Contacts of the strand formed by residues 155 - 159 (chain D) in PDB entry 2BM9
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 LEU 155 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D LEU* 4.5 0.4 - - - +
82D PRO* 4.5 0.6 - - - +
84D THR* 3.1 30.3 - - + +
86D VAL* 5.5 4.9 - - + -
151D MET* 5.1 6.1 - - + -
152D ALA 4.0 9.2 - - - +
153D HIS* 4.3 11.9 - - + +
154D PRO* 1.3 76.7 - - - +
156D ILE* 1.3 78.8 + - - +
157D PHE* 3.9 7.9 - - + +
176D LEU* 3.8 33.2 - - + -
177D LEU* 4.1 23.1 - - + -
181D ASP* 3.0 19.7 + - - +
182D TYR 3.1 20.8 + - - -
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Residues in contact with ILE 156 (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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73D TYR* 4.8 2.9 - - + -
76D MET* 3.9 18.2 - - + -
77D LEU* 3.8 20.9 - - + -
80D LEU* 4.0 15.3 - - + -
82D PRO* 3.7 27.6 - - + -
84D THR 3.0 7.3 + - - -
85D ILE* 3.4 13.8 - - + +
86D VAL* 2.9 28.4 + - - +
99D PHE* 6.0 0.2 - - + -
155D LEU* 1.3 80.5 - - - +
157D PHE* 1.3 63.6 + - - +
158D ILE* 4.1 12.3 - - + -
182D TYR* 3.7 15.9 - - + -
184D ILE* 4.0 26.5 - - + -
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Residues in contact with PHE 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D VAL* 4.0 27.6 - - + -
88D LEU* 3.9 30.1 - - + -
145D PHE* 4.2 15.5 - + - -
148D LEU* 4.8 5.6 - - + -
155D LEU* 3.9 7.4 - - + +
156D ILE* 1.3 74.2 - - - +
158D ILE* 1.3 74.9 + - - +
159D ASP* 4.6 0.9 - - - -
168D ILE* 3.9 18.6 - - + -
171D TRP* 5.0 4.0 - + - -
172D ALA* 5.3 1.3 - - + -
176D LEU* 4.2 24.5 - - + -
177D LEU* 4.8 2.0 - - + -
182D TYR 2.9 12.7 + - - +
183D PHE* 3.3 44.3 + + + -
184D ILE* 2.8 28.6 + - - +
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Residues in contact with ILE 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D LYS* 4.7 0.7 - - - -
73D TYR* 3.6 26.5 - - + +
85D ILE* 4.1 7.6 - - + -
86D VAL 3.1 13.8 + - - +
87D GLU* 3.4 24.2 - - + +
88D LEU* 3.1 29.6 + - - +
99D PHE* 3.5 38.4 - - + -
156D ILE* 4.1 10.5 - - + -
157D PHE* 1.3 85.4 - - - +
159D ASP* 1.3 65.9 + - - +
160D ASN* 3.6 11.0 - - - +
184D ILE* 3.3 12.3 - - + +
186D GLU* 3.7 9.2 - - + +
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Residues in contact with ASP 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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88D LEU* 3.6 23.7 - - + +
139D CYS* 5.7 0.2 - - - -
157D PHE* 4.3 5.5 - - + -
158D ILE* 1.3 76.7 - - - +
160D ASN* 1.3 72.4 + - - +
161D ALA 4.0 0.2 + - - -
162D HIS* 2.6 44.4 + - - +
165D THR* 2.6 41.0 + - + +
183D PHE* 5.2 4.5 - - + -
184D ILE 2.9 11.3 + - - +
185D ILE* 4.0 12.8 - - + +
186D GLU 3.6 13.5 + - - -
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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
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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