Contacts of the strand formed by residues 148 - 154 (chain J) in PDB entry 6IY6
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 VAL 148 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139J HIS* 4.3 4.3 - - + +
142J LEU* 4.0 15.0 - - + +
143J CYS* 3.6 39.0 - - - +
146J PHE* 3.5 23.6 + - + +
147J ARG* 1.3 71.6 - - - +
149J LEU* 1.3 59.3 + - - +
150J SER* 3.2 13.4 + - - +
181J TYR* 4.3 7.5 - - - -
183J LEU* 3.3 19.1 - - + +
184J GLY 4.7 0.2 - - - -
185J PHE* 3.6 33.7 - - + +
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Residues in contact with LEU 149 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350H GLU* 5.9 2.2 - - - +
602H PO4 5.6 5.8 - - - +
148J VAL* 1.3 67.0 - - - +
150J SER* 1.3 66.0 + - - +
151J THR* 3.9 15.4 + - + -
180J ASP* 6.0 0.4 - - - +
181J TYR* 3.8 51.0 - - + +
183J LEU 3.0 11.7 + - - +
184J GLY* 3.7 5.6 - - - -
185J PHE 3.2 18.9 + - - +
186J THR* 5.4 0.3 + - - -
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Residues in contact with SER 150 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139J HIS* 3.1 37.6 + - - -
143J CYS* 4.8 2.3 - - - -
148J VAL* 3.2 9.5 + - - -
149J LEU* 1.3 76.6 - - - +
151J THR* 1.3 67.1 + - - +
169J PHE* 4.0 16.8 - - - +
185J PHE* 3.3 12.3 - - - -
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Residues in contact with THR 151 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602H PO4 3.7 22.1 + - - +
149J LEU* 4.3 18.6 + - + +
150J SER* 1.3 79.1 - - - +
152J VAL* 1.3 64.3 + - - +
153J HIS* 3.6 18.4 + - - -
169J PHE* 4.4 1.1 - - - -
185J PHE 3.0 4.8 + - - +
186J THR* 3.5 20.1 + - - -
187J LEU* 3.0 26.9 + - - +
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Residues in contact with VAL 152 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342H PRO* 3.2 17.3 - - - +
151J THR* 1.3 70.5 - - - +
153J HIS* 1.3 69.1 + - - +
165J LEU 3.8 2.2 - - - +
166J LEU* 3.2 32.3 - - + +
167J LYS* 5.0 1.8 - - + -
168J CYS* 4.1 10.8 - - - +
169J PHE* 3.3 38.6 - - + +
187J LEU* 3.3 7.9 - - + +
189J TRP* 3.6 33.2 - - + +
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Residues in contact with HIS 153 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340H LEU* 3.9 25.2 - - + +
342H PRO* 2.8 42.9 + - + +
343H THR 4.8 0.2 - - - -
344H LEU* 4.6 4.5 - - + -
602H PO4 3.1 38.9 + - - -
151J THR* 3.6 11.2 + - - -
152J VAL* 1.3 85.5 + - - +
154J THR* 1.3 65.5 + - - +
166J LEU* 5.3 0.9 - - - -
186J THR* 3.8 21.5 - - + +
187J LEU 3.0 6.9 + - - +
188J ILE* 3.5 16.3 - - + -
189J TRP* 2.9 30.2 + - - -
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Residues in contact with THR 154 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339H PHE* 5.6 0.3 - - - -
340H LEU* 3.3 5.3 - - - -
341H GLU* 2.8 50.9 + - + +
342H PRO* 3.8 5.9 - - - +
153J HIS* 1.3 72.8 + - - +
155J HIS* 1.3 71.8 + - - +
158J VAL 4.1 9.4 - - - +
159J LYS* 5.7 1.1 - - - -
160J SER 5.7 1.1 - - - +
161J VAL* 3.5 33.2 - - + +
166J LEU* 3.1 27.9 - - + +
189J TRP* 3.6 7.1 - - - +
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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