Contacts of the strand formed by residues 319 - 325 (chain A) in PDB entry 2JLF
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 LEU 319 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A ARG* 6.0 1.3 - - - +
317A TRP* 3.9 3.4 - - - +
318A SER* 1.3 80.6 - - - +
320A CYS* 1.3 70.1 + - - +
321A VAL* 3.9 16.4 - - + -
457A LEU 3.6 0.2 - - - +
458A GLY* 3.2 7.4 - - - -
459A TRP* 3.1 35.8 + - + -
465A LEU* 4.4 8.3 - - + +
468A GLY* 3.6 34.3 - - - +
469A HIS* 3.6 35.4 - - + +
472A PHE* 3.6 31.2 - - + -
509A PRO* 3.9 5.6 - - + -
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Residues in contact with CYS 320 (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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74A ARG* 5.6 0.7 - - - +
314A VAL* 3.9 11.9 - - + -
317A TRP* 3.7 26.7 - - + -
319A LEU* 1.3 80.4 - - - +
321A VAL* 1.3 68.7 + - - +
322A ALA 4.1 1.8 + - - -
456A MET* 3.6 32.8 - - - -
457A LEU 3.3 2.0 - - - -
472A PHE* 3.9 14.7 - - - -
501A LEU* 3.9 1.6 - - - -
503A TYR* 3.1 28.0 + - - +
509A PRO* 3.7 14.1 - - + +
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Residues in contact with VAL 321 (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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319A LEU* 3.9 16.8 - - + -
320A CYS* 1.3 79.4 - - - +
322A ALA* 1.3 69.5 + - - +
323A THR* 3.5 10.9 + - + +
456A MET* 4.4 1.1 - - - -
457A LEU* 2.8 36.4 + - + -
459A TRP* 3.5 31.0 - - + -
471A LEU* 6.0 1.1 - - + -
472A PHE* 4.0 31.0 - - + +
475A LEU* 3.8 28.7 - - + -
490A TYR* 5.2 0.9 - - + -
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Residues in contact with ALA 322 (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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73A GLY 5.6 0.2 - - - +
320A CYS* 4.0 2.6 + - - -
321A VAL* 1.3 71.9 - - - +
323A THR* 1.3 61.2 + - - +
455A ALA 3.8 5.4 - - - -
456A MET* 3.9 21.7 - - + +
472A PHE* 5.7 1.8 - - - -
490A TYR* 3.5 8.0 - - - +
491A GLN* 2.8 35.4 + - + +
494A GLY* 3.9 28.0 - - - -
1664A MN 4.4 1.3 - - - +
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Residues in contact with THR 323 (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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321A VAL* 3.8 15.3 - - + +
322A ALA* 1.3 76.6 - - - +
324A ASP* 1.3 67.0 + - - +
410A TYR* 3.1 32.9 + - + -
413A MET* 5.2 1.8 - - + -
453A ASP 4.9 1.5 - - - +
454A ASP* 4.6 0.7 - - - +
455A ALA* 3.3 16.1 + - - +
457A LEU* 3.8 31.0 - - + -
475A LEU* 5.5 5.2 - - + -
488A ILE* 4.2 8.3 - - + -
489A SER 3.3 12.1 - - - +
490A TYR* 4.4 0.7 - - - +
491A GLN* 3.6 9.0 - - - +
1664A MN 3.6 13.3 + - - -
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Residues in contact with ASP 324 (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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323A THR* 1.3 84.1 + - - +
325A VAL* 1.3 79.1 + - - +
326A SER 4.1 0.3 + - - -
453A ASP* 4.4 7.2 - - - +
487A LYS 3.7 0.7 - - - +
488A ILE* 3.6 6.4 - - - +
489A SER* 3.0 41.5 + - - +
490A TYR 4.1 10.1 - - - +
491A GLN* 4.3 19.3 + - - +
492A HIS 5.4 0.2 + - - -
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Residues in contact with VAL 325 (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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324A ASP* 1.3 88.7 + - - +
326A SER* 1.3 73.9 + - - +
327A ASP 3.3 2.9 + - - -
328A HIS* 4.0 9.7 + - + -
406A MET* 3.4 29.8 - - + -
410A TYR* 3.4 13.7 - - - +
453A ASP* 3.8 32.7 + - + +
486A MET* 3.9 31.4 - - + -
487A LYS 3.7 10.8 - - - +
488A ILE* 4.2 4.9 - - + -
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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