Contacts of the strand formed by residues 84 - 88 (chain B) 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 THR 84 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B PRO* 3.2 3.7 + - - +
83B ARG* 1.3 86.2 + - - +
85B ILE* 1.3 65.6 + - - +
86B VAL* 4.0 13.7 - - + -
110B CYS* 3.6 0.9 - - - -
111B GLN* 3.1 17.3 + - - +
113B ILE* 4.0 4.7 - - + -
151B MET* 3.5 25.4 - - + +
152B ALA* 3.1 22.9 + - - +
154B PRO 3.4 1.6 + - - -
155B LEU* 3.3 27.0 - - + -
156B ILE 3.1 25.6 + - - +
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Residues in contact with ILE 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B LEU* 4.0 22.2 - - + -
82B PRO* 4.1 11.2 - - + -
84B THR* 1.3 76.6 - - - +
86B VAL* 1.3 70.3 + - - +
87B GLU* 4.2 2.2 - - + +
99B PHE* 3.4 55.4 - - + +
110B CYS* 3.8 18.9 - - - -
111B GLN 2.9 7.1 + - - +
112B VAL* 3.4 13.0 - - + -
113B ILE* 2.9 27.0 + - - +
156B ILE* 3.4 12.6 - - + +
158B ILE* 4.0 16.6 - - + -
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Residues in contact with VAL 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B THR* 4.0 17.3 - - + -
85B ILE* 1.3 81.9 - - - +
87B GLU* 1.3 62.6 + - - +
88B LEU* 5.5 0.4 - - + -
113B ILE* 3.4 10.5 - - + +
115B ILE* 4.1 22.7 - - + -
148B LEU* 4.2 15.5 - - + -
155B LEU* 4.1 10.8 - - + -
156B ILE 2.9 14.2 + - - +
157B PHE* 3.5 34.5 - - + -
158B ILE* 2.6 36.2 + - - +
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Residues in contact with GLU 87 (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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65B LYS* 2.9 31.2 + - - -
85B ILE* 4.2 2.0 - - + +
86B VAL* 1.3 74.4 - - - +
88B LEU* 1.3 61.2 + - - +
89B GLY 3.4 14.8 - - - +
95B SER* 3.1 10.5 - - - -
96B LEU* 3.6 30.3 - - + -
99B PHE* 3.6 11.9 - - + -
113B ILE 3.0 6.7 + - - +
114B GLY* 3.4 2.6 - - - -
115B ILE* 3.1 25.8 + - - +
158B ILE* 3.2 17.1 - - + +
160B ASN* 2.5 28.5 + - - +
301B SAM 3.1 7.2 - - - +
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Residues in contact with LEU 88 (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 VAL* 5.5 1.1 - - + -
87B GLU* 1.3 72.6 + - - +
89B GLY* 1.3 59.8 + - - +
115B ILE* 3.6 23.1 - - + +
137B GLY 5.8 0.4 - - - +
139B CYS* 3.8 28.0 - - - -
145B PHE* 3.8 20.9 - - + -
157B PHE* 4.7 14.1 - - + -
158B ILE 3.0 16.6 + - - +
159B ASP* 3.9 16.8 - - - +
160B ASN* 2.7 29.8 + - - -
161B ALA* 3.2 18.2 + - + -
168B ILE* 3.8 20.2 - - + -
301B SAM 4.4 8.7 - - + -
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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