Contacts of the strand formed by residues 339 - 347 (chain B) in PDB entry 1JEQ
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 CYS 339 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247B TRP* 3.5 10.9 - - - -
249B CYS* 3.8 11.2 - - - -
250B ARG 5.5 0.2 - - - -
337B GLY 3.9 2.7 - - - +
338B LYS* 1.3 79.4 - - - +
340B PHE* 1.3 64.2 + - - +
341B SER* 3.7 16.8 - - - +
394B ARG* 3.5 47.6 - - - -
395B TYR* 3.8 1.9 - - - -
396B ALA* 3.0 33.6 + - - -
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Residues in contact with PHE 340 (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 TRP* 4.0 10.3 - + + -
249B CYS* 3.9 16.8 - - - -
250B ARG 4.0 7.8 + - - +
251B LEU* 3.3 36.4 - - + +
252B THR* 3.3 17.0 + - - -
261B ILE* 3.9 11.0 - - + -
339B CYS* 1.3 73.3 - - - +
341B SER* 1.3 61.6 + - - +
362B LEU* 5.8 0.9 - - + -
364B VAL* 3.9 28.0 - - + -
393B VAL* 4.3 26.5 - - + -
394B ARG 3.3 8.1 - - - -
395B TYR* 3.8 22.7 - + + -
408B ALA* 4.5 12.3 - - + -
419B LEU* 5.4 0.7 - - + -
421B TYR* 4.1 22.4 - + + -
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Residues in contact with SER 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509A PRO* 3.7 26.1 - - - +
252B THR* 3.2 23.3 - - - -
339B CYS* 3.7 21.0 - - - +
340B PHE* 1.3 73.8 - - - +
342B VAL* 1.3 63.2 + - - +
343B LEU* 3.7 0.9 + - - +
393B VAL* 3.5 3.6 - - - -
394B ARG* 2.9 36.4 + - - +
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Residues in contact with VAL 342 (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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509A PRO* 3.5 12.1 - - - +
514A MET* 3.3 21.3 - - + +
251B LEU* 3.6 17.3 - - + -
252B THR 2.8 23.5 + - - +
253B ILE* 3.6 23.1 - - + -
254B GLY 5.1 0.3 + - - -
341B SER* 1.3 71.5 - - - +
343B LEU* 1.3 63.4 + - - +
344B GLY* 3.5 22.7 - - - +
345B PHE* 3.8 26.2 - - + -
380B LEU* 5.6 1.6 - - + -
391B ALA* 4.6 6.5 - - + -
392B ILE 4.0 4.7 - - - +
393B VAL* 4.3 12.8 - - + -
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Residues in contact with LEU 343 (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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469A LEU* 5.4 1.0 - - - +
471A PHE* 4.2 9.5 - - + -
478A PHE* 3.5 37.7 - - + -
506A LEU 4.8 1.1 - - - +
507A THR* 3.1 30.3 - - - +
508A LEU 3.7 3.1 - - - +
509A PRO* 3.5 31.9 - - + +
510A LYS 5.8 0.3 + - - -
514A MET* 4.3 15.3 - - - +
342B VAL* 1.3 74.4 - - - +
344B GLY* 1.3 58.6 + - - +
392B ILE* 2.9 28.0 + - + +
393B VAL 4.7 3.8 - - - -
394B ARG* 4.4 9.2 - - + +
405B VAL* 4.6 8.7 - - + -
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Residues in contact with GLY 344 (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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469A LEU* 3.5 14.1 - - - -
471A PHE* 3.4 16.9 - - - -
514A MET* 5.6 0.2 - - - -
342B VAL* 3.5 5.2 - - - +
343B LEU* 1.3 82.3 - - - +
345B PHE* 1.3 71.0 + - - -
391B ALA* 3.5 4.7 - - - -
392B ILE 2.9 24.0 + - - +
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Residues in contact with PHE 345 (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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465A ILE* 5.0 1.3 - - + -
466A VAL* 3.6 48.5 - - + +
469A LEU* 3.0 45.9 + - + +
470A ARG* 3.6 1.7 - - - -
471A PHE* 3.2 24.4 + - - +
253B ILE* 4.2 19.7 - - + -
342B VAL* 3.8 21.1 - - + -
344B GLY* 1.3 75.0 - - - -
346B CYS* 1.3 67.8 + - - +
380B LEU* 3.8 18.2 - - + -
384B LEU* 3.6 19.1 - - + -
389B MET* 4.2 4.7 - - + -
390B VAL 3.0 12.3 - - - +
391B ALA* 4.0 16.4 - - + -
392B ILE 4.8 0.2 - - - +
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Residues in contact with CYS 346 (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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471A PHE* 3.0 20.9 - - + +
473A TYR* 3.7 26.7 - - + +
345B PHE* 1.3 79.9 - - - +
347B LYS* 1.3 73.9 + - - +
350B GLN* 3.8 7.2 - - - +
351B VAL* 4.1 2.9 - - - -
389B MET* 3.1 16.1 - - - +
390B VAL* 2.8 45.4 + - - +
392B ILE* 4.0 18.4 - - - -
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Residues in contact with LYS 347 (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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470A ARG* 4.5 19.5 - - - +
346B CYS* 1.3 79.2 - - - +
348B SER* 1.3 67.0 + - - +
349B SER* 3.6 18.6 - - - +
350B GLN* 3.1 37.3 + - + +
351B VAL 4.0 0.9 + - - -
388B ASP* 4.0 8.1 - - - +
389B MET* 3.5 13.9 - - + +
390B VAL* 4.2 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