Contacts of the strand formed by residues 404 - 412 (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 GLN 404 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507A THR* 5.9 0.2 - - - -
360B GLN* 5.2 6.2 + - - +
394B ARG* 3.1 10.4 - - - +
395B TYR* 2.6 63.4 + - + +
402B ASN 4.1 8.9 + - - +
403B PRO* 1.3 79.3 - - - +
405B VAL* 1.3 63.8 + - - +
421B TYR* 3.0 26.0 + - - +
423B GLN* 2.9 45.1 + - - +
426B PHE* 4.4 3.4 - - - -
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Residues in contact with VAL 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A TYR* 5.4 0.4 - - + -
478A PHE* 3.9 35.2 - - + -
507A THR* 3.8 24.9 - - + -
343B LEU* 4.6 4.7 - - + -
392B ILE* 4.0 14.8 - - + -
393B VAL 3.2 5.6 - - - +
394B ARG* 5.1 1.1 - - - -
404B GLN* 1.3 79.6 - - - +
406B GLY* 1.3 61.1 + - - +
421B TYR* 4.1 1.8 - - - -
423B GLN* 3.8 3.9 - - - +
424B LEU* 2.8 36.0 + - + +
425B PRO 5.3 3.6 - - - +
426B PHE* 3.7 30.2 - - + -
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Residues in contact with GLY 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B ILE* 3.3 7.4 - - - +
393B VAL* 2.7 35.6 + - - -
405B VAL* 1.3 76.5 - - - +
407B VAL* 1.3 58.2 + - - -
421B TYR* 3.8 14.3 + - - -
422B VAL 3.3 12.6 - - - -
423B GLN* 3.9 0.4 - - - -
424B LEU* 3.4 15.7 - - - -
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Residues in contact with VAL 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A LYS* 5.9 0.9 - - - +
351B VAL* 4.0 17.5 - - + -
356B PHE* 4.0 26.5 - - + -
390B VAL* 3.9 21.5 - - + -
391B ALA 3.3 9.4 - - - +
392B ILE* 4.6 1.3 - - + +
393B VAL* 4.8 0.2 - - - -
406B GLY* 1.3 73.9 - - - -
408B ALA* 1.3 67.3 + - - +
409B PHE* 3.8 20.4 - - + -
420B VAL 3.3 0.7 - - - +
421B TYR* 3.2 8.8 - - - -
422B VAL* 2.9 47.7 + - + +
424B LEU* 3.7 9.8 - - + +
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Residues in contact with ALA 408 (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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340B PHE* 4.5 12.6 - - + -
384B LEU* 4.1 6.1 - - - +
390B VAL* 3.9 1.0 - - - +
391B ALA* 2.8 37.8 + - + +
393B VAL* 4.2 18.2 - - + -
407B VAL* 1.3 75.4 - - - +
409B PHE* 1.3 60.3 + - - +
419B LEU* 4.1 27.4 - - + -
420B VAL 3.3 6.7 - - - -
421B TYR* 4.9 2.5 - - + -
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Residues in contact with PHE 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A LYS* 4.0 42.6 - - + +
359A HIS* 4.1 18.8 - - + -
356B PHE* 4.2 12.1 - + - -
390B VAL* 3.2 25.4 - - + -
407B VAL* 3.8 15.9 - - + -
408B ALA* 1.3 73.5 - - - +
410B PRO* 1.3 80.3 - - + +
411B HIS* 5.5 0.7 - - + -
419B LEU* 3.4 4.8 - - - -
420B VAL* 3.0 66.4 + - + +
422B VAL* 3.8 17.3 - - + -
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Residues in contact with PRO 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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381B ILE* 3.3 30.1 - - + +
384B LEU* 3.6 21.3 - - + -
385B ASP* 3.6 31.2 - - + +
389B MET 3.9 9.6 - - - +
390B VAL* 4.2 0.4 - - + -
409B PHE* 1.3 102.7 - - + +
411B HIS* 1.3 60.1 + - - +
412B ILE* 4.2 1.3 - - + -
418B CYS 3.9 5.6 - - - +
419B LEU* 3.9 4.7 - - + -
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Residues in contact with HIS 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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357A LYS* 6.1 0.2 - - - -
359A HIS* 3.4 40.3 + + - -
363B LYS* 3.7 22.6 + - - -
381B ILE* 4.6 0.2 - - - +
409B PHE* 5.5 1.0 - - + -
410B PRO* 1.3 74.8 + - - +
412B ILE* 1.3 61.1 + - - +
413B LYS* 3.7 28.0 + - + +
416B TYR* 3.8 19.1 + + - +
417B GLU* 3.6 2.8 - - - -
418B CYS* 3.0 51.6 + - - +
420B VAL* 3.9 17.2 - - + +
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Residues in contact with ILE 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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451A LYS* 3.7 10.3 - - - +
381B ILE* 3.8 19.1 - - + -
382B HIS* 3.8 24.5 - - + +
385B ASP* 3.6 41.1 - - + +
410B PRO* 5.0 0.7 - - + -
411B HIS* 1.3 78.9 + - - +
413B LYS* 1.3 87.8 + - - +
416B TYR 4.1 1.3 - - - -
417B GLU* 3.6 22.9 - - + +
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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
------------------------------------------------------------
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