Contacts of the helix formed by residues 150 - 164 (chain B) in PDB entry 5B2R
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 ASP 150 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B VAL* 4.5 4.3 - - - +
119B PHE* 3.8 12.3 - - + -
149B ALA* 1.3 73.0 - - - +
151B LEU* 1.3 65.2 + - - +
152B ARG* 2.9 67.1 + - - +
153B LEU* 2.9 33.3 + - + +
154B ILE* 3.1 10.4 + - - +
430B TYR* 4.4 1.1 - - - -
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Residues in contact with LEU 151 (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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86B PHE* 3.9 17.5 - - + -
89B GLU* 3.9 40.4 - - + +
90B MET* 3.5 24.9 - - + +
93B VAL* 4.3 18.8 - - + +
149B ALA 3.3 4.7 + - - -
150B ASP* 1.3 74.4 + - - +
152B ARG* 1.3 57.8 + - - +
154B ILE* 3.6 12.7 + - + +
155B TYR* 3.0 21.3 + - - +
430B TYR* 3.7 41.4 + - + +
432B PHE* 3.9 12.1 - - + -
433B LEU* 4.7 2.0 - - + -
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Residues in contact with ARG 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B MET* 3.7 27.6 - - - -
93B VAL* 3.9 17.3 + - + +
94B ASP* 2.9 35.4 + - - +
97B PHE* 3.7 22.6 - - + -
118B ILE* 3.4 23.5 + - + +
119B PHE* 3.4 34.5 + - + +
150B ASP* 2.9 36.5 + - - +
151B LEU* 1.3 74.7 - - - +
153B LEU* 1.3 62.5 + - - +
155B TYR* 3.4 2.3 + - - +
156B LEU* 3.1 33.2 + - - +
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Residues in contact with LEU 153 (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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118B ILE* 4.0 12.3 - - + -
119B PHE* 4.0 24.2 - - + -
128B TYR* 3.6 30.5 - - + -
132B TYR* 4.5 15.0 - - + +
138B LEU* 3.6 35.9 - - + +
142B LEU* 3.6 11.4 - - + +
149B ALA* 5.5 1.3 - - + -
150B ASP* 2.9 25.5 + - + +
152B ARG* 1.3 75.6 - - - +
154B ILE* 1.3 64.1 + - - +
156B LEU* 3.4 6.1 + - + -
157B ALA 3.1 18.2 + - - -
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Residues in contact with ILE 154 (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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86B PHE* 4.2 8.5 - - + -
142B LEU* 4.0 10.5 - - + +
149B ALA* 3.6 25.6 - - + +
150B ASP 3.1 9.7 + - - +
151B LEU* 3.7 13.7 - - + +
153B LEU* 1.3 76.8 - - - +
155B TYR* 1.3 64.0 + - - +
157B ALA* 3.3 1.6 + - - +
158B LEU* 3.0 46.6 + - + +
422B ILE* 4.3 11.7 - - + -
423B LEU* 5.8 0.2 - - + -
426B GLN* 3.5 36.8 - - + +
430B TYR* 3.6 17.0 - - + -
433B LEU* 4.2 10.5 - - + -
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Residues in contact with TYR 155 (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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47A A 6.4 0.4 - - - -
48A A 4.6 2.4 + - - -
79B ILE* 3.3 15.6 - - - +
82B LEU* 3.5 28.0 - - + -
83B GLN* 3.0 38.1 + - + +
86B PHE* 3.8 26.2 - + + -
90B MET* 4.1 6.7 - - + -
97B PHE* 3.7 15.5 - + - -
98B PHE* 3.7 18.2 - + - -
101B LEU* 3.7 20.9 - - + -
151B LEU 3.0 17.7 + - - +
152B ARG 3.6 4.3 - - - +
153B LEU 3.3 0.2 - - - -
154B ILE* 1.3 76.7 - - - +
156B LEU* 1.3 68.5 + - + +
158B LEU* 3.7 2.2 - - - +
159B ALA* 2.8 46.0 + - + +
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Residues in contact with LEU 156 (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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46A A 5.0 5.8 - - - +
47A A 4.5 21.2 + - - -
97B PHE* 4.0 14.4 - - + -
101B LEU* 4.4 12.3 - - + -
118B ILE* 3.8 42.2 - - + -
128B TYR* 5.4 3.6 - - - +
135B ILE* 4.3 9.6 - - + +
138B LEU* 4.7 6.3 - - + -
152B ARG 3.1 21.6 + - - +
153B LEU* 3.9 11.4 - - + +
154B ILE 3.3 0.2 - - - -
155B TYR* 1.3 91.9 - - + +
157B ALA* 1.3 58.8 + - - +
159B ALA* 3.8 3.7 - - + +
160B HIS* 2.9 31.5 + - - +
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Residues in contact with ALA 157 (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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135B ILE* 4.5 5.6 - - - -
