Contacts of the strand formed by residues 139 - 143 (chain D) in PDB entry 4CJM
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 THR 139 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57D LEU* 5.6 3.4 - - + -
131D GLU* 3.8 27.4 - - + +
132D LYS 3.3 9.0 - - - +
133D VAL* 4.0 15.5 - - - +
134D LEU* 4.8 0.7 - - - -
137D ASN 5.2 1.2 + - - -
138D TYR* 1.3 75.6 - - - +
140D ALA* 1.3 72.8 + - - +
141D LEU* 4.7 8.1 - - + -
172D VAL 3.6 3.3 - - - +
173D HIS* 3.7 0.8 - - - -
174D PHE* 2.8 45.6 + - + +
175D MET* 5.5 0.2 - - - -
176D LYS* 4.5 19.3 + - + +
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Residues in contact with ALA 140 (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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130D ILE 3.6 1.0 - - - +
131D GLU* 3.6 3.6 - - - -
132D LYS* 2.8 37.7 + - + +
134D LEU* 4.1 23.3 - - + +
138D TYR 4.2 0.6 + - - -
139D THR* 1.3 78.6 - - - +
141D LEU* 1.3 63.7 + - - +
142D MET 4.0 0.7 - - - -
150D TYR* 4.1 22.7 - - + -
167D GLU* 4.7 0.9 - - + -
172D VAL* 3.6 19.3 - - + +
174D PHE* 4.9 0.2 - - - -
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Residues in contact with LEU 141 (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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57D LEU* 3.9 21.1 - - + -
66D ILE* 5.3 0.7 - - + -
97D VAL* 4.0 26.7 - - + -
99D ILE* 3.6 25.6 - - + -
108D LEU* 5.3 0.7 - - + -
129D PHE* 4.2 6.1 - - + -
130D ILE 3.5 2.7 - - - +
131D GLU* 4.2 18.4 - - + +
139D THR* 4.7 8.1 - - + -
140D ALA* 1.3 82.1 - - - +
142D MET* 1.3 61.7 + - - +
150D TYR* 3.4 4.2 - - - -
151D VAL* 2.9 57.7 + - + +
172D VAL 4.5 3.2 + - - -
174D PHE* 5.0 11.1 - - + -
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Residues in contact with MET 142 (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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129D PHE* 3.2 4.7 - - - -
130D ILE* 2.7 76.3 + - + +
132D LYS* 6.6 0.2 - - + -
140D ALA 4.0 0.4 - - - -
141D LEU* 1.3 73.4 - - - +
143D SER* 1.3 74.0 + - - +
147D SER* 3.7 19.5 - - - +
148D GLY* 3.3 23.3 - - - +
149D TRP 3.3 13.7 - - - +
150D TYR* 3.5 35.1 - - + -
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Residues in contact with SER 143 (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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110D MET* 4.0 24.3 + - - +
125D LYS 5.1 0.2 + - - -
126D GLU 5.2 1.9 + - - -
128D VAL 4.0 2.4 + - - -
129D PHE* 3.7 16.5 - - - -
130D ILE* 4.7 0.2 - - - -
142D MET* 1.3 82.1 - - - +
144D ALA* 1.3 61.3 + - - +
145D LYS* 3.1 8.5 + - - +
146D TYR* 2.9 52.0 + - - +
147D SER* 3.8 3.3 + - - -
149D TRP 2.8 14.4 + - - -
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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