Contacts of the strand formed by residues 148 - 153 (chain B) in PDB entry 3FBK
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 148 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B LEU* 3.6 20.4 - - + -
40B SER* 3.2 0.7 - - - -
41B ILE* 2.9 34.0 + - + +
136B PHE* 4.1 21.1 - - + -
140B SER 6.0 0.4 - - - +
141B LEU* 3.5 31.2 - - + -
147B GLU* 1.3 105.8 - - - +
149B SER* 1.3 61.3 + - - +
152B TYR* 3.1 39.7 - - + +
164B HIS* 5.6 2.9 - - + +
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Residues in contact with SER 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LEU 3.3 9.1 + - - -
40B SER* 4.0 11.7 + - - -
53B ILE* 5.8 2.1 - - - +
147B GLU* 3.8 15.2 + - - -
148B ILE* 1.3 81.5 - - - +
150B GLY* 1.3 59.7 + - - +
152B TYR* 3.9 8.7 + - - -
169B ARG* 2.9 23.2 + - - -
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Residues in contact with GLY 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ARG* 3.4 11.9 - - - +
39B LEU 3.0 30.1 + - - -
53B ILE* 6.1 0.4 - - - +
149B SER* 1.3 77.6 + - - +
151B TRP* 1.3 65.8 + - - -
152B TYR* 3.4 12.4 - - - -
169B ARG* 3.9 12.1 - - - -
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Residues in contact with TRP 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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36B GLN* 3.5 28.9 - - + -
37B LEU 3.5 13.9 - - - -
38B ARG* 3.7 30.2 - - + +
54B GLU* 3.6 42.0 - - + -
55B GLY 4.0 2.9 - - - -
56B LYS* 3.5 56.8 - - + +
150B GLY* 1.3 73.9 - - - -
152B TYR* 1.3 57.1 + - - +
166B LYS* 3.6 6.9 - - - +
167B VAL* 2.8 49.5 + - + +
169B ARG* 5.8 0.4 - - - -
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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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36B GLN* 3.2 4.3 - - - -
37B LEU 2.8 33.7 + - - +
39B LEU* 4.2 12.6 - - + -
134B MSE 3.5 24.7 - - + +
136B PHE* 4.1 8.5 - + - -
148B ILE* 3.1 41.2 - - + +
149B SER 3.9 6.7 + - - -
150B GLY* 3.4 27.6 - - - -
151B TRP* 1.3 74.8 - - - +
153B TYR* 1.3 61.3 + - - +
164B HIS* 3.8 25.9 + + + -
165B LEU 3.5 8.3 - - - +
166B LYS* 3.5 40.2 - - + +
167B VAL* 3.7 5.6 - - - -
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Residues in contact with TYR 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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33B GLY* 5.5 9.4 - - - -
35B GLY 3.7 3.8 - - - -
36B GLN* 3.8 32.1 - - + -
134B MSE 3.5 19.2 - - - +
152B TYR* 1.3 72.1 - - - +
154B LEU* 1.3 63.0 + - - +
155B LEU* 3.5 26.2 + - + +
165B LEU* 2.8 38.5 + - + +
166B LYS 3.7 17.0 - - - -
167B VAL* 3.6 25.1 - - + +
168B ALA 4.9 2.0 + - - -
170B ARG* 5.5 4.5 + - - -
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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