Contacts of the strand formed by residues 147 - 152 (chain B) in PDB entry 1EFP
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 147 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B ALA 4.6 1.3 - - - +
145B THR 3.2 1.4 - - - -
146B PHE* 1.3 76.5 - - - +
148B SER* 1.3 59.8 + - - +
150B VAL* 4.0 11.7 - - + -
159B VAL* 3.7 25.1 - - + -
160B THR 3.6 6.3 - - - -
178B VAL* 3.8 17.0 - - + -
179B THR 3.0 17.7 + - - +
181B ASP* 3.2 24.3 + - - +
184B LEU* 3.9 14.1 - - + +
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Residues in contact with SER 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B PHE 4.7 0.4 - - - -
147B ALA* 1.3 72.9 - - - +
149B LYS* 1.3 62.2 + - - +
160B THR* 2.8 21.6 + - - -
161B ARG 5.0 0.2 - - - -
162B GLU* 3.1 28.9 + - - -
167B LEU* 5.1 3.6 - - - +
181B ASP* 5.3 0.2 - - - -
183B ARG* 3.9 25.6 + - - +
184B LEU* 3.2 32.4 - - - +
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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
----------------------------------------------------------
147B ALA 3.7 0.2 - - - -
148B SER* 1.3 81.8 - - - +
150B VAL* 1.3 67.0 + - - +
151B GLU* 3.7 34.7 + - + +
158B LYS 3.6 1.2 - - - +
159B VAL* 3.2 6.8 - - - +
160B THR* 3.0 45.1 + - + +
184B LEU* 3.7 4.0 - - - +
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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
----------------------------------------------------------
45B GLU* 4.3 22.8 + - + +
49B LEU* 4.9 8.7 - - + +
52B LYS* 5.0 7.1 + - - -
116B LEU* 5.7 7.9 - - + -
118B ILE* 6.3 2.9 - - + -
147B ALA* 4.0 22.0 - - + -
149B LYS* 1.3 81.2 - - - +
151B GLU* 1.3 60.6 + - - +
152B ILE* 3.4 24.2 + - + +
157B ALA* 4.6 11.9 - - + -
158B LYS 3.9 1.8 - - - -
159B VAL* 4.5 7.9 - - + +
178B VAL* 4.3 21.1 - - + -
184B LEU* 4.4 15.8 - - + +
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Residues in contact with GLU 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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52B LYS* 6.2 0.9 - - - +
149B LYS* 3.7 33.5 + - + +
150B VAL* 1.3 71.3 - - - +
152B ILE* 1.3 64.0 + - - +
153B GLU* 3.3 20.8 + - - +
157B ALA* 4.4 0.7 - - - -
158B LYS* 2.9 60.8 + - + +
160B THR* 5.0 5.4 - - - +
169B THR* 5.8 0.3 - - - +
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Residues in contact with ILE 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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1B MET* 3.5 39.3 - - + -
49B LEU* 3.7 30.5 - - + -
52B LYS* 5.7 2.0 - - - +
54B GLN* 3.9 31.9 + - + +
116B LEU* 4.4 14.4 - - + -
150B VAL* 3.4 11.0 + - + +
151B GLU* 1.3 72.4 - - - +
153B GLU* 1.3 63.7 + - - +
154B GLY 4.7 3.6 - - - +
156B LYS 4.2 0.9 - - - +
157B ALA* 3.8 12.6 - - + -
174B LEU* 3.5 28.5 - - + -
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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