Contacts of the helix formed by residues 139 - 150 (chain C) in PDB entry 3CB4
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 ASP 139 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104C ALA* 3.0 23.5 + - - +
105C GLY 5.7 0.4 - - - +
137C ALA 3.6 4.4 + - - +
138C ALA* 1.3 74.7 - - - +
140C PRO* 1.3 64.8 - - - +
141C GLU* 3.4 8.3 + - - +
142C ARG* 3.2 64.4 + - - +
143C VAL* 3.3 14.9 + - - +
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Residues in contact with PRO 140 (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 ALA* 4.3 8.5 - - + -
130C LEU* 4.0 17.0 - - + +
133C ILE* 4.8 16.2 - - + -
138C ALA* 4.1 6.7 - - + +
139C ASP* 1.3 88.5 - - - +
141C GLU* 1.3 74.2 + - - +
143C VAL* 4.1 1.7 - - + +
144C ALA* 3.2 27.0 + - - +
160C ARG* 3.6 28.2 + - - +
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Residues in contact with GLU 141 (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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139C ASP* 3.4 5.4 + - - +
140C PRO* 1.3 92.6 - - - +
142C ARG* 1.3 64.6 + - - +
144C ALA* 3.2 8.0 + - - +
145C GLU* 3.0 34.0 + - - +
160C ARG* 3.3 25.3 + - - -
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Residues in contact with ARG 142 (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 ALA 4.5 2.0 + - - -
105C GLY 4.9 7.1 + - - -
106C GLN 4.9 4.6 + - - -
139C ASP* 3.2 58.0 + - - +
141C GLU* 1.3 78.2 - - - +
143C VAL* 1.3 77.5 + - - +
145C GLU* 3.4 19.6 + - + +
146C GLU* 3.2 43.7 + - + +
437C ASN* 5.9 5.4 - - - +
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Residues in contact with VAL 143 (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 VAL* 3.9 26.7 - - + -
103C ASP 4.1 4.0 - - - +
104C ALA* 3.3 24.5 - - - +
106C GLN 4.9 0.4 - - - +
107C GLY* 4.4 13.7 - - - +
108C VAL* 6.2 0.2 - - + -
130C LEU* 4.0 18.2 - - + -
139C ASP 3.3 20.5 + - - +
140C PRO 4.2 2.9 - - - +
141C GLU 3.2 0.4 - - - -
142C ARG* 1.3 85.9 - - - +
144C ALA* 1.3 65.3 + - - +
146C GLU* 3.1 13.6 + - + +
147C ILE* 3.1 25.8 + - + +
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Residues in contact with ALA 144 (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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130C LEU* 4.8 8.5 - - + +
140C PRO 3.2 19.5 + - - +
141C GLU* 3.2 9.1 + - - +
143C VAL* 1.3 77.2 - - - +
145C GLU* 1.3 62.5 + - + +
147C ILE* 3.5 11.9 + - - +
148C GLU* 3.3 23.9 + - - +
155C ALA* 4.2 26.1 - - + +
156C THR* 5.8 1.6 - - + -
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Residues in contact with GLU 145 (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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141C GLU* 3.0 25.4 + - - +
142C ARG* 3.4 19.0 + - + +
144C ALA* 1.3 78.1 - - + +
146C GLU* 1.3 57.2 + - + +
148C GLU* 3.8 4.1 + - - +
149C ASP* 3.1 29.8 + - - +
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Residues in contact with GLU 146 (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* 4.2 6.4 - - - -
108C VAL* 3.8 31.0 + - + +
142C ARG* 3.2 38.2 + - + +
143C VAL* 3.1 15.6 + - + +
145C GLU* 1.3 77.7 - - + +
147C ILE* 1.3 61.0 + - + +
149C ASP* 4.1 4.9 - - - -
150C ILE* 2.8 49.8 + - + +
437C ASN* 5.9 1.4 + - - -
438C GLN* 4.7 17.7 + - + +
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Residues in contact with ILE 147 (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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100C LEU* 4.4 9.9 - - + -
102C VAL* 3.8 31.2 - - + -
108C VAL* 5.4 5.6 - - + -
128C PRO* 4.9 9.2 - - + -
129C VAL 5.6 1.1 - - - +
130C LEU* 4.0 22.7 - - + -
143C VAL* 3.1 19.5 + - + +
144C ALA* 3.9 8.3 - - - +
145C GLU 3.5 0.2 - - - -
146C GLU* 1.3 75.6 - - + +
148C GLU* 1.3 63.3 + - - +
151C VAL* 3.1 27.6 + - + +
152C GLY 3.1 18.0 + - - -
153C ILE* 3.6 29.2 + - + -
155C ALA* 4.1 13.9 - - + -
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Residues in contact with GLU 148 (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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144C ALA 3.3 13.6 + - - +
145C GLU* 4.1 5.2 - - - +
146C GLU 3.3 0.4 - - - -
147C ILE* 1.3 78.7 - - - +
149C ASP* 1.3 61.0 + - - +
152C GLY* 3.6 14.2 - - - -
153C ILE 3.3 17.9 - - - +
154C ASP* 3.6 12.5 - - - +
155C ALA* 3.0 26.5 + - - +
156C THR* 3.9 19.3 + - - +
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Residues in contact with ASP 149 (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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145C GLU 3.1 20.0 + - - +
146C GLU* 3.1 7.5 + - - +
148C GLU* 1.3 79.4 - - - +
150C ILE* 1.3 65.8 + - + +
152C GLY* 4.4 2.1 + - - -
434C TYR 4.5 0.9 - - - +
435C HIS* 3.2 49.0 + - + +
436C GLY 4.7 0.5 + - - -
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Residues in contact with ILE 150 (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 VAL* 3.9 24.0 - - + -
113C LEU* 4.0 17.5 - - + -
117C TYR* 3.1 30.7 + - - +
146C GLU* 2.8 32.6 + - + +
149C ASP* 1.3 74.8 - - + +
151C VAL* 1.3 65.6 + - + +
409C LEU* 4.3 20.4 - - + -
435C HIS* 3.6 45.7 + - + +
438C GLN* 4.9 10.8 - - + +
440C ALA* 5.4 1.1 - - + -
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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