Contacts of the strand formed by residues 141 - 145 (chain A) in PDB entry 1JS6
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 GLY 141 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A PHE 2.9 21.4 + - - +
134A ALA* 3.9 15.9 - - - -
140A GLY* 1.3 75.3 - - - -
142A GLY* 1.3 59.3 + - - -
315A TRP* 3.4 2.3 - - - -
316A VAL 3.1 26.1 + - - -
343A ILE* 4.4 1.8 - - - -
349A TRP* 3.8 17.2 - - - -
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Residues in contact with GLY 142 (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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116A THR* 4.7 1.9 + - - +
119A MET* 3.6 21.4 - - - +
120A ASP* 5.5 1.4 + - - -
134A ALA* 5.2 1.2 - - - +
141A GLY* 1.3 74.6 - - - -
143A VAL* 1.3 55.2 + - - -
314A MET 3.1 11.2 - - - -
315A TRP* 3.7 14.1 - - - -
343A ILE* 4.4 1.8 - - - +
346A TYR* 2.6 31.9 + - - -
349A TRP* 4.0 3.6 - - - -
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Residues in contact with VAL 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A GLU* 3.3 14.8 - - - +
119A MET* 3.6 7.0 - - - +
142A GLY* 1.3 74.3 - - - -
144A ILE* 1.3 76.4 + - - +
145A GLN* 3.4 25.4 + - - +
314A MET* 2.8 40.9 + - + +
322A LEU* 4.9 2.9 - - + -
346A TYR* 3.4 26.5 - - + +
349A TRP* 3.5 28.0 - - + +
350A GLN* 5.0 2.2 - - - +
355A ARG* 3.6 6.1 - - - +
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Residues in contact with ILE 144 (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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115A GLU* 2.9 33.7 + - + +
119A MET* 4.4 6.7 - - - -
143A VAL* 1.3 77.5 - - - +
145A GLN* 1.3 72.0 + - - +
311A CYS* 4.3 15.9 - - - -
312A SER 3.3 8.5 - - - +
313A ALA* 5.5 0.2 - - - -
350A GLN* 4.0 2.9 - - - +
355A ARG* 3.4 8.5 + - - -
358A ARG* 3.3 45.1 + - + +
359A SER* 3.8 24.2 - - - +
362A MET* 3.4 33.9 - - - -
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Residues in contact with GLN 145 (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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143A VAL* 3.4 19.0 + - - +
144A ILE* 1.3 80.6 - - - +
146A GLY* 1.3 64.1 + - - +
147A SER 3.3 16.6 - - - +
150A GLU* 4.7 5.8 - - + +
151A ALA* 4.0 11.4 - - + +
154A VAL* 3.9 18.1 - - - +
311A CYS* 4.0 1.2 - - - -
312A SER* 2.7 35.5 + - - +
314A MET* 4.0 29.5 - - + -
349A TRP 2.8 28.9 + - - -
350A GLN* 3.6 19.6 - - - +
351A LEU 4.8 0.5 + - - -
352A PRO* 5.8 0.2 - - - +
358A ARG* 3.9 5.0 + - - +
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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