Contacts of the helix formed by residues 140 - 153 (chain B) in PDB entry 4I5L
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 140 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138B SER 4.2 1.2 + - - -
139B VAL* 1.3 73.9 - - - +
141B VAL* 1.3 64.2 + - - +
142B ASP* 3.7 8.5 + - - +
143B ALA* 3.2 38.9 + - + +
144B VAL* 3.3 14.7 + - - +
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Residues in contact with VAL 141 (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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139B VAL* 3.2 17.8 + - + +
140B ASN* 1.3 73.4 + - - +
142B ASP* 1.3 59.8 + - - +
144B VAL* 3.1 6.8 + - - +
145B ILE* 2.8 56.0 + - + +
204B ARG* 4.2 18.6 - - + +
207B LEU* 4.2 31.0 - - + +
208B GLN* 4.9 15.5 - - + +
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Residues in contact with ASP 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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140B ASN* 3.3 8.2 - - - +
141B VAL* 1.3 87.0 - - - +
143B ALA* 1.3 56.5 + - - +
145B ILE* 3.4 11.0 + - - +
146B SER* 2.9 29.5 + - - -
204B ARG* 5.9 1.4 + - - -
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Residues in contact with ALA 143 (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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140B ASN* 3.2 34.8 + - + +
142B ASP* 1.3 74.4 - - - +
144B VAL* 1.3 61.7 + - + +
146B SER* 3.3 7.1 + - - -
147B LYS* 3.0 28.6 + - - +
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Residues in contact with VAL 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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139B VAL* 5.1 7.6 - - + -
140B ASN 3.3 13.6 + - - +
141B VAL* 3.1 7.0 + - - +
143B ALA* 1.3 74.3 - - + +
145B ILE* 1.3 65.0 + - - +
147B LYS* 3.1 6.6 + - - +
148B ILE* 2.8 40.3 + - + +
171B ALA 4.1 14.4 - - - +
172B CYS* 4.2 9.2 - - - +
203B TRP* 3.9 18.2 - - - +
207B LEU* 3.9 16.4 - - + -
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Residues in contact with ILE 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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141B VAL* 2.8 38.8 + - + +
142B ASP* 3.7 12.1 - - - +
144B VAL* 1.3 72.8 - - - +
146B SER* 1.3 57.0 - - - +
148B ILE* 3.2 17.6 + - + +
149B GLU* 2.8 44.9 + - - +
200B VAL* 3.8 29.2 - - + +
204B ARG* 4.1 41.7 - - + +
207B LEU* 4.7 5.4 - - + -
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Residues in contact with SER 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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142B ASP 2.9 17.8 + - - -
143B ALA* 3.5 8.7 - - - -
145B ILE* 1.3 76.0 - - - +
147B LYS* 1.3 62.9 + - - +
149B GLU* 3.1 15.3 + - - +
150B SER* 3.0 23.5 + - - -
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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 ALA 3.0 17.2 + - - +
144B VAL* 3.6 6.1 - - - +
146B SER* 1.3 77.4 + - - +
148B ILE* 1.3 59.9 + - - +
150B SER* 3.5 11.4 + - - -
151B THR* 2.9 38.0 + - - -
170B LYS 5.6 1.1 - - - -
171B ALA* 3.9 29.4 - - + +
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Residues in contact with ILE 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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144B VAL* 2.8 32.6 + - + +
145B ILE* 3.5 14.6 - - + +
147B LYS* 1.3 71.3 - - - +
149B GLU* 1.3 59.3 + - - +
151B THR* 3.2 3.1 + - - -
152B PHE* 2.9 54.1 + - + -
168B VAL* 5.3 1.6 - - + +
171B ALA* 4.4 15.3 - - + +
172B CYS* 4.0 18.6 - - - -
196B VAL* 4.8 0.4 - - + -
199B PHE* 3.9 11.2 - - + -
200B VAL* 3.7 20.6 - - + -
203B TRP* 3.6 33.7 - - + -
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Residues in contact with GLU 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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145B ILE* 2.8 32.9 + - - +
146B SER* 3.1 15.7 + - - +
148B ILE* 1.3 77.0 - - - +
150B SER* 1.3 57.7 + - - +
152B PHE* 3.4 3.5 + - - +
153B ALA* 3.0 24.9 + - - +
158B GLU* 5.1 1.9 - - - +
196B VAL* 4.0 22.9 - - + +
200B VAL* 4.2 10.2 - - + +
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Residues in contact with SER 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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146B SER 3.0 11.6 + - - -
147B LYS* 3.5 17.0 + - - -
149B GLU* 1.3 73.3 - - - +
151B THR* 1.3 69.1 + - - +
153B ALA* 3.3 20.7 + - - +
154B ARG* 3.7 10.7 + - - +
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Residues in contact with THR 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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147B LYS* 2.9 27.1 + - - -
148B ILE* 3.2 5.1 + - - -
150B SER* 1.3 77.4 + - - +
152B PHE* 1.3 63.3 + - - +
154B ARG* 3.1 34.3 + - - +
155B PHE* 3.6 23.0 - - + -
167B LEU* 4.2 29.4 - - + +
168B VAL* 4.5 6.1 - - + +
171B ALA* 3.5 16.6 - - + +
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Residues in contact with PHE 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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148B ILE* 2.9 46.5 + - + +
149B GLU 3.9 1.3 - - - +
151B THR* 1.3 67.6 - - - +
153B ALA* 1.3 56.6 + - - +
154B ARG 3.0 5.4 - - - -
155B PHE* 3.0 34.6 + + - +
158B GLU* 3.4 32.1 - - + +
160B ALA* 3.6 20.4 - - + -
165B MET* 5.2 0.4 - - - -
168B VAL* 3.7 20.9 - - + -
194B VAL* 3.4 24.2 - - + -
195B SER 3.9 0.9 - - - -
196B VAL* 3.5 40.4 - - + -
199B PHE* 3.6 29.8 - + + -
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Residues in contact with ALA 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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149B GLU 3.0 14.3 + - - +
150B SER* 3.4 17.7 - - - +
151B THR 3.2 0.6 - - - -
152B PHE* 1.3 75.7 - - - +
154B ARG* 1.3 59.4 + - - +
155B PHE 3.3 3.5 - - - +
158B GLU* 3.8 23.1 - - - +
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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