Contacts of the helix formed by residues 101 - 111 (chain C) in PDB entry 2B5F
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 ASN 101 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85C ILE* 6.1 1.1 - - + -
99C HIS 3.4 9.6 - - - +
100C ILE* 1.3 82.4 - - + +
102C PRO* 1.4 69.9 - - - +
103C ALA* 2.8 20.6 + - - +
104C VAL* 3.1 23.7 + - + +
105C THR* 3.1 13.5 + - - -
126C GLN* 3.3 8.6 - - - -
175C LEU* 3.5 20.4 - - - +
221C ILE* 2.7 25.1 + - - +
222C ASN* 3.3 26.3 - - - +
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Residues in contact with PRO 102 (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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101C ASN* 1.4 83.6 - - - +
103C ALA* 1.3 56.0 + - - +
105C THR* 3.4 1.3 + - - -
106C PHE* 2.8 28.9 + - - +
123C MET* 3.6 28.8 - - + +
126C GLN* 2.9 22.0 - - + +
127C CYS* 4.4 10.8 - - - -
222C ASN* 3.5 15.7 - - - +
223C PRO* 4.2 7.6 - - + -
224C ALA* 3.5 30.1 - - + +
246C TRP* 4.8 2.7 - - + -
250C PHE* 4.1 13.5 - - + -
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Residues in contact with ALA 103 (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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101C ASN* 2.8 17.3 + - - +
102C PRO* 1.3 71.4 - - - +
104C VAL* 1.3 60.8 + - - +
106C PHE* 3.6 6.5 - - - +
107C GLY* 2.9 23.6 + - - -
172C THR* 4.0 11.2 - - + -
176C VAL* 4.2 2.9 - - + +
221C ILE 4.7 0.4 - - - +
223C PRO* 3.9 4.5 - - + +
249C PRO* 3.8 41.7 - - + +
250C PHE* 4.2 5.2 - - + -
253C ALA* 3.4 11.8 - - - +
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Residues in contact with VAL 104 (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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98C GLY 5.2 0.4 - - - +
99C HIS* 4.2 22.7 - - + +
101C ASN* 3.1 34.6 + - + +
103C ALA* 1.3 75.3 - - - +
105C THR* 1.3 65.4 + - - +
107C GLY* 3.3 2.5 + - - -
108C LEU* 3.1 40.2 + - + +
175C LEU* 4.2 13.9 - - + -
176C VAL* 4.5 9.0 - - + +
179C VAL* 4.2 31.9 - - + -
197C LEU* 5.2 3.4 - - + -
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Residues in contact with THR 105 (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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99C HIS* 3.1 26.0 + - + +
101C ASN 3.1 3.7 + - - -
102C PRO* 3.7 10.3 - - - -
104C VAL* 1.3 78.6 - - - +
106C PHE* 1.3 57.4 + - - +
108C LEU* 3.3 2.4 + - - +
109C PHE* 2.8 28.1 + - - +
114C VAL* 4.9 6.3 - - + +
119C ALA* 3.6 39.9 - - + +
122C TYR* 4.0 11.2 - - + +
123C MET* 4.4 3.8 - - + -
126C GLN* 3.1 23.5 + - - -
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Residues in contact with PHE 106 (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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102C PRO 2.8 21.1 + - - +
103C ALA* 3.6 6.3 - - - +
104C VAL 3.2 0.2 - - - -
105C THR* 1.3 73.5 - - - +
107C GLY* 1.4 62.8 + - - +
109C PHE* 3.2 19.6 + + - +
110C LEU* 3.0 60.6 + - + +
123C MET* 4.0 14.3 - - + +
250C PHE* 3.5 65.3 - + + -
253C ALA* 4.2 5.4 - - + -
254C ALA* 4.5 2.9 - - + -
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Residues in contact with GLY 107 (chain C).
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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103C ALA 2.9 15.6 + - - -
104C VAL 3.8 2.5 - - - -
106C PHE* 1.4 77.4 - - - +
108C LEU* 1.3 60.2 + - - +
110C LEU* 3.3 10.4 + - - +
111C ALA* 3.2 16.5 + - - +
176C VAL* 4.7 3.6 - - - -
180C PHE* 3.4 21.0 - - - -
253C ALA* 4.2 21.8 - - - -
257C ALA* 3.8 2.7 - - - +
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Residues in contact with LEU 108 (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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99C HIS* 2.9 39.9 - - + +
104C VAL* 3.1 25.6 + - + +
105C THR 3.8 3.6 - - - +
107C GLY* 1.3 74.7 - - - +
109C PHE* 1.4 57.4 + - - +
111C ALA* 2.9 31.6 - - - +
113C LYS* 3.3 20.3 + - + +
114C VAL* 4.3 13.5 - - + -
176C VAL* 6.5 0.2 - - + -
179C VAL* 4.5 18.4 - - + -
180C PHE* 3.9 27.8 - - + -
183C THR* 4.5 9.9 - - - +
197C LEU* 5.2 7.4 - - + -
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Residues in contact with PHE 109 (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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105C THR 2.8 14.4 + - - +
106C PHE* 3.3 22.7 - + + +
108C LEU* 1.4 71.4 - - - +
110C LEU* 1.3 88.6 + - + +
111C ALA 3.0 2.1 + - - -
112C ARG* 3.1 17.5 + - - +
114C VAL* 3.9 23.4 - - + +
115C SER* 4.0 2.7 - - - -
116C LEU* 3.7 52.0 - - + -
119C ALA* 4.3 14.1 - - + -
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Residues in contact with LEU 110 (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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106C PHE* 3.0 54.5 + - + +
107C GLY 3.3 6.7 + - - +
109C PHE* 1.3 89.9 - - + +
111C ALA* 1.3 57.1 + - - +
112C ARG* 3.1 5.5 + - - +
253C ALA 4.8 0.7 - - - +
254C ALA* 3.3 44.0 - - + +
257C ALA* 4.3 11.0 - - + -
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Residues in contact with ALA 111 (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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107C GLY 3.2 9.7 + - - +
108C LEU 2.9 10.9 + - - +
109C PHE 3.0 0.6 - - - -
110C LEU* 1.3 76.0 - - - +
112C ARG* 1.3 53.5 + - - +
113C LYS* 2.4 41.1 + - + +
180C PHE* 3.8 24.9 - - + -
257C ALA* 5.0 4.9 - - + +
260C HIS* 5.8 4.0 - - + -
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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