Contacts of the strand formed by residues 133 - 138 (chain B) in PDB entry 3PEJ
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 133 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B ILE* 3.8 33.2 - - + +
107B ALA* 3.8 20.4 - - + -
108B ALA* 4.1 7.0 - - - +
111B LEU* 3.6 20.9 - - + -
132B GLU* 1.4 71.5 - - - +
134B ARG* 1.3 61.1 + - - +
135B ILE* 4.3 13.5 - - + -
146B ILE* 4.1 16.6 - - + -
147B THR 3.4 9.9 - - - +
148B ASP* 4.5 0.4 - - + -
271B ILE* 4.2 10.8 - - + -
273B PHE* 5.0 1.8 - - + -
274B PRO 2.9 8.9 + - - +
275B ILE* 3.3 27.9 - - + -
276B TYR* 2.8 32.7 + - - +
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Residues in contact with ARG 134 (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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299A PRO* 3.7 20.1 - - - +
2B SO4 2.8 47.7 + - - +
128B GLU* 4.9 4.8 + - - -
130B LYS* 4.6 9.3 - - - +
132B GLU* 2.8 25.8 + - + +
133B ILE* 1.3 77.0 - - - +
135B ILE* 1.3 62.9 + - - +
136B SER 4.1 0.2 + - - -
145B SER 3.6 2.9 - - - +
146B ILE* 3.6 0.9 - - - -
147B THR* 2.6 50.4 + - - +
149B THR* 3.6 28.5 - - - +
276B TYR* 3.5 7.6 - - + -
326B TRP* 3.6 30.9 - - + -
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Residues in contact with ILE 135 (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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100B LEU* 4.8 7.0 - - + -
104B ILE* 4.3 21.1 - - + -
133B ILE* 4.6 4.0 - - + -
134B ARG* 1.3 74.5 - - - +
136B SER* 1.3 63.2 + - - +
144B LEU* 4.1 10.1 - - + -
145B SER 3.4 6.5 - - - +
146B ILE* 4.3 20.2 - - + -
260B LEU* 4.1 16.6 - - + -
264B ILE* 3.7 33.9 - - + -
275B ILE* 3.8 20.4 - - + -
276B TYR 2.8 12.4 + - - +
277B LEU* 3.3 20.1 - - + +
278B LEU 3.0 25.1 + - - -
326B TRP* 3.6 1.8 - - - -
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Residues in contact with SER 136 (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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2B SO4 4.3 15.1 + - - -
134B ARG 4.1 0.4 + - - -
135B ILE* 1.3 75.4 - - - +
137B ALA* 1.3 58.6 + - - +
144B LEU* 3.6 5.7 - - - +
145B SER* 2.7 48.5 + - - +
242B ARG* 4.8 3.1 + - - -
260B LEU* 5.5 0.4 - - - -
277B LEU* 5.1 1.1 - - - -
278B LEU* 3.7 36.3 - - - +
326B TRP* 4.1 5.7 - - - -
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Residues in contact with ALA 137 (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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3B SO4 3.6 1.9 + - - -
136B SER* 1.3 75.0 - - - +
138B ASN* 1.3 54.7 + - - +
139B LYS* 3.8 2.8 - - + +
143B ILE 3.4 5.8 - - - +
144B LEU* 4.3 3.8 - - + +
255B LEU* 3.5 33.9 - - + +
260B LEU* 4.2 20.1 - - + +
278B LEU 4.9 5.2 + - - +
324B LYS* 2.8 31.4 + - - -
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Residues in contact with ASN 138 (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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3B SO4 4.0 6.9 + - - -
137B ALA* 1.3 69.5 - - - +
139B LYS* 1.4 52.1 + - - +
140B GLU* 3.2 12.0 + - - +
141B LYS* 3.1 57.0 + - + +
142B ASN* 2.8 30.5 + - - -
143B ILE* 2.7 25.8 + - + +
255B LEU* 4.1 1.3 - - - -
324B LYS* 4.6 1.8 - - - +
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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