Contacts of the strand formed by residues 348 - 355 (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 SER 348 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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345M VAL* 3.3 16.8 + - - -
346M ASP* 4.1 0.3 - - - -
347M PHE* 1.3 78.3 - - - +
349M ALA* 1.3 58.7 + - - +
374M LEU* 3.8 3.3 - - - +
489M LEU 3.2 6.5 - - - -
490M HIS* 3.6 22.0 - - - -
1104N HIS* 5.4 0.3 + - - -
1105N ALA* 3.5 0.3 - - - -
1106N ARG* 2.8 35.0 + - - +
1127N GLY* 4.0 1.9 - - - -
1128N LEU* 3.1 39.2 + - - +
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Residues in contact with ALA 349 (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* 1.3 74.4 - - - +
350M ARG* 1.3 55.4 + - - +
370M ILE* 3.7 22.9 - - + -
374M LEU* 4.1 7.4 - - + -
468M PHE* 4.1 5.8 - - + -
489M LEU* 2.7 36.4 + - + +
1104N HIS 2.9 16.8 - - - +
1105N ALA* 3.4 17.9 - - + -
1128N LEU* 3.0 13.2 - - - +
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Residues in contact with ARG 350 (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 4.5 4.8 + - - -
215 C 3.6 36.6 + - - -
225 BRU 6.3 0.2 - - - -
96 G 4.4 11.3 - - - +
349M ALA* 1.3 72.9 - - - +
351M THR* 1.3 77.2 + - - +
447M GLN* 4.1 9.9 + - - +
468M PHE* 3.5 2.7 - - - -
486M GLU* 3.1 49.1 + - - +
487M MET* 3.2 16.1 - - - +
488M ASN* 2.7 60.3 + - - +
1102N LYS 4.1 1.4 - - - +
1103N ILE* 3.8 0.9 - - - -
1104N HIS* 2.7 30.0 + - + +
1128N LEU* 3.5 20.6 - - + +
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Residues in contact with THR 351 (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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350M ARG* 1.3 88.3 - - - +
352M VAL* 1.3 73.2 + - - +
367M PRO* 5.0 1.9 - - + +
370M ILE* 3.8 17.7 - - + -
466M SER 3.8 2.4 + - - +
468M PHE* 3.1 29.4 + - + -
486M GLU* 3.1 12.8 - - - +
487M MET 3.0 24.8 + - - +
1102N LYS* 5.3 0.2 - - - -
1103N ILE* 3.0 47.3 - - + +
1104N HIS 3.7 3.1 - - - +
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Residues in contact with VAL 352 (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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351M THR* 1.3 82.1 - - - +
353M ILE* 1.3 74.7 + - - +
354M SER* 5.7 0.4 - - - -
467M THR* 2.9 30.5 - - + +
468M PHE 3.2 7.3 + - - -
484M GLY* 4.5 18.8 - - - +
485M ASP 3.4 12.1 - - - +
486M GLU* 4.2 14.1 - - + -
977N GLY* 4.2 16.4 - - - +
989N THR* 4.7 6.1 - - - +
1098N MET 6.0 0.2 - - - -
1099N VAL* 3.6 26.3 - - + +
1102N LYS* 4.3 18.2 - - + +
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Residues in contact with ILE 353 (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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351M THR 4.2 0.2 - - - +
352M VAL* 1.3 88.4 - - - +
354M SER* 1.3 62.3 + - - +
468M PHE* 3.2 15.3 - - + +
470M LEU* 3.3 17.5 - - + -
480M ALA* 3.6 24.2 - - + -
481M ASP 3.8 6.7 - - - +
482M PHE* 3.2 26.4 - - + +
485M ASP* 2.9 17.3 + - + +
487M MET* 3.1 66.2 - - + +
989N THR* 4.5 0.3 + - - -
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Residues in contact with SER 354 (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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352M VAL* 5.7 0.2 - - - -
353M ILE* 1.3 75.5 - - - +
355M GLY* 1.3 69.6 + - - +
467M THR* 3.2 27.5 + - - +
468M PHE 3.2 3.2 + - - -
469M ARG* 3.4 22.2 + - - +
470M LEU 3.3 18.4 + - - -
482M PHE* 3.3 15.3 - - - -
838N SER* 5.5 1.3 - - - -
976N ILE* 4.6 1.9 - - - +
977N GLY* 6.4 0.2 - - - -
989N THR* 4.9 1.6 - - - -
990N ILE 4.2 19.3 - - - -
991N GLY* 4.5 3.1 - - - -
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Residues in contact with GLY 355 (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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354M SER* 1.3 74.3 - - - +
356M ASP* 1.3 57.9 + - - -
357M PRO* 4.3 3.1 - - - +
469M ARG* 3.1 18.4 + - - -
470M LEU 3.5 5.6 - - - -
472M LEU* 4.8 7.9 - - - -
482M PHE* 2.9 36.5 - - - -
832N GLY 5.5 1.6 - - - -
833N TYR* 4.4 14.8 + - - +
835N GLN* 6.2 1.3 - - - -
838N SER* 5.0 1.4 + - - -
991N GLY* 5.3 0.3 - - - -
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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