Contacts of the strand formed by residues 145 - 149 (chain B) in PDB entry 5I75
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 145 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143B PRO 3.7 4.4 + - - -
144B PRO* 1.3 72.3 - - - +
146B VAL* 1.3 62.2 + - - +
147B TYR* 3.7 32.9 + - - -
166B LEU 3.6 1.0 - - - +
167B VAL* 3.5 3.8 - - - -
168B LYS* 2.9 54.0 + - - +
169B GLY 4.8 0.5 + - - -
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Residues in contact with VAL 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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144B PRO* 3.7 11.1 + - + +
145B SER* 1.3 72.8 - - - +
147B TYR* 1.3 74.8 + - - +
148B PRO* 4.1 0.2 - - - +
165B CYS* 5.3 1.1 - - + -
166B LEU 3.5 7.0 - - - +
167B VAL* 4.8 1.3 - - + -
220B CYS* 4.9 7.0 - - - -
222B VAL* 3.6 48.9 - - + -
231B VAL* 3.8 31.6 - - + +
233B LYS* 3.8 27.4 - - + +
143C GLU* 3.7 12.8 - - - +
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Residues in contact with TYR 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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145B SER* 3.8 31.4 + - - -
146B VAL* 1.3 89.4 - - - +
148B PRO* 1.3 69.3 - - + +
149B LEU* 5.7 0.4 - - + -
165B CYS* 5.1 0.4 - - - -
166B LEU* 2.9 50.5 + - + +
168B LYS* 4.8 15.9 + - + +
141C SER* 4.1 2.7 - - - +
143C GLU* 3.7 19.3 - - + -
144C GLN* 3.5 55.9 - - + +
147C SER* 2.9 28.5 + - - -
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Residues in contact with PRO 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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146B VAL 4.1 1.1 - - - +
147B TYR* 1.3 86.2 - - - +
149B LEU* 1.3 65.2 + - - +
150B ALA* 3.8 3.4 - - + +
165B CYS* 4.5 11.7 - - - -
233B LYS* 4.8 11.6 - - + -
234B LYS 4.8 12.6 - - - +
235B LEU* 4.6 12.1 - - + -
236B GLU 6.0 0.7 - - - +
141C SER* 2.9 45.0 + - - +
143C GLU* 3.2 38.6 - - + +
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Residues in contact with LEU 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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147B TYR* 3.7 1.1 + - + +
148B PRO* 1.3 81.0 - - - +
150B ALA* 1.3 61.7 + - - +
151B PRO* 3.9 2.9 - - - +
164B GLY* 2.9 35.9 + - - +
165B CYS 4.1 10.5 - - - +
166B LEU* 3.7 39.3 - - + +
203B SER* 5.0 1.1 - - - -
235B LEU* 3.4 6.0 - - - +
138C PHE* 4.1 18.6 - - + -
139C PRO 4.7 13.0 - - - +
140C PRO* 5.4 0.4 - - + -
141C SER 5.2 2.7 - - - +
144C GLN* 5.3 3.8 - - - +
151C SER 5.1 4.0 - - - +
153C VAL* 3.9 31.4 - - + -
155C PHE* 4.4 20.6 - - + -
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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