Contacts of the strand formed by residues 408 - 413 (chain B) 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 LEU 408 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B PHE* 4.2 15.5 - - + -
246B THR 4.0 1.8 - - - +
247B SER 3.4 24.9 - - - +
248B CYS* 3.8 23.8 - - - +
249B CYS* 3.9 16.2 - - + +
274B TYR* 4.5 0.8 + - + -
403B GLU 5.3 0.2 - - - +
404B VAL* 3.4 23.6 - - - +
405B THR 5.1 0.7 + - - -
406B LEU* 3.3 3.9 + - - +
407B GLY* 1.3 78.0 - - - +
409B VAL* 1.3 69.0 + - - +
410B CYS* 4.3 2.7 - - - -
447B ARG* 3.7 36.8 - - + +
448B PHE 3.3 30.1 - - - +
449B ALA* 3.9 5.6 - - + -
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Residues in contact with VAL 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385B SER* 3.4 33.7 - - - +
388B PHE* 3.7 34.1 - - + -
389B GLU* 4.1 12.3 - - + -
392B VAL* 4.8 2.0 - - + -
400B VAL* 4.7 5.6 - - + -
404B VAL* 3.7 21.8 - - + -
408B LEU* 1.3 80.2 - - - +
410B CYS* 1.3 72.4 + - - +
411B PHE* 3.8 5.6 + - + +
446B LEU 3.7 1.0 - - - +
447B ARG* 3.6 0.9 - - - -
448B PHE* 2.8 42.7 + - + +
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Residues in contact with CYS 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247B SER 3.3 26.7 - - - -
248B CYS* 3.5 23.6 - - + -
400B VAL* 3.5 7.9 - - - +
401B CYS* 2.7 40.4 + - + -
402B ALA* 4.7 7.4 + - + +
404B VAL* 5.1 2.8 - - - +
408B LEU* 4.3 4.7 + - - -
409B VAL* 1.3 76.9 - - - +
411B PHE* 1.3 54.6 + - - +
438B CYS* 4.8 1.1 - - - -
440B LEU* 4.5 5.4 - - + -
445B VAL* 3.6 18.4 - - + -
446B LEU 3.4 4.3 - - - -
447B ARG* 4.2 13.2 - - - -
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Residues in contact with PHE 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388B PHE* 4.0 22.7 - + - -
392B VAL* 3.9 24.2 - - + -
398B PHE* 4.0 21.8 - + - -
399B GLU 3.2 11.2 - - - +
400B VAL* 4.8 0.2 - - - -
401B CYS* 3.9 1.6 - - - -
409B VAL* 4.1 7.9 - - + -
410B CYS* 1.3 76.1 - - - +
412B ARG* 1.3 67.2 + - - +
423B LEU* 4.8 2.9 - - + -
435B LEU* 4.0 18.4 - - + -
445B VAL* 3.5 3.3 - - - +
446B LEU* 2.9 78.9 + - + +
448B PHE* 4.3 6.5 - - + -
464B TRP* 4.7 3.6 - + - -
467B ILE* 4.1 26.5 - - + -
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Residues in contact with ARG 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398B PHE* 3.2 8.9 - - - +
399B GLU* 2.8 56.9 + - + +
401B CYS* 3.7 19.1 - - - -
411B PHE* 1.3 84.1 - - - +
413B LEU* 1.3 68.7 + - - +
415B GLY 3.4 21.0 + - - +
416B SER* 3.4 23.2 - - - +
417B ASP* 3.0 21.6 + - - +
420B ASN* 3.3 21.8 - - - +
443B GLN* 3.2 33.3 + - - +
444B PHE 3.1 22.0 + - - +
445B VAL* 4.4 0.9 - - - -
446B LEU* 5.2 1.3 - - - +
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Residues in contact with LEU 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397B ARG* 3.7 20.0 - - + +
398B PHE* 3.4 36.9 - - + -
411B PHE* 5.2 0.6 - - - -
412B ARG* 1.3 74.7 + - - +
414B LYS* 1.3 68.9 + - - +
415B GLY* 3.0 3.8 + - - -
419B LEU* 3.3 29.3 - - + +
420B ASN* 2.6 32.5 + - - +
423B LEU* 4.1 17.1 - - + +
471B ALA* 3.9 21.1 - - + -
474B LEU* 4.3 12.1 - - + -
475B LEU* 4.4 15.3 - - + -
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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