Contacts of the strand formed by residues 148 - 154 (chain B) in PDB entry 4K8T
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 ALA 148 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B PHE* 3.3 20.9 - - + +
3B ASP 4.6 0.2 - - - +
5B LEU* 3.9 24.5 - - + +
144B VAL 3.1 12.9 + - - +
145B VAL 3.2 7.3 + - - +
146B ALA 3.5 1.0 + - - -
147B ASP* 1.3 78.1 - - - +
149B LYS* 1.3 67.0 + - - +
150B VAL* 3.3 9.5 + - - +
151B THR* 4.4 3.7 + - - +
179B ARG* 3.1 25.1 - - - +
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Residues in contact with LYS 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0B THR* 3.7 21.7 + - + +
2B PHE 3.0 16.1 + - - +
3B ASP* 3.1 31.7 + - - +
147B ASP 4.2 0.2 + - - -
148B ALA* 1.3 72.1 - - - +
150B VAL* 1.4 62.7 + - + +
179B ARG* 3.5 15.3 - - - +
180B GLU* 3.2 24.6 + - - +
287B THR* 3.0 41.3 + - + +
288B GLN* 4.9 2.2 + - - -
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Residues in contact with VAL 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B ASP 2.9 7.2 + - - +
4B VAL* 3.3 8.6 - - + +
5B LEU* 2.8 32.9 + - - +
148B ALA* 4.1 3.5 - - - +
149B LYS* 1.4 81.9 - - + +
151B THR* 1.3 61.8 + - - +
152B TYR* 4.4 3.4 - - + +
180B GLU* 3.4 12.1 - - + +
181B MSE 4.8 0.2 - - - -
182B SER* 3.9 28.0 - - - +
209B ILE* 5.1 4.7 - - + -
283B LEU* 4.2 16.6 - - + -
286B TYR* 4.2 21.1 - - + -
287B THR* 3.5 27.1 - - + -
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Residues in contact with THR 151 (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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5B LEU* 3.2 37.7 - - + +
7B VAL* 4.4 11.7 - - + -
145B VAL* 3.7 16.7 + - - +
148B ALA* 4.4 4.6 + - - +
149B LYS 4.4 0.2 - - - -
150B VAL* 1.3 73.0 - - - +
152B TYR* 1.3 56.7 + - - +
153B PHE* 5.6 1.6 - - + -
167B ILE* 5.9 0.7 - - + -
170B CYS* 4.3 16.6 - - + -
174B ALA* 4.8 2.3 - - - +
179B ARG* 5.6 0.6 - - - +
180B GLU 3.1 7.5 + - - -
181B MSE 3.3 30.6 - - + +
182B SER 2.8 31.3 + - - +
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Residues in contact with TYR 152 (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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4B VAL* 4.6 2.0 - - + -
5B LEU 2.6 13.1 + - - +
6B THR* 3.0 27.0 - - + -
7B VAL* 2.8 26.2 + - - +
58B SER* 4.9 3.7 + - - -
59B ALA* 4.5 11.2 - - + -
62B THR* 3.8 24.6 + - + -
150B VAL* 4.7 1.3 - - + -
151B THR* 1.3 73.9 - - - +
153B PHE* 1.3 65.3 + - - +
154B GLU* 5.3 0.4 - - + -
182B SER* 3.2 29.6 - - - -
184B THR* 3.3 38.9 - - + +
211B PHE* 3.6 25.4 - + - +
275B GLY 5.1 0.9 + - - -
276B ASP* 5.0 2.9 + - - -
279B ALA* 3.6 18.7 - - + +
283B LEU* 3.7 20.9 - - + -
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Residues in contact with PHE 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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7B VAL* 3.4 11.4 - - + +
151B THR* 5.6 0.9 - - + -
152B TYR* 1.3 80.9 - - - +
154B GLU* 1.3 70.5 + - - +
157B LEU* 4.2 1.3 - - + -
158B TRP* 3.6 24.9 - + - -
167B ILE* 3.6 40.4 - - + -
181B MSE 3.6 31.0 - - + -
182B SER 2.9 31.3 + - - -
183B MSE 3.2 33.4 - - + -
184B THR* 3.0 27.0 + - - +
201B LEU* 3.9 8.7 - - + -
206B LYS 5.1 0.2 - - - -
207B VAL* 3.6 21.8 - - + -
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Residues in contact with GLU 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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7B VAL 3.4 3.9 + - - +
8B GLY* 3.3 15.2 - - - -
9B ASN* 3.0 21.3 + - - -
57B GLY 4.0 1.2 - - - -
58B SER* 3.2 19.0 + - - +
59B ALA* 2.7 41.2 + - + +
152B TYR* 5.5 0.7 - - + -
153B PHE* 1.3 83.5 - - - +
155B GLY* 1.3 64.0 + - - +
156B TYR* 3.6 15.0 - - + +
157B LEU* 3.0 24.0 + - + +
158B TRP* 4.3 1.4 - - - -
184B THR* 3.7 9.9 - - + -
186B SER* 3.7 6.5 - - - +
401B ADN 3.2 21.3 - - - -
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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