Contacts of the helix formed by residues 148 - 158 (chain B) in PDB entry 4A69
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 ASN 148 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61B PHE* 4.0 10.2 - - + -
62B HIS* 2.9 16.9 + - - +
133B LEU 3.8 11.6 - - - +
134B HIS* 3.3 22.2 + - - +
136B ALA* 2.8 30.6 + - + +
147B VAL* 1.3 70.1 - - - +
149B ASP* 1.3 61.9 + - - +
150B ILE* 3.3 12.1 + - - +
151B VAL* 3.1 27.4 + - - +
152B ILE* 3.3 22.7 + - - +
176B GLY 3.8 13.9 - - - -
177B VAL* 3.9 2.0 - - - +
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Residues in contact with ASP 149 (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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107B TYR* 3.6 14.2 - - + -
108B THR* 3.8 35.8 - - - +
111B SER* 2.6 35.7 + - - +
112B LEU 5.5 0.2 + - - -
131B GLY* 3.2 5.6 - - - -
132B GLY 2.9 19.8 + - - -
133B LEU* 2.9 27.2 + - - -
147B VAL 3.1 4.8 + - - -
148B ASN* 1.3 72.1 - - - +
150B ILE* 1.3 58.4 + - - +
152B ILE* 3.5 2.9 + - - +
153B GLY* 2.9 26.7 + - - -
293B LEU* 4.0 4.0 - - - +
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Residues in contact with ILE 150 (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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132B GLY* 3.6 25.1 - - - -
134B HIS* 3.5 24.9 - - + -
148B ASN* 3.2 6.4 + - - +
149B ASP* 1.3 76.1 - - - +
151B VAL* 1.3 55.7 + - - +
153B GLY* 3.2 1.9 + - - -
154B ILE* 2.8 57.2 + - + +
166B TYR* 3.4 43.7 - - + +
177B VAL* 3.7 11.0 - - + -
253B VAL* 4.4 5.6 - - + -
255B GLN* 3.7 3.4 - - - +
293B LEU* 3.7 23.3 - - + -
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Residues in contact with VAL 151 (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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61B PHE* 3.6 35.2 - - + -
148B ASN* 3.1 31.8 + - + +
150B ILE* 1.3 74.8 - - - +
152B ILE* 1.3 58.6 + - - +
154B ILE* 3.2 1.7 + - - +
155B LEU* 2.8 42.2 + - + +
176B GLY 4.2 0.4 - - - +
177B VAL* 4.0 13.9 - - + -
180B ALA* 3.6 24.0 - - + -
181B PHE* 3.7 25.4 - - + -
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Residues in contact with ILE 152 (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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57B ASP 4.1 13.9 - - - +
58B MET* 3.6 31.0 - - - +
60B ARG* 3.7 14.6 + - + +
61B PHE* 4.2 17.7 - - + +
62B HIS* 4.4 3.1 - - + -
108B THR* 3.8 17.3 - - + -
112B LEU* 4.3 24.0 - - + -
147B VAL* 3.7 26.5 - - + -
148B ASN 3.3 10.6 + - - +
149B ASP* 3.8 7.4 - - - +
150B ILE 3.3 0.2 - - - -
151B VAL* 1.3 77.3 - - - +
153B GLY* 1.3 60.9 + - - +
155B LEU* 3.4 6.6 + - - +
156B GLU* 3.2 17.7 + - - +
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Residues in contact with GLY 153 (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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111B SER* 4.7 7.9 - - - -
112B LEU* 4.8 5.8 - - - +
115B ALA* 3.6 15.6 - - - +
149B ASP 2.9 16.0 + - - -
150B ILE* 3.7 2.9 - - - -
152B ILE* 1.3 74.0 - - - +
154B ILE* 1.3 60.5 + - - +
156B GLU* 3.2 7.5 + - - +
157B LEU* 3.0 31.5 + - - +
291B LEU* 5.3 6.7 - - - -
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Residues in contact with ILE 154 (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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150B ILE* 2.8 42.0 + - + +
151B VAL 3.9 2.7 - - - +
153B GLY* 1.3 70.3 - - - +
155B LEU* 1.3 66.6 + - - +
157B LEU* 3.1 6.3 + - - +
158B LEU* 3.0 23.7 + - + +
164B VAL* 4.1 15.7 - - + -
166B TYR* 4.1 25.8 - - + -
177B VAL* 4.4 1.6 - - + -
181B PHE* 3.8 20.6 - - + -
187B VAL* 3.7 32.3 - - + -
253B VAL* 3.9 23.6 - - + -
291B LEU* 6.1 0.2 - - + -
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Residues in contact with LEU 155 (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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60B ARG* 3.8 40.4 + - + +
61B PHE* 4.2 10.3 - - + -
151B VAL* 2.8 38.6 + - + +
152B ILE* 3.7 7.2 - - - +
154B ILE* 1.3 73.3 - - - +
156B GLU* 1.3 60.5 + - - +
158B LEU* 3.6 19.4 + - + +
159B LYS* 3.8 13.2 + - - +
181B PHE* 3.8 23.3 - - + -
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Residues in contact with GLU 156 (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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60B ARG* 2.6 42.7 + - - +
112B LEU* 3.7 15.7 - - + -
115B ALA* 4.3 8.1 - - + -
116B THR* 3.7 25.8 - - + +
119B ASN* 2.8 18.3 + - - +
152B ILE 3.2 5.0 + - - +
153B GLY 3.2 10.0 + - - +
154B ILE 3.1 0.4 - - - -
155B LEU* 1.3 75.0 - - - +
157B LEU* 1.3 64.2 + - - +
159B LYS* 3.2 37.0 + - - +
505B GOL 5.5 1.3 - - - -
506B GOL 2.6 31.6 + - - +
501C I0P 4.8 5.3 + - - -
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Residues in contact with LEU 157 (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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115B ALA* 3.7 33.9 - - + +
118B LEU* 4.3 7.6 - - + -
119B ASN* 3.6 13.2 - - - +
153B GLY 3.0 19.3 + - - +
154B ILE* 3.1 8.9 + - + +
156B GLU* 1.3 76.0 - - - +
158B LEU* 1.3 51.6 + - - +
160B TYR 3.1 3.6 + - - -
161B HIS* 2.8 40.6 + - + +
164B VAL* 4.2 18.6 - - + -
251B CYS* 3.6 29.4 - - - -
253B VAL* 3.6 30.7 - - + -
291B LEU* 4.8 4.0 - - + -
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Residues in contact with LEU 158 (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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154B ILE* 3.0 20.8 + - + +
155B LEU* 3.8 17.5 - - + +
156B GLU 3.2 0.6 - - - -
157B LEU* 1.3 70.3 - - - +
159B LYS* 1.3 65.4 + - - +
160B TYR 3.1 3.1 + - - -
161B HIS 3.6 8.7 + - - +
164B VAL* 3.8 11.9 - - + -
181B PHE* 4.3 14.6 - - + -
186B ARG* 2.8 78.4 + - + +
187B VAL* 3.7 22.0 - - + -
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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