 3.7 33.0 - - + -
43A GLY 4.9 2.4 + - - -
155B LYS* 3.1 23.1 - - + +
156B LEU 3.5 0.7 - - - -
157B PHE* 1.4 112.3 - - + +
159B ASN* 1.3 58.3 + - + +
160B PHE 3.0 0.2 - - - -
161B LEU* 2.9 25.6 + - + +
162B LYS* 2.9 13.7 + - - +
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Residues in contact with ASN 159 (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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149B LEU* 5.5 0.9 - - - +
156B LEU* 2.6 50.4 - - - +
158B PRO* 1.3 79.9 - - + +
160B PHE* 1.3 58.5 + - - +
162B LYS* 3.1 44.2 - - - +
163B LEU* 3.1 21.9 - - - +
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Residues in contact with PHE 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B ILE* 3.7 28.9 - - + -
124B PHE* 4.0 12.1 - - + -
125B ILE* 3.1 49.6 - - + +
128B TYR* 4.0 18.6 - + + -
144B ILE* 4.9 2.9 - - + -
145B PHE* 3.5 35.0 - + - -
148B ALA* 4.2 14.8 - - + -
149B LEU* 3.9 28.9 - - + -
156B LEU 4.0 0.7 - - - +
157B PHE 3.0 13.7 - - - +
158B PRO 3.0 0.2 - - - -
159B ASN* 1.3 81.3 + - - +
161B LEU* 1.3 63.1 + - + +
162B LYS 3.3 0.2 - - - -
163B LEU* 3.0 8.3 + - - +
164B ARG 2.9 22.9 + - - -
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Residues in contact with LEU 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A GLU* 4.3 6.1 - - - +
43A GLY* 3.8 27.6 - - - -
128B TYR* 3.6 40.4 - - + +
142B TYR* 6.4 0.9 - - + -
145B PHE* 4.1 9.4 - - + -
157B PHE* 2.9 41.5 + - + +
158B PRO* 2.9 11.1 + - + +
160B PHE* 1.3 79.0 - - + +
162B LYS* 1.3 56.7 + - - +
164B ARG* 3.0 20.1 + - - +
165B ASP* 2.9 32.8 + - - +
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Residues in contact with LYS 162 (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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43A GLY* 5.3 2.6 - - - +
71A HIS* 4.9 6.0 - - + -
158B PRO 2.9 9.1 + - - +
159B ASN* 3.1 45.4 + - + +
161B LEU* 1.3 76.1 - - - +
163B LEU* 1.3 67.3 + - - +
165B ASP* 3.3 14.5 + - - +
166B GLN* 2.9 53.1 + - - +
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Residues in contact with LEU 163 (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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121B ILE* 4.4 26.7 - - + -
125B ILE* 3.8 10.9 - - + +
149B LEU* 6.5 0.4 - - + -
159B ASN* 3.1 23.8 - - - +
160B PHE* 3.0 14.2 + - - +
162B LYS* 1.3 94.9 - - - +
164B ARG* 1.3 59.1 + - - +
166B GLN* 3.2 21.0 + - + +
167B LEU* 2.9 28.6 + - - +
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Residues in contact with ARG 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A GLY* 4.7 0.6 - - - -
44A VAL 2.8 34.2 + - - +
46A SER* 4.6 4.8 + - - -
49A ILE* 3.5 21.0 - - + +
125B ILE* 3.3 35.6 - - + +
128B TYR* 3.3 41.3 - - + -
129B LEU* 4.1 27.6 - - + +
132B THR* 3.8 12.1 + - - +
160B PHE 2.9 7.9 + - - +
161B LEU* 3.0 21.1 + - - +
163B LEU* 1.3 77.8 - - - +
165B ASP* 1.3 76.9 + - - +
167B LEU* 3.2 6.1 + - + +
168B TRP* 2.9 27.3 + - + +
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Residues in contact with ASP 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A GLY* 4.4 1.9 - - - -
44A VAL* 3.3 40.0 + - + +
49A ILE* 4.8 2.3 - - - +
71A HIS* 4.3 15.2 - - + +
161B LEU 2.9 17.7 + - - +
162B LYS* 3.5 15.9 - - - +
