Contacts of the strand formed by residues 152 - 157 (chain B) in PDB entry 4U7B
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 ILE 152 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B PHE* 3.6 17.6 + - + +
149B LEU* 3.1 17.7 + - + +
150B HIS 3.4 1.6 - - - +
151B ARG* 1.3 77.9 - - - +
153B VAL* 1.3 68.1 + - - +
154B THR* 5.0 1.3 - - - +
198B ASP* 3.5 20.1 - - - +
199B GLN 4.5 1.0 + - - -
245B ILE* 3.6 27.6 - - + +
247B LEU* 3.5 41.1 - - + -
271B LEU* 4.6 4.3 - - + -
326B ILE* 3.5 41.3 - - + -
329B LEU* 5.3 5.2 - - + -
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Residues in contact with VAL 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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151B ARG 4.6 1.6 - - - +
152B ILE* 1.3 76.5 - - - +
154B THR* 1.3 67.8 + - - +
196B TRP* 4.8 6.3 - - + -
197B TRP 3.5 20.6 - - - +
198B ASP* 4.4 5.2 - - + -
203B ILE* 4.4 14.4 - - + -
226B LEU* 5.4 2.9 - - + -
230B LEU* 4.7 16.6 - - + -
244B VAL* 3.5 26.7 - - + -
245B ILE 2.8 17.7 + - - +
246B PHE* 3.4 17.7 - - + -
247B LEU 3.1 21.1 + - - -
268B TRP* 5.8 1.1 - - + -
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Residues in contact with THR 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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152B ILE* 5.0 2.5 - - - -
153B VAL* 1.3 76.2 - - - +
155B GLY* 1.3 60.4 + - - +
196B TRP* 3.0 8.6 - - - +
197B TRP* 2.7 76.5 + - + +
246B PHE* 5.0 1.1 - - - -
247B LEU* 2.6 41.8 + - - +
248B HIS* 4.8 0.2 - - - -
281B ALA* 6.0 0.2 - - - -
282B PRO* 4.2 11.9 - - + +
283B SER* 3.4 9.6 + - - +
326B ILE* 4.3 8.1 - - + -
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Residues in contact with GLY 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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154B THR* 1.3 81.2 + - - +
156B ASP* 1.3 65.7 + - - +
195B VAL 2.8 15.9 - - - -
196B TRP* 3.6 17.4 - - - -
197B TRP* 4.5 0.2 - - - -
246B PHE* 5.1 0.4 - - - -
247B LEU 3.5 11.1 + - - +
248B HIS* 4.0 14.5 - - - +
249B ALA 4.8 0.7 + - - -
283B SER* 3.7 8.7 + - - -
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Residues in contact with ASP 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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155B GLY* 1.3 76.7 - - - +
157B GLU* 1.3 96.9 + - - +
194B CYS* 3.8 0.9 - - - +
195B VAL 3.0 26.6 + - - +
196B TRP* 4.9 3.9 - - - +
249B ALA* 4.4 22.0 - - - +
254B HIS* 5.7 5.0 + - - -
281B ALA* 5.0 3.7 - - + +
283B SER* 3.8 10.8 + - - -
284B ASP* 3.1 26.0 - - - +
288B PHE* 3.7 23.8 - - + -
57D T 4.2 11.3 + - - +
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Residues in contact with GLU 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 ASP* 1.3 100.7 + - - +
158B LYS* 1.3 62.3 + - - +
192B MET* 3.5 28.9 - - + +
193B LEU 3.3 11.2 - - - +
194B CYS* 3.9 15.5 - - - +
196B TRP* 5.7 2.3 - - - -
214B VAL* 3.6 27.1 - - - +
219B TYR* 4.6 6.1 - - - -
222B GLN* 5.6 0.3 - - - +
253B SER* 5.1 0.5 + - - -
254B HIS* 3.2 32.3 + - + -
284B ASP* 5.5 0.2 - - - +
288B PHE* 4.1 3.2 - - - -
56D A 4.7 1.9 + - - -
57D T 4.2 10.7 + - - +
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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