Contacts of the helix formed by residues 135 - 149 (chain C) in PDB entry 2BZN
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 135 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A SER* 3.5 12.8 - - - -
24A LEU* 5.2 7.0 - - - -
25A LYS 6.0 0.4 - - - -
317A THR* 6.6 0.2 - - - -
132C ASN* 3.8 19.1 + - - +
133C GLY 3.4 0.4 - - - +
134C TYR* 1.3 78.8 - - - +
136C GLU* 1.3 58.5 + - - +
137C HIS* 3.7 11.4 + - - +
138C PHE* 3.0 36.0 + - - +
139C VAL* 3.2 15.1 + - - +
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Residues in contact with GLU 136 (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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21A ARG* 3.0 41.8 + - - +
22A SER 2.7 19.2 + - - +
23A THR* 2.9 31.5 + - - +
24A LEU 5.6 0.2 - - - +
134C TYR 3.7 0.4 + - - -
135C SER* 1.3 69.5 - - - +
137C HIS* 1.3 65.1 + - - +
139C VAL* 3.4 2.8 + - - +
140C GLU* 3.1 41.0 + - + +
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Residues in contact with HIS 137 (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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24A LEU 5.0 5.7 + - - +
25A LYS* 4.5 20.0 - - - +
105C THR* 4.3 33.8 + - - +
135C SER* 3.1 11.3 - - - +
136C GLU* 1.3 79.8 - - - +
138C PHE* 1.3 61.6 + - - +
140C GLU* 3.5 5.0 + - + +
141C PHE* 3.1 26.7 + + + +
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Residues in contact with PHE 138 (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* 3.6 21.8 - - + -
128C LEU* 3.7 18.4 - - + -
129C ASP 4.6 0.2 - - - -
130C VAL* 3.6 22.4 - - + -
132C ASN 4.4 6.1 - - - +
133C GLY* 3.7 24.7 - - - +
135C SER* 3.0 23.1 + - - +
137C HIS* 1.3 74.1 + - - +
139C VAL* 1.3 60.1 + - - +
141C PHE* 3.2 19.8 + + - +
142C VAL* 2.9 41.7 + - + +
156C ALA* 3.9 8.7 - - + -
157C GLY* 3.7 37.7 - - - -
168C LEU* 3.9 14.6 - - + -
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Residues in contact with VAL 139 (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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21A ARG* 4.2 8.1 - - - +
133C GLY 4.8 0.4 - - - +
135C SER 3.2 8.8 + - - +
136C GLU* 3.6 10.1 - - - +
138C PHE* 1.3 75.6 - - - +
140C GLU* 1.3 62.4 + - - +
142C VAL* 3.3 5.0 + - - +
143C LYS* 3.1 41.3 + - - +
164C MET* 3.4 33.2 - - + -
167C GLU* 3.8 21.5 - - - +
168C LEU* 4.0 17.7 - - + -
171C SER* 3.5 21.5 - - - +
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Residues in contact with GLU 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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21A ARG* 5.7 0.5 + - - -
136C GLU* 3.1 30.6 + - + +
137C HIS* 4.0 5.6 - - + +
138C PHE 3.2 0.2 - - - -
139C VAL* 1.3 76.3 - - - +
141C PHE* 1.3 61.9 + - - +
143C LYS* 2.5 45.3 + - - +
144C ASP* 3.0 34.1 + - - +
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Residues in contact with PHE 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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103C SER* 4.3 0.2 - - - -
104C GLY 3.4 25.4 - - - -
105C THR* 3.5 34.5 - - + -
110C PHE* 3.9 28.5 - + + -
128C LEU* 3.7 34.5 - - + -
129C ASP 5.9 0.2 - - - -
137C HIS* 3.1 21.0 + + + +
138C PHE* 3.2 14.6 + + - +
140C GLU* 1.3 75.3 - - - +
142C VAL* 1.3 66.1 + - - +
144C ASP* 3.2 11.3 + - + +
145C VAL* 3.0 46.6 + - + +
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Residues in contact with VAL 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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128C LEU* 4.2 14.1 - - + -