164B ARG* 1.3 98.8 + - - +
166B GLN* 1.3 57.5 + - - +
168B TRP* 3.3 15.6 - - + +
169B ASP* 2.9 33.7 + - - +
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Residues in contact with GLN 166 (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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71A HIS* 4.8 9.2 - - + -
162B LYS* 2.9 42.7 + - - +
163B LEU* 3.2 22.6 + - + +
165B ASP* 1.3 75.6 - - - +
167B LEU* 1.3 60.5 + - - +
169B ASP* 3.0 15.8 + - - +
170B ARG* 2.9 27.3 + - - +
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Residues in contact with LEU 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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107B TYR* 4.7 7.9 - - + +
108B PHE* 5.8 0.2 - - + -
111B ALA* 4.0 15.3 - - + -
113B PHE* 3.7 30.5 - - + -
122B ASN* 5.0 0.4 - - - +
125B ILE* 3.7 22.2 - - + +
126B ALA* 3.6 36.8 - - + -
129B LEU* 4.5 13.5 - - + -
163B LEU 2.9 13.5 + - - +
164B ARG* 3.5 7.9 - - - +
166B GLN* 1.3 75.2 - - - +
168B TRP* 1.3 63.0 + - - +
170B ARG* 3.0 15.1 + - + +
171B ILE* 3.2 19.9 + - + +
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Residues in contact with TRP 168 (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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44A VAL* 4.7 13.5 - - + -
48A ALA 4.7 0.2 - - - -
49A ILE* 3.7 33.8 - - + +
52A ILE* 3.5 50.5 - - + -
53A SER* 3.2 22.4 + - - -
69A VAL* 5.3 0.2 - - + -
76A LEU* 5.2 6.1 - - + -
129B LEU* 4.2 20.2 - - + +
164B ARG 2.9 14.5 + - - +
165B ASP* 3.3 18.6 - - + +
167B LEU* 1.3 76.6 - - - +
169B ASP* 1.3 59.0 + - - +
171B ILE* 3.4 18.7 - - + +
173B TYR* 2.9 77.6 + + - -
175B ALA* 4.4 3.4 - - + +
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Residues in contact with ASP 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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70A ILE 4.9 0.2 - - - +
71A HIS* 2.7 38.7 + - - +
165B ASP 2.9 20.8 + - - +
166B GLN* 3.0 16.7 + - - +
168B TRP* 1.3 77.5 - - - +
170B ARG* 1.3 60.1 + - - +
172B ASP* 3.7 6.3 + - - -
173B TYR* 2.8 39.4 + - - +
558C MET* 3.4 32.0 - - + +
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Residues in contact with ARG 170 (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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110B ARG 4.2 5.5 - - - +
111B ALA* 2.5 30.8 + - + +
112B LYS* 2.8 26.5 + - - +
113B PHE* 3.4 15.2 - - - -
114B THR* 4.8 0.8 - - - +
117B GLU* 2.6 41.7 + - - -
122B ASN* 5.8 0.2 - - - +
166B GLN 2.9 11.4 + - - +
167B LEU* 3.0 13.2 + - - +
169B ASP* 1.3 76.1 - - - +
171B ILE* 1.3 58.2 + - - +
172B ASP* 3.1 10.7 + - - -
558C MET* 5.4 3.0 - - - +
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Residues in contact with ILE 171 (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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107B TYR* 3.6 27.1 - - + +
110B ARG* 3.8 22.6 - - + +
111B ALA* 3.6 30.5 - - + +
129B LEU* 4.2 12.3 - - + -
167B LEU* 3.5 16.4 - - + +
168B TRP* 3.4 27.1 - - + +
170B ARG* 1.3 75.6 - - - +
172B ASP* 1.3 67.0 + - - +
173B TYR 3.8 4.5 - - - +
174B ARG* 3.3 41.8 + - - +
175B ALA 4.2 0.7 - - - +
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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