Contacts of the strand formed by residues 133 - 138 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A ILE* 3.8 33.0 - - + +
107A ALA* 3.8 14.8 - - + -
108A ALA* 4.1 6.3 - - - +
111A LEU* 3.6 21.3 - - + -
132A GLU* 1.4 71.5 - - - +
134A ARG* 1.3 61.9 + - - +
135A ILE* 4.6 13.2 - - + -
146A ILE* 4.1 22.0 - - + -
147A THR 3.4 10.3 - - - +
148A ASP* 4.5 0.2 - - + -
271A ILE* 4.2 11.0 - - + -
273A PHE* 4.9 1.6 - - + -
274A PRO 2.9 9.1 + - - +
275A ILE* 3.3 28.0 - - + +
276A TYR* 2.8 32.7 + - - +
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Residues in contact with ARG 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A SO4 3.0 40.2 + - - +
128A GLU* 5.7 2.0 + - - -
130A LYS* 4.5 8.1 - - - +
132A GLU* 2.7 42.0 + - - +
133A ILE* 1.3 76.4 - - - +
135A ILE* 1.3 63.1 + - - +
136A SER* 4.1 0.7 + - - -
145A SER 3.6 3.3 - - - +
146A ILE* 3.6 0.7 - - - -
147A THR* 2.6 57.6 + - - +
148A ASP* 5.9 0.4 - - - +
149A THR* 3.8 21.6 - - - +
237A LEU* 5.7 2.2 - - - +
276A TYR* 3.5 7.6 - - + -
326A TRP* 3.6 28.1 - - + -
299B PRO* 3.6 19.0 - - - +
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Residues in contact with ILE 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A LEU* 4.7 7.0 - - + -
104A ILE* 4.3 21.5 - - + -
133A ILE* 4.6 4.3 - - + -
134A ARG* 1.3 76.3 - - - +
136A SER* 1.3 61.7 + - - +
144A LEU* 4.3 8.1 - - + -
145A SER 3.4 7.6 - - - +
146A ILE* 4.3 19.7 - - + -
260A LEU* 4.0 17.3 - - + -
264A ILE* 3.7 32.3 - - + -
275A ILE* 3.8 22.2 - - + -
276A TYR 2.8 11.8 + - - +
277A LEU* 3.3 20.6 - - + +
278A LEU 3.0 25.5 + - - -
326A TRP* 3.6 1.4 - - - -
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Residues in contact with SER 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A SO4 4.1 15.2 + - - -
134A ARG 4.1 0.4 + - - -
135A ILE* 1.3 75.4 - - - +
137A ALA* 1.3 57.8 + - - +
144A LEU* 3.7 5.8 - - - +
145A SER* 2.7 50.8 + - - +
242A ARG* 4.8 3.3 + - - -
260A LEU* 5.5 0.9 - - - -
277A LEU* 5.1 1.3 - - - -
278A LEU* 3.7 36.3 - - - +
326A TRP* 4.1 6.3 - - - -
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Residues in contact with ALA 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A SER* 1.3 75.7 - - - +
138A ASN* 1.3 53.3 + - - +
139A LYS* 3.8 3.8 + - + +
143A ILE 3.4 5.4 - - - -
144A LEU* 4.0 11.9 - - + +
255A LEU* 3.8 41.7 - - + +
260A LEU* 4.2 7.8 - - + +
278A LEU 4.9 5.0 + - - +
324A LYS* 2.8 31.2 + - - +
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Residues in contact with ASN 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A ALA* 1.3 69.9 - - - +
139A LYS* 1.4 51.2 + - - +
140A GLU* 3.2 12.0 + - - +
141A LYS* 3.1 46.1 + - + +
142A ASN* 2.8 29.8 + - - -
143A ILE* 2.7 27.0 + - + +
255A LEU* 4.2 1.6 - - - -
324A LYS* 4.6 5.4 - - - +
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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