138C PHE* 2.9 46.3 + - + +
139C VAL* 3.5 9.2 - - - +
141C PHE* 1.3 75.9 - - - +
143C LYS* 1.3 62.4 + - - +
145C VAL* 3.2 3.3 + - - +
146C ARG* 3.0 22.2 + - - +
154C ILE* 4.7 5.6 - - + +
156C ALA* 4.1 10.8 - - + -
168C LEU* 4.1 11.0 - - + +
171C SER* 3.8 12.6 - - - +
172C GLY 4.2 1.1 - - - -
173C ALA* 3.7 34.5 - - + +
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Residues in contact with LYS 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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139C VAL* 3.1 18.1 + - - +
140C GLU* 2.5 48.5 + - - +
141C PHE 3.3 0.2 - - - -
142C VAL* 1.3 78.0 - - - +
144C ASP* 1.3 58.4 + - - +
146C ARG* 3.4 3.6 + - - +
147C LYS* 2.9 44.6 + - - +
167C GLU* 5.5 1.2 + - - -
171C SER* 3.3 41.3 - - - +
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Residues in contact with ASP 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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110C PHE* 5.7 2.7 - - + -
140C GLU* 3.0 20.3 + - - +
141C PHE* 3.2 14.6 + - + +
143C LYS* 1.3 74.3 - - - +
145C VAL* 1.3 63.7 + - + +
147C LYS* 3.4 22.8 + - - +
148C ARG* 3.0 29.5 + - - +
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Residues in contact with VAL 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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110C PHE* 3.6 27.1 - - + -
126C ILE* 4.0 22.0 - - + -
128C LEU* 4.0 21.1 - - + -
141C PHE* 3.0 39.2 + - + +
142C VAL 3.2 3.6 + - - +
144C ASP* 1.3 73.5 - - + +
146C ARG* 1.3 56.2 + - - +
148C ARG* 3.2 5.8 + - - +
149C PHE* 2.7 40.0 + - + +
154C ILE* 4.0 14.8 - - + -
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Residues in contact with ARG 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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40C ASN* 3.8 9.6 - - + +
41C SER* 3.7 9.6 - - - +
142C VAL 3.0 16.5 + - - +
143C LYS 3.6 5.8 - - - +
145C VAL* 1.3 73.6 - - - +
147C LYS* 1.3 65.0 + - - +
149C PHE 3.1 17.0 + - - -
150C PRO* 3.2 40.7 + - - +
152C HIS 2.9 21.8 + - - -
154C ILE* 3.6 22.4 - - + +
171C SER 4.3 1.8 - - - +
172C GLY* 2.8 41.9 + - - -
174C ASP* 2.6 34.4 + - - -
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Residues in contact with LYS 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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143C LYS* 2.9 31.6 + - - +
144C ASP* 3.6 27.8 + - - +
145C VAL 3.3 0.2 - - - -
146C ARG* 1.3 78.6 - - - +
148C ARG* 1.3 63.2 + - - +
150C PRO* 3.7 10.3 - - - +
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Residues in contact with ARG 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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110C PHE* 4.2 8.1 - - + -
114C GLU* 2.9 31.8 + - - +
118C GLU* 5.9 2.4 + - - +
144C ASP 3.0 18.1 + - - +
145C VAL* 3.7 5.4 - - - +
147C LYS* 1.3 78.6 - - + +
149C PHE* 1.3 96.7 + - + +
150C PRO* 3.4 6.3 - - - +
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Residues in contact with PHE 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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110C PHE* 4.0 17.9 - + - -
114C GLU* 4.2 13.0 - - + -
117C LEU* 3.7 32.8 - - + -
118C GLU 5.8 0.2 - - - -
126C ILE* 3.9 19.3 - - + -
145C VAL* 2.7 23.9 + - + +
146C ARG* 3.1 18.2 + - - +
148C ARG* 1.3 127.5 - - + +
150C PRO* 1.3 65.3 - - - +
151C GLN 3.2 4.4 + - - -
152C HIS* 3.2 40.3 + + + +
154C ILE* 4.6 0.9 - - - +
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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