Contacts of the strand formed by residues 155 - 159 (chain G) in PDB entry 2BM8
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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80G LEU* 4.5 1.3 - - - +
82G PRO* 4.7 0.2 - - - -
84G THR* 3.3 20.4 - - + +
86G VAL* 4.6 4.5 - - + -
151G MET* 4.0 26.2 - - + -
152G ALA 4.1 4.3 - - - +
153G HIS* 3.9 18.8 - - + +
154G PRO* 1.3 76.1 - - - +
156G ILE* 1.3 69.3 + - - +
157G PHE* 3.7 26.7 - - + +
176G LEU* 3.9 31.6 - - + -
177G LEU* 4.1 16.8 - - + -
181G ASP* 3.0 14.6 + - - +
182G TYR 3.1 22.0 + - - -
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Residues in contact with ILE 156 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73G TYR* 4.7 2.5 - - + -
76G MET* 3.9 15.9 - - + -
77G LEU* 3.6 31.0 - - + -
80G LEU* 3.9 17.5 - - + -
82G PRO* 3.9 15.9 - - + -
84G THR 3.1 6.1 + - - -
85G ILE* 3.4 12.1 - - + +
86G VAL 2.9 26.9 + - - +
99G PHE* 5.9 0.2 - - + -
155G LEU* 1.3 79.2 - - - +
157G PHE* 1.3 59.3 + - - +
158G ILE* 3.8 17.9 - - + -
182G TYR* 3.7 13.0 - - + -
184G ILE* 3.6 29.8 - - + -
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Residues in contact with PHE 157 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86G VAL* 3.6 28.9 - - + -
88G LEU* 4.3 22.4 - - + -
115G ILE* 5.2 0.2 - - + -
145G PHE* 3.7 33.7 - + - -
148G LEU* 5.4 2.2 - - + -
155G LEU* 3.7 10.0 - - + +
156G ILE* 1.3 72.6 - - - +
158G ILE* 1.3 66.7 + - - +
159G ASP* 4.7 0.7 - - - -
168G ILE* 4.0 13.0 - - + -
171G TRP* 4.3 10.8 - + - -
172G ALA* 5.3 0.2 - - + -
176G LEU* 3.8 18.6 - - + -
177G LEU* 4.7 3.4 - - + -
182G TYR 2.9 13.6 + - - +
183G PHE* 3.3 42.5 - + + -
184G ILE* 2.9 25.5 + - - +
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Residues in contact with ILE 158 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73G TYR* 3.5 31.9 - - + +
85G ILE* 4.3 7.4 - - + -
86G VAL 2.8 14.1 + - - +
87G GLU* 3.9 8.5 - - - +
88G LEU* 3.0 28.2 + - - +
99G PHE* 3.5 36.8 - - + -
156G ILE* 3.8 17.9 - - + -
157G PHE* 1.3 80.7 - - - +
159G ASP* 1.3 62.5 + - - +
160G ASN* 3.4 26.6 + - - +
184G ILE* 3.6 7.2 - - + +
186G GLU* 3.7 11.7 - - + +
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Residues in contact with ASP 159 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88G LEU* 3.6 22.3 - - + +
157G PHE* 4.1 1.9 + - + -
158G ILE* 1.3 70.3 - - - +
160G ASN* 1.3 61.6 + - - +
161G ALA 3.1 5.4 + - - -
162G HIS* 3.0 45.6 + - - -
163G ALA 4.9 0.5 + - - +
165G THR* 3.4 29.0 + - + +
168G ILE* 5.7 0.4 - - - +
183G PHE* 4.7 9.0 - - + -
184G ILE 2.7 17.8 + - - +
185G ILE* 3.7 13.9 - - + +
186G GLU* 3.2 24.1 + - - +
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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