Contacts of the strand formed by residues 308 - 311 (chain B) in PDB entry 1JRX
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 ALA 308 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B ASP 3.0 8.9 + - - +
129B VAL* 3.1 9.0 - - + -
130B VAL 2.8 30.8 + - - -
289B VAL* 3.9 1.1 - - - -
306B ALA* 3.3 3.1 - - - +
307B ASP* 1.3 82.7 - - + +
309B VAL* 1.4 62.4 + - - +
528B GLY 3.1 12.3 - - - +
530B TYR* 4.0 6.5 - - + -
564B ALA* 3.9 34.1 - - + +
567B TYR* 4.2 4.0 - - + -
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Residues in contact with VAL 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B VAL* 3.3 12.8 - - + +
132B VAL* 3.9 10.3 - - + -
281B VAL* 4.0 9.4 - - + -
289B VAL* 3.7 19.5 - - + +
291B GLY* 3.9 19.3 - - - +
292B ILE* 4.0 21.8 - - + -
306B ALA* 5.1 0.4 - - + -
308B ALA* 1.4 78.5 - - - +
310B ILE* 1.3 62.9 + - - +
311B LEU* 3.7 27.8 - - + -
528B GLY 2.8 7.5 + - - +
529B LEU* 3.6 9.5 - - + +
530B TYR* 2.9 27.5 + - - +
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Residues in contact with ILE 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B VAL* 3.4 27.4 - - + -
130B VAL 2.9 8.9 + - - -
131B VAL* 3.6 13.1 - - + +
132B VAL* 2.8 29.3 + - - +
141B ALA* 3.8 25.1 - - + +
309B VAL* 1.3 72.5 - - - +
311B LEU* 1.3 73.8 + - - +
312B ALA* 3.4 2.7 + - + -
530B TYR* 3.5 20.2 - - + +
532B ALA* 4.4 7.6 - - + -
560B ALA* 3.7 15.9 - - + +
561B GLY* 3.6 30.5 - - - -
564B ALA* 3.6 10.3 - - + -
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Residues in contact with LEU 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B VAL* 3.6 32.8 - - + -
281B VAL* 4.3 2.0 - - + -
292B ILE* 4.8 0.4 - - + -
309B VAL* 3.7 12.8 - - + -
310B ILE* 1.3 72.4 - - - +
312B ALA* 1.3 57.2 + - - +
313B THR* 3.5 9.9 - - + +
345B GLY 4.4 9.6 - - - +
348B VAL* 4.1 20.0 - - + -
349B ALA* 3.9 35.9 - - + +
510B VAL* 5.8 0.7 - - + -
518B VAL* 5.4 1.6 - - + -
529B LEU* 3.5 25.4 - - + -
530B TYR 2.7 14.5 + - - +
531B GLY* 3.4 2.9 - - - -
532B ALA 2.9 26.0 + - - -
535B VAL* 3.3 13.6 - - + +
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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
------------------------------------------------------------
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