Contacts of the strand formed by residues 155 - 163 (chain B) in PDB entry 5D9I
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 THR 155 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153B ASN 3.5 9.1 + - - +
154B ARG* 1.3 81.3 - - - +
156B LEU* 1.3 69.2 + - - +
202B ARG* 2.8 59.9 + - + +
203B HIS* 3.3 11.2 - - - -
204B ARG* 3.8 22.0 - - + +
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Residues in contact with LEU 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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147B SER* 4.9 4.3 - - - -
154B ARG* 3.2 48.2 - - - +
155B THR* 1.3 82.4 - - - +
157B ALA* 1.3 65.3 + - - +
158B CYS 3.7 5.2 - - - +
159B PHE* 3.3 17.1 - - + -
202B ARG* 3.1 8.9 - - - +
203B HIS 2.9 26.0 + - - -
205B VAL* 4.0 13.0 - - + -
225B GLY* 3.5 35.2 - - - -
226B VAL 4.2 9.0 - - - +
227B ASN* 4.8 2.5 - - - +
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Residues in contact with ALA 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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156B LEU* 1.3 76.0 - - - +
158B CYS* 1.3 60.3 + - - +
159B PHE* 3.9 3.6 - - - -
198B LEU* 3.3 10.1 - - + +
199B THR* 3.0 52.5 + - - +
200B PRO 5.7 0.2 - - - -
201B HIS 4.2 5.4 - - - +
202B ARG* 4.2 11.9 - - + +
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Residues in contact with CYS 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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156B LEU* 3.7 4.3 - - - +
157B ALA* 1.3 81.0 - - - +
159B PHE* 1.3 72.0 + - - +
196B PHE* 3.5 38.8 - - - -
197B PHE 3.3 9.0 - - - -
198B LEU* 3.8 7.4 - - + -
225B GLY* 3.7 1.0 - - - -
226B VAL* 2.9 40.0 + - - +
229B GLU* 3.5 31.0 - - + +
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Residues in contact with PHE 159 (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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156B LEU* 3.3 34.1 - - + -
157B ALA* 3.9 4.5 - - - -
158B CYS* 1.3 85.9 - - - +
160B ALA* 1.3 62.1 + - - +
196B PHE* 3.6 4.3 - - - -
197B PHE* 3.0 63.1 + + + -
199B THR* 3.9 15.9 - - + -
203B HIS* 3.4 20.9 - + + -
205B VAL* 3.8 22.0 - - + -
208B ILE* 3.7 35.2 - - + -
223B CYS* 5.2 2.0 - - - -
224B LYS 3.5 8.3 - - - +
225B GLY* 4.1 10.3 - - - -
226B VAL* 3.6 6.7 - - - +
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Residues in contact with ALA 160 (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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138B PHE* 3.5 24.4 - - + -
146B LEU* 4.5 1.3 - - + -
159B PHE* 1.3 74.8 - - - +
161B ILE* 1.3 66.9 + - - +
194B ILE* 4.5 1.8 - - + -
195B LEU 3.1 11.2 - - - +
196B PHE* 4.8 2.5 - - - -
223B CYS* 3.4 5.2 - - - -
224B LYS 2.9 33.3 + - - +
226B VAL* 3.7 9.4 - - + +
232B MET* 3.7 21.1 - - + -
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Residues in contact with ILE 161 (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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138B PHE* 3.9 2.7 - - - -
160B ALA* 1.3 75.6 - - - +
162B TYR* 1.4 61.2 + - - +
163B THR* 3.9 17.5 + - + +
171B LEU* 4.0 13.9 - - + -
175B ILE* 5.5 1.8 - - + -
193B ASN 3.9 0.5 - - - +
194B ILE* 3.1 6.9 - - - +
195B LEU* 2.8 46.9 + - + +
197B PHE* 3.7 22.0 - - + -
208B ILE* 4.8 3.8 - - + -
212B ALA* 4.6 9.6 - - + -
221B LEU* 3.8 28.5 - - + -
222B ILE 3.2 1.6 - - - -
223B CYS* 3.1 45.1 - - + -
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Residues in contact with TYR 162 (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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135B PRO* 3.6 27.4 - - + +
137B ASP 3.3 29.8 - - - -
138B PHE* 3.6 26.4 - + + -
139B PRO* 3.8 19.2 - - + +
161B ILE* 1.4 71.0 - - - +
163B THR* 1.3 66.0 + - - +
189B SER* 3.9 18.8 + - - -
190B TYR* 5.5 2.8 - - - -
192B HIS* 3.7 29.5 - + + +
193B ASN 3.4 14.1 - - - -
194B ILE* 3.5 11.2 - - + -
220B PHE* 3.4 14.7 - + - -
221B LEU* 3.4 1.7 - - - +
222B ILE* 2.7 45.2 + - + +
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Residues in contact with THR 163 (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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161B ILE* 3.9 16.2 - - + +
162B TYR* 1.3 78.3 - - - +
164B THR* 1.4 65.9 + - - +
167B LYS* 3.3 20.3 + - + +
168B ALA* 3.7 33.9 - - + +
171B LEU* 4.5 2.9 - - + -
192B HIS* 3.3 5.4 - - - +
193B ASN 3.0 31.5 + - - +
195B LEU* 5.6 0.2 - - + -
220B PHE* 2.6 36.3 + - - -
221B LEU* 4.0 10.8 - - + -
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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