Contacts of the strand formed by residues 111 - 116 (chain E) 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 GLN 111 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83E ARG 2.8 14.1 + - - +
84E THR* 3.4 15.6 - - + +
85E ILE 3.3 19.5 + - - -
109E ASP* 5.8 2.0 - - - +
110E CYS* 1.3 72.9 - - - +
112E VAL* 1.3 65.7 + - - +
113E ILE* 4.2 6.5 - - + +
131E ASN* 3.3 46.3 + - - +
133E THR* 3.8 19.0 + - - -
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Residues in contact with VAL 112 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85E ILE* 3.6 19.3 - - + +
87E GLU* 5.4 1.1 - - + -
96E LEU* 3.8 40.6 - - + +
99E PHE* 3.7 17.5 - - + -
100E ARG* 3.7 36.3 - - + +
110E CYS* 4.9 4.5 - - - +
111E GLN* 1.3 75.2 + - - +
113E ILE* 1.3 66.1 + - - +
131E ASN 3.0 12.9 + - - +
132E ILE* 3.4 8.0 - - + -
133E THR* 3.0 23.4 + - - -
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Residues in contact with ILE 113 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84E THR* 3.7 26.9 - - + -
85E ILE 3.1 10.2 + - - +
86E VAL* 3.3 11.1 - - + +
87E GLU 2.8 28.1 + - - +
111E GLN* 4.2 8.5 - - + +
112E VAL* 1.3 83.2 - - - +
114E GLY* 1.3 67.0 + - - +
115E ILE* 4.2 12.8 - - + -
133E THR* 3.3 26.0 - - + +
135E HIS* 4.2 14.1 - - + +
148E LEU* 4.5 8.1 - - + -
151E MET* 4.0 24.0 - - + -
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Residues in contact with GLY 114 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87E GLU 3.4 5.8 - - - -
90E VAL* 4.0 20.0 - - - -
96E LEU* 4.1 17.7 - - - +
112E VAL 4.3 0.2 - - - -
113E ILE* 1.3 73.6 - - - +
115E ILE* 1.3 64.9 + - - +
132E ILE* 5.8 0.2 - - - +
133E THR 3.3 7.6 + - - +
134E LEU* 3.6 8.6 - - - +
135E HIS* 3.0 25.2 + - - +
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Residues in contact with ILE 115 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86E VAL* 3.7 27.6 - - + -
87E GLU 3.2 7.7 + - - +
88E LEU* 3.5 18.0 - - + +
89E GLY* 2.5 33.8 + - - -
90E VAL* 4.1 0.6 - - - +
113E ILE* 4.2 6.3 - - + -
114E GLY* 1.3 78.3 - - - +
116E ASP* 1.3 63.5 + - - +
135E HIS* 3.4 23.8 - - + +
137E GLY 4.2 5.6 - - - +
139E CYS* 6.1 0.4 - - - -
144E THR* 3.6 29.4 - - + +
145E PHE* 4.6 15.5 - - + -
148E LEU* 3.9 24.5 - - + -
157E PHE* 5.1 0.9 - - + -
301E SAM 5.7 0.4 - - + -
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Residues in contact with ASP 116 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90E VAL* 2.9 20.6 + - + +
91E TYR 3.7 1.4 + - - -
115E ILE* 1.3 79.4 - - - +
117E ARG* 1.3 62.5 + - - +
118E ASP* 2.8 42.4 + - - +
119E LEU* 3.8 20.3 - - + +
135E HIS 3.2 10.8 + - - +
136E GLN* 3.3 3.8 - - - +
137E GLY 3.2 18.6 + - - -
301E SAM 2.6 55.9 + - - -
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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