Contacts of the strand formed by residues 127 - 132 (chain D) in PDB entry 3CJC
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 GLU 127 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92D LEU* 3.2 26.2 - - + +
117D LYS* 3.7 16.3 + - - -
118D PHE 3.4 12.3 - - - +
119D SER* 4.6 5.6 - - - +
125D VAL* 3.0 14.5 - - - +
126D LYS* 1.3 90.0 - - + +
128D PHE* 1.3 61.5 + - - +
160D LEU* 3.2 25.1 - - + +
162D ASP* 4.1 2.3 - - - +
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Residues in contact with PHE 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D LEU* 5.4 2.2 - - + -
3D ILE* 4.4 14.1 - - + -
34D ILE* 4.4 12.1 - - + -
89D VAL* 5.2 0.7 - - + -
118D PHE* 2.9 47.5 + - + +
120D SER* 3.6 29.6 - - - -
123D THR* 5.3 0.4 - - - -
125D VAL* 3.7 22.7 - - + -
127D GLU* 1.3 81.6 - - - +
129D ALA* 1.3 70.6 + - - +
130D ILE* 3.5 27.4 - - + -
160D LEU* 3.3 12.2 - - - +
162D ASP* 3.6 11.9 - - + +
164D MET* 5.2 3.1 - - + -
221D LEU* 4.5 14.6 - - + -
259D LEU* 4.8 11.4 - - + -
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Residues in contact with ALA 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D VAL* 4.5 4.5 - - + -
116D VAL 3.5 5.4 - - - +
117D LYS* 4.5 0.4 - - - +
128D PHE* 1.3 73.9 - - - +
130D ILE* 1.3 64.5 + - - +
154D VAL* 4.4 3.1 - - + -
158D TRP* 3.9 22.2 - - + -
160D LEU* 3.2 10.9 - - + +
162D ASP 3.0 7.5 + - - -
163D VAL* 3.4 28.4 - - + -
164D MET* 2.8 29.8 + - - +
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Residues in contact with ILE 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D ILE* 4.6 8.3 - - + -
34D ILE* 4.2 18.6 - - + -
82D PHE* 4.0 16.6 - - + -
114D ALA 3.7 2.6 - - - +
116D VAL 3.0 28.5 + - - +
118D PHE* 3.5 32.8 - - + -
128D PHE* 3.5 24.9 - - + -
129D ALA* 1.3 81.4 - - - +
131D VAL* 1.3 61.2 + - - +
132D ALA* 3.4 3.4 + - - +
164D MET* 3.1 15.7 - - + +
166D MET* 3.4 33.2 - - + -
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Residues in contact with VAL 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D PRO* 3.8 19.7 - - + -
114D ALA 4.1 3.1 - - - -
115D VAL* 3.9 24.0 - - + +
129D ALA 4.2 0.2 - - - -
130D ILE* 1.3 70.0 - - - +
132D ALA* 1.3 62.9 + - - +
133D LEU* 4.0 1.0 + - - +
147D LEU* 4.3 15.7 - - + +
150D VAL* 3.8 28.5 - - + -
151D TYR 5.5 0.9 - - - +
154D VAL* 4.7 4.3 - - + -
163D VAL* 3.8 21.5 - - + -
164D MET 2.7 10.8 + - - +
165D LEU* 3.4 14.6 - - + +
166D MET 3.1 26.2 + - - +
169D PHE* 5.4 0.3 - - - -
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Residues in contact with ALA 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D LEU* 3.7 26.9 - - + -
80D TYR* 4.1 11.5 - - + -
82D PHE* 3.5 29.2 - - + -
113D PRO* 3.4 24.3 - - - +
114D ALA 3.3 12.5 + - - +
130D ILE* 3.4 2.1 + - + -
131D VAL* 1.3 72.1 - - - +
133D LEU* 1.3 64.0 + - - +
166D MET* 3.5 7.0 - - + -
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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