Contacts of the strand formed by residues 84 - 88 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C PRO* 3.1 3.2 + - - +
83C ARG* 1.3 84.8 + - - +
85C ILE* 1.3 67.4 + - - +
86C VAL* 4.0 16.6 - - + -
110C CYS* 3.7 0.9 - - - -
111C GLN* 3.5 18.5 - - + +
113C ILE* 4.8 5.4 - - + -
151C MET* 3.9 26.5 - - + +
152C ALA* 2.5 36.4 + - - +
154C PRO 3.3 2.1 + - - +
155C LEU* 3.4 11.3 - - + +
156C ILE 3.2 23.2 + - - -
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Residues in contact with ILE 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C LEU* 4.0 8.1 - - + -
82C PRO* 3.9 17.9 - - + -
84C THR* 1.3 78.6 - - - +
86C VAL* 1.3 64.8 + - - +
87C GLU 4.1 1.1 - - - +
99C PHE* 3.6 56.5 - - + -
103C THR* 3.8 18.2 - - + -
110C CYS* 3.6 19.6 - - - -
111C GLN 3.4 6.2 + - - +
112C VAL* 3.4 8.2 - - + +
113C ILE* 2.8 32.1 + - - +
156C ILE* 3.6 14.8 - - + +
158C ILE* 4.4 8.1 - - + -
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Residues in contact with VAL 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C THR* 4.0 7.4 - - + -
85C ILE* 1.3 86.9 - - - +
87C GLU* 1.3 61.2 + - - +
88C LEU* 5.2 0.4 - - + +
113C ILE* 3.2 20.2 - - + +
115C ILE* 4.5 17.7 - - + -
148C LEU* 5.0 1.6 - - + -
151C MET* 3.7 28.5 - - + -
155C LEU* 3.9 15.5 - - + -
156C ILE 3.1 8.4 + - - +
157C PHE* 3.8 29.1 - - + -
158C ILE* 3.0 30.2 + - - +
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Residues in contact with GLU 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C LYS* 2.9 30.1 + - - -
85C ILE* 4.1 1.4 - - + +
86C VAL* 1.3 73.3 - - - +
88C LEU* 1.3 59.9 + - - +
89C GLY 3.5 8.5 + - - +
95C SER* 3.2 21.9 + - - +
96C LEU* 3.3 25.8 - - + +
99C PHE* 3.4 22.9 - - + -
112C VAL* 5.2 0.4 - - - +
113C ILE 2.7 9.0 + - - +
114C GLY* 3.3 3.6 - - - -
115C ILE* 3.2 23.6 + - - +
158C ILE* 3.5 9.9 - - - +
160C ASN* 3.0 30.1 + - - +
301C SAM 3.2 7.6 + - - +
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Residues in contact with LEU 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C VAL* 4.9 0.9 - - + +
87C GLU* 1.3 73.5 + - - +
89C GLY* 1.3 61.1 + - - +
115C ILE* 4.3 24.2 - - + +
139C CYS* 3.6 28.5 - - - -
145C PHE* 4.0 19.5 - - + -
157C PHE* 3.8 32.3 - - + -
158C ILE 3.0 20.8 + - - +
159C ASP* 3.6 18.4 - - - +
160C ASN 2.9 21.9 + - - -
161C ALA* 3.0 14.6 + - + +
163C ALA 5.8 0.4 - - - +
168C ILE* 4.4 8.7 - - + -
301C SAM 4.9 1.6 - - + -
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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