Contacts of the helix formed by residues 135 - 149 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21C ARG* 5.3 0.2 - - - -
22C SER* 3.6 16.2 - - - -
24C LEU 6.0 1.6 - - - -
317C THR* 6.3 1.1 - - - -
132D ASN* 3.8 17.0 + - - +
133D GLY 3.4 0.8 - - - -
134D TYR* 1.3 79.3 - - - +
136D GLU* 1.3 65.7 + - - +
137D HIS* 3.7 11.5 + - - +
138D PHE* 3.1 32.2 + - - +
139D VAL* 3.1 16.6 + - - +
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Residues in contact with GLU 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C ARG* 2.6 44.4 + - - +
22C SER 2.9 18.7 + - - +
23C THR* 4.0 21.6 - - + +
135D SER* 1.3 72.2 - - - +
137D HIS* 1.3 64.3 + - - +
138D PHE 3.1 0.2 + - - -
139D VAL* 3.2 3.6 + - - +
140D GLU* 3.0 43.5 + - + +
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Residues in contact with HIS 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C LYS* 6.3 3.8 - - - +
105D THR* 3.8 33.6 + - - +
106D GLY* 4.5 9.6 - - - -
135D SER* 3.1 10.4 + - - +
136D GLU* 1.3 81.5 - - - +
138D PHE* 1.3 60.9 + - - +
140D GLU* 3.5 6.5 + - + +
141D PHE* 3.1 23.4 + + - +
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Residues in contact with PHE 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D GLY 6.3 0.2 - - - -
105D THR* 3.8 20.6 - - + -
128D LEU* 3.8 22.2 - - + -
130D VAL* 3.6 24.0 - - + -
132D ASN 4.3 7.0 - - - +
133D GLY* 3.5 26.5 - - - +
135D SER* 3.1 22.9 + - - +
137D HIS* 1.3 75.9 + - - +
139D VAL* 1.3 64.7 - - - +
141D PHE* 3.1 9.0 + + + +
142D VAL* 2.9 42.1 + - + +
156D ALA* 4.0 2.0 - - + -
157D GLY 3.5 37.7 - - - -
168D LEU* 4.1 15.0 - - + -
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Residues in contact with VAL 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C ARG* 4.1 15.3 - - - +
133D GLY 4.8 0.2 - - - +
135D SER 3.1 9.4 + - - +
136D GLU* 3.5 8.3 - - - +
138D PHE* 1.3 75.6 - - - +
140D GLU* 1.3 60.0 + - - +
142D VAL* 3.1 6.7 + - - +
143D LYS* 3.0 46.9 + - - +
164D MET* 3.6 31.6 - - + -
167D GLU* 4.1 13.2 - - + +
168D LEU* 3.9 17.0 - - + -
171D SER* 3.4 22.4 - - - +
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Residues in contact with GLU 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D GLU* 3.0 39.7 + - + +
137D HIS* 3.9 6.3 - - + +
139D VAL* 1.3 76.3 - - + +
141D PHE* 1.3 55.9 + - - +
143D LYS* 3.3 37.9 + - - +
144D ASP* 3.0 36.2 + - - +
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Residues in contact with PHE 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D SER* 4.0 7.4 - - - -
104D GLY 3.2 23.8 - - - -
105D THR* 3.8 18.4 - - + -
106D GLY* 3.6 32.1 - - - -
110D PHE* 3.8 31.9 - + + -
128D LEU* 3.9 20.6 - - + -
137D HIS* 3.1 16.7 + + + +
138D PHE* 3.1 13.6 + + - +
140D GLU* 1.3 73.9 - - - +
142D VAL* 1.3 65.1 + - - +
144D ASP* 3.2 11.5 + - + +
145D VAL* 3.0 43.9 + - + +
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Residues in contact with VAL 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D LEU* 4.1 12.3 - - + -
138D PHE* 2.9 47.6 + - + +
139D VAL* 3.4 9.0 - - - +
141D PHE* 1.3 74.7 - - - +
