Contacts of the strand formed by residues 152 - 157 (chain D) in PDB entry 5Y7K
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 152 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D TYR 4.6 1.7 - - - +
129D THR* 4.6 2.0 - - - -
130D ALA 3.5 21.6 + - - +
132D TYR* 3.6 19.8 + - + -
148D ILE* 3.3 10.1 - - + +
149D PRO* 2.4 31.9 + - - +
150D ASN 3.2 0.4 - - - -
151D ASN* 1.3 78.7 - - - +
153D GLN* 1.3 62.7 + - - +
154D TRP 3.7 10.5 - - - +
155D VAL* 3.5 32.1 - - + -
166D TYR* 4.0 12.0 - - + -
167D VAL 3.7 8.5 - - - +
168D TRP* 4.2 5.7 - - - -
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Residues in contact with GLN 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D TYR* 3.8 11.8 - - - +
129D THR* 5.7 3.1 - - + +
132D TYR* 4.8 2.9 + - - -
151D ASN 4.0 10.3 - - - +
152D THR* 1.3 73.3 - - - +
154D TRP* 1.3 61.7 + - - +
167D VAL* 2.8 23.0 + - + +
169D ASN* 3.3 11.3 + - - +
170D ASN* 2.9 44.5 + - - -
195D TYR* 6.0 0.4 - - - -
198D ILE* 3.5 10.4 - - + +
211D TYR* 3.0 52.4 + - + +
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Residues in contact with TRP 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126D HIS 5.7 0.9 - - - -
128D TYR* 4.3 28.3 - + - -
132D TYR* 4.7 4.2 + - - -
152D THR* 3.5 2.3 + - - +
153D GLN* 1.3 84.9 - - - +
155D VAL* 1.3 81.2 + - - +
156D THR* 3.7 20.4 - - - +
166D TYR* 3.0 8.1 - - - +
167D VAL* 2.9 29.0 + - + -
197D GLY 4.9 1.8 - - - -
198D ILE* 4.1 16.4 - - + -
210D ALA* 6.4 0.9 - - + -
211D TYR* 4.6 16.8 - + + -
212D SER* 3.1 43.9 + - - -
214D LEU* 4.1 20.0 - - + -
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Residues in contact with VAL 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D LEU* 3.6 28.9 - - + +
132D TYR* 3.8 28.9 + - + -
148D ILE* 4.2 14.4 - - + -
152D THR* 3.5 20.9 - - + -
154D TRP* 1.3 97.8 - - - +
156D THR* 1.3 68.4 + - - +
157D TRP* 6.1 0.2 - - + -
164D LEU* 4.0 21.5 - - + -
165D ALA 3.7 4.5 - - - +
166D TYR* 3.9 9.6 - - + -
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Residues in contact with THR 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D LEU* 6.2 0.2 - - - -
154D TRP* 3.7 23.7 - - - +
155D VAL* 1.3 78.2 - - - +
157D TRP* 1.3 74.3 + - - +
164D LEU* 3.8 5.8 - - - +
165D ALA 3.1 35.9 + - - +
214D LEU* 4.1 16.2 - - + -
216D TRP* 3.9 19.3 + - + +
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Residues in contact with TRP 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D SER* 3.1 40.0 + - - -
107D ILE 4.1 9.0 - - - -
108D SER* 3.7 22.2 - - - +
109D PRO* 3.9 8.5 - - + -
113D PHE* 3.6 26.2 - + + -
114D ILE 4.4 0.7 - - - -
115D LEU* 3.7 33.3 - - + +
134D ILE* 4.5 7.6 - - + -
156D THR* 1.3 89.3 + - - +
158D SER* 1.3 69.8 + - - +
159D PRO* 4.0 0.5 - - - +
162D HIS* 3.2 30.5 - - + -
163D LYS 3.4 21.3 - - - -
164D LEU* 3.6 28.5 - - + +
178D PRO* 4.6 2.9 - - + -
216D TRP* 3.4 9.5 - - - -
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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