Contacts of the strand formed by residues 366 - 375 (chain B) in PDB entry 3IJE
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 366 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90B LEU* 4.9 0.9 - - + -
92B LEU* 3.5 31.2 - - + -
362B LEU* 3.7 19.5 - - + +
363B PRO* 3.0 25.5 + - + +
364B GLU 3.4 3.8 - - - +
365B GLU* 1.3 78.2 - - - +
367B SER* 1.3 64.8 + - - +
368B LEU* 4.5 2.5 - - + -
401B ALA* 4.4 14.8 - - + -
402B LYS 3.5 14.6 - - - +
403B VAL* 3.7 9.2 - - + +
414B PHE* 3.9 29.6 - - + -
429B VAL* 4.1 13.7 - - + -
431B PHE* 4.1 10.5 - - + -
551B SER* 3.0 16.1 + - - -
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Residues in contact with SER 367 (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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362B LEU* 5.1 1.6 - - - -
365B GLU 4.6 2.9 + - - -
366B LEU* 1.3 73.1 - - - +
368B LEU* 1.3 66.5 + - - +
369B SER* 5.3 0.4 + - - -
400B GLU* 3.4 2.9 - - - +
401B ALA* 3.5 2.8 - - - -
402B LYS* 2.9 40.0 + - - +
404B ARG* 6.2 0.2 - - - +
549B CYS 5.1 2.3 + - - -
550B ASP 4.6 0.9 - - - -
551B SER* 2.7 39.4 + - - -
552B ASP 5.2 1.6 - - - -
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Residues in contact with LEU 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B PHE* 5.2 1.8 - - + -
359B VAL* 4.9 5.6 - - + -
362B LEU* 3.5 42.4 - - + +
366B LEU* 4.5 9.4 - - + -
367B SER* 1.3 82.6 - - - +
369B SER* 1.3 64.1 + - - +
370B PHE* 4.1 24.0 - - + -
399B ILE* 3.7 24.2 - - + -
400B GLU 3.3 4.9 - - - +
401B ALA* 4.6 5.6 - - + -
414B PHE* 4.2 13.9 - - + -
416B ILE* 3.9 20.6 - - + -
552B ASP* 5.3 4.9 + - - +
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Residues in contact with SER 369 (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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367B SER 5.3 0.5 + - - -
368B LEU* 1.3 77.4 + - - +
370B PHE* 1.3 63.8 + - - +
398B SER 3.4 1.2 - - - +
399B ILE* 3.2 8.7 - - - +
400B GLU* 3.0 53.9 + - - -
1K NAG 3.4 11.7 - - - +
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Residues in contact with PHE 370 (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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357B LEU* 4.9 5.2 - - + -
359B VAL* 4.2 17.9 - - + -
368B LEU* 4.1 35.2 - - + -
369B SER* 1.3 77.6 - - - +
371B ASN* 1.3 59.2 + - - +
382B GLY* 2.7 39.7 + - - -
383B LEU 3.1 21.6 + - - +
384B LYS* 3.7 41.1 - - + -
397B PHE* 4.9 9.2 - + + -
398B SER 3.3 2.0 - - - -
399B ILE* 3.5 39.0 - - + -
416B ILE* 4.6 8.7 - - + -
1K NAG 4.7 0.4 - - - -
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Residues in contact with ASN 371 (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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369B SER* 6.0 0.2 - - - -
370B PHE* 1.3 82.7 - - - +
372B ALA* 1.3 60.6 + - - +
373B THR 4.2 0.4 + - - -
379B VAL* 3.7 25.0 - - + +
380B ILE 3.8 3.6 - - - -
381B PRO* 3.2 17.5 - - + +
382B GLY 3.3 1.9 + - - -
383B LEU 3.5 2.7 - - - +
397B PHE* 3.3 7.1 - - - +
398B SER* 2.9 37.2 + - - -
1K NAG 1.5 67.0 + - - +
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Residues in contact with ALA 372 (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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371B ASN* 1.3 73.4 - - - +
373B THR* 1.3 60.9 + - - +
374B CYS* 4.0 1.0 + - - -
378B GLU 3.7 0.5 - - - +
379B VAL* 3.4 1.5 - - - -
380B ILE* 2.8 54.2 + - + +
383B LEU* 3.2 28.0 + - + +
386B CYS* 4.0 13.7 - - - -
396B SER 3.8 3.4 - - - -
397B PHE* 3.8 16.4 - - + -
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Residues in contact with THR 373 (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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371B ASN 4.2 0.6 + - - -
372B ALA* 1.3 69.5 - - - +
374B CYS* 1.3 62.0 + - - +
376B ASN 3.9 21.1 - - - +
377B ASN* 4.2 11.8 + - - +
378B GLU 3.6 10.5 - - - +
379B VAL* 3.6 22.5 - - - +
395B VAL* 3.8 1.0 - - - -
396B SER* 2.8 54.0 + - - +
397B PHE* 4.8 0.2 - - - +
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Residues in contact with CYS 374 (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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372B ALA* 4.0 4.9 - - - -
373B THR* 1.3 87.4 - - - +
375B LEU* 1.3 62.6 + - - +
376B ASN 4.1 1.5 + - - -
378B GLU 3.9 2.6 + - - -
380B ILE* 5.7 3.5 - - + +
386B CYS* 2.0 53.4 - - + -
387B MET 5.8 0.7 - - - +
389B LEU* 4.9 2.2 - - + -
394B THR 5.4 2.1 - - - +
395B VAL* 3.8 22.5 - - + +
396B SER 4.4 2.2 - - - -
397B PHE* 4.5 1.6 - - - -
633B ARG* 3.5 26.5 + - - +
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Residues in contact with LEU 375 (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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374B CYS* 1.3 78.4 + - + +
376B ASN* 1.3 94.0 + - - +
377B ASN 3.0 0.2 + - - -
378B GLU* 2.9 40.5 + - + +
629B ASN 4.2 2.9 - - - +
630B THR* 3.4 26.0 - - + -
633B ARG* 3.5 34.1 - - + +
634B TYR* 3.2 37.0 - - + +
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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