Contacts of the helix formed by residues 101 - 112 (chain F) in PDB entry 2BWJ
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 GLU 101 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72F SER* 5.2 6.4 - - - -
99F PRO* 3.5 6.1 - - - +
100F ARG* 1.3 78.8 - - - +
102F VAL* 1.3 63.8 + - - +
103F LYS* 3.6 27.2 - - + +
104F GLN* 3.2 47.9 + - + +
105F GLY 3.4 4.3 + - - -
162F PRO* 6.1 2.0 - - - -
163F VAL* 3.7 8.3 - - - +
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Residues in contact with VAL 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99F PRO* 5.8 0.4 - - - -
101F GLU* 1.3 73.0 - - - +
103F LYS* 1.3 58.4 + - - +
105F GLY* 3.2 3.9 + - - +
106F GLU* 3.0 47.0 + - - +
162F PRO* 3.5 37.9 - - + +
163F VAL* 4.2 3.8 - - - +
166F TYR* 3.7 34.1 - - + -
167F TYR* 6.5 0.4 - - - -
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Residues in contact with LYS 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101F GLU* 3.6 27.1 - - + +
102F VAL* 1.3 78.5 - - - +
104F GLN* 1.3 58.5 + - + +
106F GLU* 3.8 16.2 - - - +
107F GLU* 3.1 28.4 + - - +
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Residues in contact with GLN 104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C ASP* 5.6 5.5 + - - -
72F SER* 4.8 17.1 - - - -
76F LEU* 5.4 0.2 - - - +
98F TYR* 3.5 31.1 + - + +
99F PRO* 3.3 12.7 - - + +
100F ARG* 2.7 38.9 + - - +
101F GLU* 3.2 43.2 + - + +
102F VAL 3.2 0.4 - - - -
103F LYS* 1.3 75.2 - - - +
105F GLY* 1.3 60.3 + - - +
107F GLU* 3.6 5.5 + - - +
108F PHE* 2.9 28.6 + - - +
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Residues in contact with GLY 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99F PRO* 3.6 10.0 - - - +
101F GLU 3.4 4.6 + - - -
102F VAL* 3.2 7.2 + - - -
104F GLN* 1.3 78.0 - - - +
106F GLU* 1.3 62.7 + - - +
108F PHE* 3.7 5.9 - - - +
109F GLY* 3.0 20.6 + - - -
166F TYR* 4.9 4.3 + - - -
167F TYR* 3.1 29.8 + - - -
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Residues in contact with GLU 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102F VAL* 3.0 32.5 + - - +
103F LYS* 3.8 17.7 - - - +
105F GLY* 1.3 75.8 - - - +
107F GLU* 1.3 59.3 + - - +
109F GLY* 3.3 3.2 + - - -
110F ARG* 3.0 28.8 + - - +
166F TYR* 3.5 28.6 - - + +
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Residues in contact with GLU 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73F GLY* 6.3 2.2 - - - -
76F LEU* 3.7 20.4 - - + -
103F LYS 3.1 15.1 + - - +
104F GLN* 3.9 6.1 - - - +
106F GLU* 1.3 78.0 - - - +
108F PHE* 1.3 59.3 + - - +
110F ARG* 3.0 46.2 + - - +
111F ARG* 2.9 37.9 + - - +
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Residues in contact with PHE 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F ILE* 4.2 12.1 - - + -
15F PHE* 3.6 27.6 - + + -
76F LEU* 3.9 10.5 - - + +
79F LEU* 3.6 26.2 - - + -
83F MET* 4.3 0.4 - - + -
95F ILE* 3.7 26.2 - - + -
98F TYR* 3.9 12.3 - + + -
104F GLN 2.9 19.1 + - - +
105F GLY* 3.7 9.6 - - - +
107F GLU* 1.3 76.4 - - - +
109F GLY* 1.3 55.3 + - - +
112F ILE* 2.8 71.3 + - + +
113F GLY 3.0 39.5 + - - -
115F PRO* 5.0 2.7 - - + -
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Residues in contact with GLY 109 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5F MET* 3.8 1.6 - - - +
9F ARG* 3.5 22.7 + - - -
105F GLY 3.0 15.3 + - - -
106F GLU 3.7 3.8 - - - -
108F PHE* 1.3 76.2 - - - +
110F ARG* 1.3 61.4 + - - +
113F GLY 3.1 16.4 + - - -
114F ASP* 3.5 16.5 - - - +
115F PRO* 6.0 0.4 - - - -
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Residues in contact with ARG 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F MET* 3.3 18.0 - - - +
106F GLU 3.0 16.5 + - - +
107F GLU* 3.0 42.1 + - - +
109F GLY* 1.3 77.7 - - - +
111F ARG* 1.3 83.5 + - - +
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Residues in contact with ARG 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F MET* 3.6 14.0 - - - +
76F LEU* 3.7 26.5 - - + -
77F GLU* 5.8 4.5 - - - -
80F LYS* 3.9 22.3 + - + -
107F GLU* 2.9 21.0 + - - +
110F ARG* 1.3 113.5 - - - +
112F ILE* 1.3 64.5 + - + +
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Residues in contact with ILE 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F MET* 3.1 27.0 - - - +
8F LEU* 4.1 13.1 - - + +
9F ARG* 3.9 4.7 - - - +
13F ILE* 4.4 2.5 - - + -
76F LEU* 3.4 33.0 - - + -
79F LEU* 4.3 1.3 - - + -
80F LYS* 4.0 39.0 - - + +
83F MET* 3.7 24.2 - - + -
108F PHE* 2.8 47.2 + - + +
110F ARG 3.7 0.6 - - - -
111F ARG* 1.3 80.2 - - + +
113F GLY* 1.3 59.0 + - - +
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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