138B LEU* 4.4 6.4 - - + +
139B ARG* 4.2 17.8 - - + +
142B LEU* 3.7 21.3 - - + -
153B LEU 3.1 17.0 + - - +
154B ILE 3.8 2.2 - - - +
156B LEU* 1.3 77.4 - - - +
158B LEU* 1.3 61.4 + - - +
160B HIS* 3.4 2.3 + - - +
161B MET* 3.2 29.9 + - - +
422B ILE* 3.8 15.9 - - + -
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Residues in contact with LEU 158 (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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82B LEU* 4.1 11.7 - - + -
86B PHE* 3.9 30.7 - - + -
154B ILE* 3.0 27.8 + - + +
155B TYR 3.9 2.9 - - - +
157B ALA* 1.3 73.5 - - - +
159B ALA* 1.3 59.7 + - - +
161B MET* 3.3 3.6 + - - +
162B ILE* 2.9 33.3 + - + +
419B LEU* 3.6 40.1 - - + +
422B ILE* 4.0 22.9 - - + -
423B LEU* 3.8 24.7 - - + -
440B ILE* 4.6 6.3 - - + -
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Residues in contact with ALA 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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47A A 4.8 7.2 - - - +
79B ILE* 3.8 12.2 - - + +
82B LEU* 3.6 11.8 - - + +
155B TYR* 2.8 51.6 + - + +
156B LEU* 3.8 5.6 - - + +
158B LEU* 1.3 69.3 - - - +
160B HIS* 1.3 56.7 + - - +
162B ILE* 4.4 0.7 - - - +
163B LYS* 2.7 39.3 + - - +
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Residues in contact with HIS 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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46A A 2.9 30.1 + - - +
47A A 3.9 22.6 + - - +
135B ILE* 3.4 34.9 - - + +
136B TYR* 3.6 17.7 - + - -
139B ARG* 2.9 33.7 + - - +
156B LEU 2.9 18.8 + - - +
157B ALA 3.6 5.2 - - - +
158B LEU 3.3 0.2 - - - -
159B ALA* 1.3 76.4 - - - +
161B MET* 1.3 61.2 + - - +
163B LYS* 4.7 1.1 - - - -
164B PHE* 3.2 41.5 + + + +
403B ARG* 3.7 8.1 + - - -
415B HIS* 6.1 0.2 - + - -
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Residues in contact with MET 161 (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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139B ARG* 3.5 48.7 - - + +
157B ALA 3.2 13.5 + - - +
158B LEU* 3.6 5.6 - - - +
160B HIS* 1.3 76.5 - - - +
162B ILE* 1.3 62.9 + - - +
164B PHE 3.4 3.5 - - - -
165B ARG* 3.1 26.5 - - - +
415B HIS* 3.9 9.4 - - + +
418B GLU* 3.5 21.5 - - + +
419B LEU* 3.3 36.6 - - + -
422B ILE* 3.6 27.4 - - + -
444B LEU* 3.8 16.6 - - + +
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Residues in contact with ILE 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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78B ARG* 3.0 59.3 + - + +
79B ILE* 4.2 11.7 - - + -
82B LEU* 4.0 28.9 - - + -
158B LEU 2.9 19.7 + - - +
159B ALA* 3.9 3.6 - - - +
161B MET* 1.3 77.4 - - - +
163B LYS* 1.3 61.5 + - - +
165B ARG* 3.6 7.1 - - - +
419B LEU* 4.1 6.7 - - + -
440B ILE* 4.1 20.2 - - + +
443B ILE* 3.8 18.8 - - + +
444B LEU* 4.0 24.5 - - + +
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Residues in contact with LYS 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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19A G 4.8 2.4 + - - -
47A A 4.4 7.5 + - - +
48A A 2.7 55.0 + - - +
49A A 4.7 8.2 + - - -
75B ARG* 3.6 51.5 - - + +
78B ARG* 3.2 17.6 + - - +
79B ILE* 4.1 17.7 - - + -
159B ALA 2.7 23.1 + - - +
160B HIS* 4.7 0.7 - - - -
162B ILE* 1.3 77.5 - - - +
164B PHE* 1.3 90.2 + - + +
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Residues in contact with PHE 164 (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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19A G 3.1 25.4 + - - +
20A C 4.7 4.0 - - - +
47A A 3.6 26.9 - - - -
75B ARG* 3.9 19.7 - - - -
139B ARG* 5.4 0.2 + - - -
160B HIS* 3.2 33.9 + + + +
161B MET 3.4 6.4 - - - +
163B LYS* 1.3 107.0 - - + +
165B ARG* 1.3 55.3 + - - +
403B ARG* 3.3 38.1 - - - +
415B HIS* 3.4 23.8 + - + -
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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