Contacts of the helix formed by residues 135 - 149 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B ASN* 3.7 16.9 + - - +
133B GLY 3.4 1.4 - - - +
134B TYR* 1.3 78.1 - - - +
136B GLU* 1.3 64.8 + - - +
137B HIS* 3.8 12.6 + - - +
138B PHE* 2.9 32.2 + - - +
139B VAL* 3.0 13.6 + - - +
22D SER* 3.6 14.1 - - - -
24D LEU 6.2 1.3 - - - -
317D THR* 6.5 0.2 - - - -
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Residues in contact with GLU 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B TYR 3.7 0.8 + - - -
135B SER* 1.3 70.7 - - - +
137B HIS* 1.3 57.7 + - - +
139B VAL* 3.0 4.0 + - - +
140B GLU* 2.8 50.2 + - + +
21D ARG* 3.2 39.6 + - - +
22D SER 3.0 19.9 + - - +
23D THR* 3.4 26.9 - - + +
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Residues in contact with HIS 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B THR* 3.3 41.2 + - - +
135B SER* 3.8 10.8 + - - +
136B GLU* 1.3 79.2 - - - +
138B PHE* 1.3 63.2 + - - +
140B GLU* 3.4 7.3 + - + +
141B PHE* 3.0 22.8 + + + +
24D LEU 5.9 2.2 - - - +
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Residues in contact with PHE 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B GLY 6.3 0.2 - - - -
105B THR* 3.8 14.6 - - + -
128B LEU* 3.7 28.9 - - + -
129B ASP 4.5 0.2 - - - -
130B VAL* 3.8 29.6 - - + -
132B ASN 4.4 5.8 - - - +
133B GLY* 3.7 26.9 - - - +
135B SER* 2.9 27.1 + - - +
137B HIS* 1.3 69.3 + - - +
139B VAL* 1.3 65.1 + - - +
141B PHE* 3.1 11.0 + + + +
142B VAL* 3.0 36.4 + - + +
156B ALA* 3.9 10.3 - - + -
157B GLY 3.6 30.7 - - - -
168B LEU* 4.1 16.4 - - + -
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Residues in contact with VAL 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B GLY 4.9 0.4 - - - +
135B SER 3.0 13.6 + - - +
136B GLU* 3.3 9.6 - - - +
138B PHE* 1.3 74.8 - - - +
140B GLU* 1.3 64.9 + - - +
142B VAL* 3.2 13.5 + - - +
143B LYS* 3.2 30.5 + - - +
164B MET* 3.5 31.9 - - + -
167B GLU* 4.0 20.0 - - + +
168B LEU* 4.1 16.2 - - + -
171B SER* 3.4 23.2 - - - +
21D ARG* 4.1 7.6 - - - +
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Residues in contact with GLU 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B GLU* 2.8 37.1 + - + +
137B HIS* 3.8 6.5 - - + +
139B VAL* 1.3 72.6 - - - +
141B PHE* 1.3 65.4 + - - +
143B LYS* 2.8 41.1 + - - +
144B ASP* 3.1 34.5 + - - +
21D ARG* 5.5 0.7 + - - -
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Residues in contact with PHE 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B SER* 4.1 5.4 - - - -
104B GLY 3.2 27.1 - - - -
105B THR* 3.7 41.5 - - + -
110B PHE* 4.0 30.1 - + + -
113B LEU* 5.9 0.2 - - + -
128B LEU* 3.9 31.2 - - + -
137B HIS* 3.0 16.4 + + + +
138B PHE* 3.1 15.7 + + - +
140B GLU* 1.3 76.6 - - - +
142B VAL* 1.3 61.2 + - - +
144B ASP* 3.3 13.5 + - + +
145B VAL* 3.0 40.9 + - + +
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Residues in contact with VAL 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B LEU* 4.1 16.6 - - + -
138B PHE* 3.0 47.2 + - + +
139B VAL* 3.2 8.5 + - - +
