Contacts of the helix formed by residues 103 - 114 (chain C) in PDB entry 3WBR
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 SER 103 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102C GLN* 1.3 74.1 - - - +
104C TRP* 1.3 52.5 + - - +
105C THR* 3.7 6.5 + - - -
106C LYS* 3.0 38.1 + - - +
107C SER* 2.7 39.7 + - - -
141C PHE* 3.5 2.7 - - - -
198C CYS 3.6 13.7 - - - -
199C HIS* 4.1 22.6 + - - -
200C VAL 4.2 4.0 - - - -
201C PRO* 4.2 2.8 - - - +
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Residues in contact with TRP 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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103C SER* 1.3 70.7 - - - +
105C THR* 1.3 73.2 + - - +
107C SER* 3.2 3.3 + - - -
108C GLN* 2.8 38.4 + - + -
118C LEU* 3.4 17.4 - - + +
141C PHE* 3.2 32.1 - + + -
142C LEU 2.8 25.0 + - - -
143C GLY 4.3 14.1 - - - -
144C LEU 4.0 6.3 + - - -
145C SER* 3.6 26.9 - - - -
180C CYS* 3.3 32.3 - - + -
181C ALA 4.8 0.2 - - - -
198C CYS* 3.0 16.5 + - + +
156G VAL* 3.9 26.9 - - + -
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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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103C SER* 3.3 6.7 + - - -
104C TRP* 1.3 95.1 - - - +
106C LYS* 1.3 64.0 + - + +
108C GLN* 3.4 4.2 + - + +
109C LYS* 3.0 23.5 + - + +
178C GLU* 5.4 4.0 + - - -
198C CYS* 4.8 3.2 + - - +
199C HIS* 6.0 3.5 - - - -
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Residues in contact with LYS 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 GLN* 3.5 32.5 - - + +
103C SER* 3.0 28.6 + - - +
105C THR* 1.3 80.1 - - + +
107C SER* 1.3 57.8 + - - +
109C LYS* 3.3 7.6 + - - +
110C ASN* 2.9 31.8 + - - +
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Residues in contact with SER 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C GLN* 3.4 19.9 + - - +
103C SER 2.7 26.6 + - - -
104C TRP* 3.5 7.4 - - - -
106C LYS* 1.3 74.2 - - - +
108C GLN* 1.3 56.3 + - - +
110C ASN* 3.2 8.9 + - - +
111C CYS* 2.9 31.4 + - - -
118C LEU* 4.0 8.7 - - - -
141C PHE* 3.8 7.1 - - - -
202C GLN 4.2 2.3 + - - -
204C SER* 3.6 30.8 + - - -
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Residues in contact with GLN 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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104C TRP* 2.8 31.5 + - + +
105C THR* 3.8 4.7 - - - +
107C SER* 1.3 68.4 - - - +
109C LYS* 1.3 61.9 + - - +
111C CYS* 3.3 1.7 + - - +
112C SER* 2.9 33.8 + - - -
116C ALA 4.5 2.0 + - - -
117C ASP* 2.8 28.1 + - - +
118C LEU* 2.9 45.5 + - + +
156G VAL* 3.5 25.9 - - + +
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Residues in contact with LYS 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* 3.0 14.7 + - + +
106C LYS* 3.4 12.6 - - - +
108C GLN* 1.3 76.5 - - - +
110C ASN* 1.3 61.1 + - - +
112C SER* 3.1 14.1 + - - -
113C VAL* 2.9 50.2 + - + +
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Residues in contact with ASN 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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98C SER* 4.9 12.5 + - - +
102C GLN* 2.1 37.1 + - - +
106C LYS 2.9 12.0 + - - +
107C SER* 3.2 10.7 + - - +
109C LYS* 1.3 80.5 - - - +
111C CYS* 1.3 61.1 + - - +
113C VAL* 3.5 7.9 + - - +
114C MET* 3.3 35.8 + - + +
206C CYS* 5.8 0.4 - - - -
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Residues in contact with CYS 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 SER 2.9 17.4 + - - -
108C GLN 3.6 7.6 - - - +
110C ASN* 1.3 75.0 - - - +
112C SER* 1.3 57.1 + - - +
114C MET* 3.1 13.3 + - - +
115C GLY 3.3 0.3 + - - -
116C ALA* 2.8 27.3 + - - -
117C ASP* 3.6 19.5 - - - +
118C LEU* 3.6 23.8 - - - +
204C SER* 5.0 1.6 - - - -
206C CYS* 2.1 55.2 - - + -
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Residues in contact with SER 112 (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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108C GLN* 2.9 25.9 + - - -
109C LYS* 3.4 17.5 + - - +
111C CYS* 1.3 78.4 - - - +
113C VAL* 1.3 57.5 + - - +
115C GLY* 2.9 19.1 + - - -
116C ALA 3.2 13.0 + - - -
117C ASP* 5.5 0.2 - - - -
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Residues in contact with VAL 113 (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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109C LYS* 2.9 46.5 + - + +
110C ASN* 3.9 9.0 - - - +
111C CYS 3.3 0.4 - - - -
112C SER* 1.3 74.6 - - - +
114C MET* 1.3 60.0 + - + +
115C GLY 3.1 1.1 + - - -
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Residues in contact with MET 114 (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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87C TRP* 3.5 33.6 - - + +
96C PHE* 3.7 37.9 - - + -
98C SER* 5.1 6.1 - - - +
110C ASN* 3.3 26.6 + - + +
111C CYS 3.1 8.8 + - - +
113C VAL* 1.3 77.0 - - + +
115C GLY* 1.3 59.0 + - - +
206C CYS* 4.0 14.8 - - - -
208C MET* 4.2 15.8 - - - +
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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