143D LYS* 1.3 64.7 + - - +
145D VAL* 3.3 2.1 + - - +
146D ARG* 3.0 22.3 + - - +
154D ILE* 4.6 6.5 - - + +
156D ALA* 4.0 11.7 - - + -
168D LEU* 4.3 9.2 - - + +
171D SER* 4.0 12.8 - - - +
172D GLY 4.2 1.8 - - - -
173D ALA* 3.7 35.0 - - + +
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Residues in contact with LYS 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C ARG* 5.8 0.6 - - - +
139D VAL* 3.0 29.7 + - - +
140D GLU* 3.4 41.5 + - - +
142D VAL* 1.3 76.8 - - - +
144D ASP* 1.3 64.8 + - - +
146D ARG* 3.3 1.7 + - - +
147D LYS* 3.0 52.4 + - + +
167D GLU* 5.2 2.6 + - - -
171D SER* 3.5 39.2 + - - +
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Residues in contact with ASP 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D PHE* 4.4 14.9 - - + -
140D GLU* 3.0 22.0 + - - +
141D PHE* 3.2 13.4 + - + +
143D LYS* 1.3 77.1 - - - +
145D VAL* 1.3 62.6 + - - +
147D LYS* 3.3 9.5 + - - +
148D ARG* 2.9 24.3 + - - +
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Residues in contact with VAL 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D PHE* 3.7 21.8 - - + -
113D LEU* 4.6 2.9 - - + -
126D ILE* 3.8 32.3 - - + -
128D LEU* 3.8 19.3 - - + -
141D PHE* 3.0 45.8 + - + +
142D VAL 3.8 3.6 - - - +
144D ASP* 1.3 75.2 - - - +
146D ARG* 1.3 58.4 + - - +
148D ARG 3.3 0.5 + - - -
149D PHE* 2.9 37.0 + - + +
154D ILE* 3.8 11.0 - - + -
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Residues in contact with ARG 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D ASN* 3.7 15.3 - - - +
41D SER* 3.7 5.1 - - - +
142D VAL 3.0 17.8 + - - +
143D LYS 3.5 5.6 - - - +
144D ASP 3.3 0.2 - - - -
145D VAL* 1.3 76.8 - - - +
147D LYS* 1.3 67.2 + - + +
149D PHE 3.1 18.0 + - - -
150D PRO* 3.3 39.4 + - - +
152D HIS 2.9 21.6 + - - -
154D ILE* 3.6 26.6 - - + +
171D SER 4.4 3.4 - - - +
172D GLY* 2.9 41.0 + - - -
174D ASP* 2.7 34.1 + - - -
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Residues in contact with LYS 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143D LYS* 3.0 56.9 + - + +
144D ASP* 3.7 8.5 - - - +
146D ARG* 1.3 82.6 - - + +
148D ARG* 1.3 61.9 + - - +
150D PRO* 4.0 10.4 - - - +
171D SER 5.2 1.6 + - - -
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Residues in contact with ARG 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D PHE* 4.0 13.9 - - + -
114D GLU* 2.4 29.2 + - - +
118D GLU* 2.9 35.8 + - - +
144D ASP 2.9 16.1 + - - +
145D VAL 3.3 3.3 + - - +
147D LYS* 1.3 78.3 - - - +
149D PHE* 1.3 97.1 + - + +
150D PRO* 3.3 8.2 - - - +
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Residues in contact with PHE 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D PHE* 4.2 13.2 - + - -
113D LEU* 4.6 6.5 - - + -
114D GLU* 3.8 25.4 - - + -
117D LEU* 3.7 33.0 - - + -
118D GLU* 5.7 0.7 - - + -
126D ILE* 3.7 16.6 - - + -
145D VAL* 2.9 24.9 + - + +
146D ARG* 3.1 19.8 + - - +
148D ARG* 1.3 125.1 - - + +
150D PRO* 1.4 61.1 - - - +
151D GLN 3.2 2.7 - - - -
152D HIS* 3.2 40.2 + + + +
154D 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