Contacts of the strand formed by residues 84 - 88 (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 THR 84 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82G PRO* 3.9 2.3 - - - +
83G ARG* 1.3 81.4 + - - +
85G ILE* 1.3 68.4 + - - +
86G VAL* 4.3 11.4 - - + -
110G CYS* 4.0 0.4 - - - -
111G GLN* 3.3 15.7 - - + +
113G ILE* 4.1 17.3 - - + -
151G MET* 3.8 21.3 - - + +
152G ALA* 2.7 37.9 + - - +
154G PRO 3.2 4.5 + - - +
155G LEU* 3.3 13.0 - - - -
156G ILE 3.1 22.3 + - - -
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Residues in contact with ILE 85 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77G LEU* 4.3 5.8 - - + -
82G PRO* 4.1 15.5 - - + -
84G THR* 1.3 79.4 - - - +
86G VAL* 1.3 66.1 + - - +
87G GLU* 4.8 0.9 - - + +
99G PHE* 3.8 51.1 - - + +
103G THR* 3.9 17.3 - - + -
110G CYS* 3.6 21.5 - - - -
111G GLN 3.0 7.3 + - - +
112G VAL* 3.3 11.3 - - + +
113G ILE* 2.8 26.7 + - - +
156G ILE* 3.4 18.6 - - + +
158G ILE* 4.3 10.5 - - + -
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Residues in contact with VAL 86 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84G THR* 4.3 8.7 - - + -
85G ILE* 1.3 77.2 - - - +
87G GLU* 1.3 67.9 + - - +
88G LEU 4.6 0.9 - - - +
113G ILE* 3.3 15.0 - - + +
115G ILE* 4.0 22.0 - - + -
148G LEU* 5.3 2.2 - - + -
151G MET* 3.9 27.4 - - - -
155G LEU* 4.6 7.6 - - + -
156G ILE 2.9 11.4 + - - +
157G PHE* 3.9 36.6 - - + -
158G ILE* 2.8 31.9 + - - +
176G LEU* 5.5 0.4 - - + -
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Residues in contact with GLU 87 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65G LYS* 3.0 34.8 + - - -
85G ILE* 4.1 1.5 + - + -
86G VAL* 1.3 77.1 - - - +
88G LEU* 1.3 61.9 + - - +
89G GLY 3.4 17.7 + - - +
90G VAL* 4.3 0.7 - - + +
95G SER* 3.7 10.6 + - - +
96G LEU* 3.4 32.8 - - + -
99G PHE* 3.8 17.0 - - + -
113G ILE 2.7 9.1 + - - +
114G GLY* 3.3 1.4 - - - -
115G ILE* 2.8 26.9 + - - +
158G ILE* 3.9 11.2 - - + +
160G ASN* 2.7 25.8 + - - +
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Residues in contact with LEU 88 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86G VAL* 4.0 1.4 - - - +
87G GLU* 1.3 69.9 - - - +
89G GLY* 1.3 62.5 + - - +
115G ILE* 3.8 28.7 - - + +
116G ASP* 5.6 0.9 - - - -
139G CYS* 3.6 27.8 - - - -
145G PHE* 3.8 29.8 - - + -
157G PHE* 4.3 17.0 - - + -
158G ILE 3.0 16.3 + - - +
159G ASP* 3.6 22.7 - - + +
160G ASN* 2.9 31.2 + - - +
161G ALA* 3.3 6.2 + - + -
163G ALA 6.3 0.2 - - - +
168G ILE* 4.0 17.5 - - + -
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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