141B PHE* 1.3 74.8 - - - +
143B LYS* 1.3 53.7 + - - +
145B VAL* 3.1 2.4 + - - +
146B ARG* 2.8 34.0 + - - +
154B ILE* 4.6 8.1 - - + +
156B ALA* 4.1 6.5 - - + -
168B LEU* 4.3 10.5 - - + +
171B SER* 3.8 18.4 - - - +
172B GLY 4.3 1.3 - - - -
173B ALA* 3.8 28.5 - - + +
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Residues in contact with LYS 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B VAL* 3.2 17.1 + - - +
140B GLU* 2.8 45.4 + - - +
142B VAL* 1.3 77.4 - - - +
144B ASP* 1.3 58.1 + - - +
146B ARG* 3.2 4.3 + - - +
147B LYS* 2.9 50.3 + - - +
171B SER* 3.6 37.5 - - - +
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Residues in contact with ASP 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B PHE* 5.2 5.0 - - + -
140B GLU* 3.1 23.1 + - - +
141B PHE* 3.5 16.1 - - + +
143B LYS* 1.3 82.4 - - - +
145B VAL* 1.3 59.5 + - + +
147B LYS* 3.5 17.4 + - - +
148B ARG* 3.1 27.4 + - - +
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Residues in contact with VAL 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B PHE* 4.0 14.6 - - + -
113B LEU* 4.9 2.5 - - + -
126B ILE* 3.8 32.5 - - + -
128B LEU* 3.9 23.8 - - + -
141B PHE* 3.0 43.5 + - + +
142B VAL 3.7 3.4 - - - +
144B ASP* 1.3 73.1 - - + +
146B ARG* 1.3 61.4 + - - +
148B ARG* 3.3 4.6 + - - +
149B PHE* 2.9 37.7 + - + +
154B ILE* 3.9 9.4 - - + +
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Residues in contact with ARG 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B ASN* 3.6 15.1 - - - +
41B SER* 3.7 4.4 - - - +
142B VAL 2.8 19.8 + - - +
143B LYS 3.2 5.1 + - - +
145B VAL* 1.3 73.6 - - - +
147B LYS* 1.3 60.4 + - - +
149B PHE 3.1 16.5 + - - -
150B PRO* 3.2 40.2 + - - +
152B HIS 2.8 22.8 + - - -
154B ILE* 3.8 18.9 - - + +
171B SER 4.2 3.4 - - - +
172B GLY* 2.9 42.4 + - - -
174B ASP* 2.7 32.7 + - - -
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Residues in contact with LYS 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B LYS* 2.9 42.9 + - - +
144B ASP* 3.6 19.5 + - - +
145B VAL 3.3 0.2 - - - -
146B ARG* 1.3 77.1 - - - +
148B ARG* 1.3 62.0 - - - +
149B PHE 3.5 0.2 + - - -
150B PRO* 3.6 10.6 - - - +
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Residues in contact with ARG 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B PHE* 4.0 15.7 - - + -
114B GLU* 3.0 27.1 + - - +
118B GLU* 3.0 35.8 + - - +
144B ASP 3.1 15.6 + - - +
145B VAL* 3.3 1.3 + - - +
147B LYS* 1.3 80.8 - - - +
149B PHE* 1.3 101.6 + - + +
150B PRO* 3.3 7.0 - - - +
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Residues in contact with PHE 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B PHE* 4.3 14.8 - + - -
113B LEU* 4.7 6.1 - - + -
114B GLU* 4.1 20.0 - - + -
117B LEU* 3.7 28.9 - - + -
118B GLU* 5.5 0.9 - - + -
126B ILE* 3.9 17.0 - - + -
145B VAL* 2.9 18.9 + - + +
146B ARG* 3.1 18.7 + - - +
148B ARG* 1.3 133.2 - - + +
150B PRO* 1.4 63.7 - - - +
151B GLN 3.2 4.0 + - - -
152B HIS* 3.3 42.6 + + + +
154B ILE* 4.8 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