Contacts of the strand formed by residues 486 - 490 (chain M) in PDB entry 2JA7
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 486 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215 C 5.0 7.8 + - - +
225 BRU 5.4 7.9 - - - +
96 G 5.2 7.4 + - - +
106 A 5.2 2.4 + - - -
350M ARG* 3.1 52.2 + - - +
351M THR* 3.1 20.1 - - - +
352M VAL* 4.2 10.1 - - + -
446M ARG* 4.4 10.7 + - - +
447M GLN 5.6 0.2 + - - -
484M GLY 3.8 5.1 + - - +
485M ASP* 1.3 77.8 - - - +
487M MET* 1.3 72.5 + - - +
1102N LYS* 4.0 36.8 + - + +
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Residues in contact with MET 487 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350M ARG* 3.2 22.9 - - - +
351M THR 3.0 7.4 + - - -
353M ILE* 3.1 45.5 - - + +
444M PHE* 3.3 40.2 - - + -
445M ASN 3.5 11.4 - - - +
446M ARG* 3.4 30.7 - - + +
468M PHE* 3.3 11.4 - - - -
470M LEU* 3.4 19.1 - - + -
478M TYR* 4.2 11.4 - - + -
480M ALA* 4.6 3.1 - - + -
486M GLU* 1.3 84.9 - - - +
488M ASN* 1.3 65.4 + - - +
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Residues in contact with ASN 488 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205 C 5.1 2.2 + - - -
215 C 5.5 0.2 - - - -
349M ALA 3.5 3.1 - - - +
350M ARG* 2.7 47.5 + - - +
443M LEU 3.9 0.3 - - - +
444M PHE* 3.4 8.1 - - - -
445M ASN* 2.8 49.9 + - - +
447M GLN* 3.3 32.5 + - - +
487M MET* 1.3 72.8 - - - +
489M LEU* 1.3 60.2 + - - +
490M HIS* 4.5 13.7 + - - +
1128N LEU* 3.9 17.0 - - + +
1129N ARG 4.7 6.5 + - - +
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Residues in contact with LEU 489 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348M SER* 3.2 8.5 - - - -
349M ALA* 2.7 40.2 + - + +
364M VAL* 5.0 2.7 - - + -
366M VAL* 4.0 22.0 - - + -
374M LEU* 4.4 19.8 - - + +
436M ILE* 6.4 0.4 - - + -
442M VAL* 3.5 34.8 - - + -
443M LEU 3.1 20.0 - - - +
444M PHE* 3.9 14.8 - - + -
460M VAL* 5.1 0.7 - - + -
468M PHE* 3.6 32.1 - - + -
488M ASN* 1.3 76.0 - - - +
490M HIS* 1.3 64.1 + - - +
491M VAL* 5.1 0.9 - - + -
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Residues in contact with HIS 490 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345M VAL* 4.2 7.6 - - + -
347M PHE 3.7 2.0 - - - -
348M SER* 3.6 20.6 - - - -
442M VAL* 3.7 5.7 - - - +
443M LEU* 2.9 55.0 + - + +
445M ASN* 4.8 1.9 + - + -
455M MET* 4.3 10.4 - - + +
488M ASN* 4.5 15.4 + - + +
489M LEU* 1.3 77.8 + - - +
491M VAL* 1.3 62.6 + - - +
492M PRO* 4.0 0.7 - - - +
501M LEU* 5.5 0.2 - - - +
1128N LEU* 4.6 10.3 - - + -
1129N ARG 4.7 11.3 + - - -
1130N PHE* 3.7 31.0 - + + -
1134N GLU* 5.4 0.6 - - - +
1146N PHE* 4.6 3.8 - - + -
1150N ARG* 3.0 32.8 + - - +
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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