Contacts of the helix formed by residues 365 - 381 (chain B) in PDB entry 2YIC
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 ASP 365 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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367A ASN* 5.8 4.4 - - - +
366B LYS* 1.4 65.2 + - - +
367B ASN* 3.5 5.4 - - - +
368B ALA* 3.5 16.7 + - - +
369B ARG* 3.1 23.0 + - - +
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Residues in contact with LYS 366 (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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365B ASP* 1.4 74.6 - - - +
367B ASN* 1.4 71.8 + - - +
369B ARG* 3.2 16.6 + - - +
370B VAL* 3.2 17.0 + - - +
414B ASP* 5.6 5.6 - - - +
419B PHE* 4.2 13.7 - - + -
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Residues in contact with ASN 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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368A ALA* 5.5 5.6 - - + -
365B ASP 3.5 3.2 - - - +
366B LYS* 1.4 81.8 - - - +
368B ALA* 1.4 60.8 + - - +
370B VAL* 3.2 3.2 + - - +
371B ILE* 3.1 37.6 + - + +
419B PHE* 3.3 36.5 - - - +
420B LYS* 5.1 4.0 + - - +
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Residues in contact with ALA 368 (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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367A ASN* 5.1 14.6 - - + +
368A ALA* 5.4 4.9 - - - +
371A ILE* 3.6 31.6 - - + +
365B ASP* 3.5 20.0 + - - +
366B LYS 3.3 0.4 - - - -
367B ASN* 1.4 76.2 - - - +
369B ARG* 1.4 62.2 + - - +
371B ILE* 3.6 6.8 + - - +
372B GLU* 3.2 23.0 + - - +
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Residues in contact with ARG 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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365B ASP 3.1 13.6 + - - +
366B LYS* 3.2 11.0 + - - +
368B ALA* 1.4 75.1 - - - +
370B VAL* 1.4 58.7 + - + +
372B GLU* 3.6 6.5 + - - +
373B LEU* 2.9 30.7 + - - +
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Residues in contact with VAL 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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366B LYS 3.3 14.1 - - - +
367B ASN* 3.2 10.8 + - - +
369B ARG* 1.4 73.3 - - + +
371B ILE* 1.4 58.5 + - + +
373B LEU* 3.1 10.1 + - + +
374B ILE* 2.8 54.6 + - + +
419B PHE* 3.7 40.2 - - + -
432B LEU* 3.8 34.1 - - + -
435B ILE* 4.9 4.3 - - + -
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Residues in contact with ILE 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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368A ALA* 3.8 30.5 - - + +
371A ILE* 3.7 27.1 - - + -
372A GLU* 4.3 24.0 - - + +
367B ASN* 3.1 32.7 + - + +
368B ALA* 4.0 3.6 - - - +
369B ARG 3.5 0.2 - - - -
370B VAL* 1.4 79.7 - - + +
372B GLU* 1.4 58.6 + - - +
374B ILE* 3.2 16.3 + - + +
375B ALA* 3.0 29.4 + - + +
419B PHE* 6.5 0.7 - - + -
420B LYS 5.4 7.9 - - - +
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Residues in contact with GLU 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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371A ILE* 5.2 9.0 - - + -
368B ALA 3.2 17.4 + - - +
369B ARG* 3.8 7.9 - - - +
371B ILE* 1.4 78.6 - - - +
373B LEU* 1.3 56.2 + - - +
375B ALA* 3.5 6.9 + - - +
376B ALA* 3.0 28.8 + - - +
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Residues in contact with LEU 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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369B ARG* 2.9 19.5 + - + +
370B VAL* 3.1 11.6 + - + +
372B GLU* 1.3 73.7 - - - +
374B ILE* 1.3 63.8 + - - +
376B ALA* 3.3 9.6 + - + +
377B TYR* 3.1 48.6 + - + -
432B LEU* 5.5 5.4 - - + -
436B LEU* 3.7 28.7 - - + -
439B LEU* 4.8 0.9 - - + -
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Residues in contact with ILE 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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370B VAL* 2.8 42.7 + - + +
371B ILE* 3.2 17.9 + - + +
373B LEU* 1.3 72.0 - - + +
375B ALA* 1.4 61.1 + - - +
377B TYR* 3.3 4.5 + - - +
378B ARG* 3.1 59.7 + - - +
435B ILE* 4.2 15.5 - - + -
439B LEU* 3.8 29.1 - - + +
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Residues in contact with ALA 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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371B ILE* 3.0 18.1 + - + +
372B GLU* 3.8 7.4 - - - +
374B ILE* 1.4 75.3 - - - +
376B ALA* 1.3 57.6 + - - +
378B ARG* 3.4 9.4 + - - +
379B ASN* 2.9 48.1 + - - +
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Residues in contact with ALA 376 (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 GLU 3.0 18.5 + - - +
373B LEU* 3.7 12.6 - - + +
374B ILE 3.3 0.2 - - - -
375B ALA* 1.3 76.5 - - - +
377B TYR* 1.4 56.1 + - + +
379B ASN* 4.7 4.3 - - - +
380B ARG* 2.8 36.6 + - + +
381B GLY 3.4 3.6 + - - -
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Residues in contact with TYR 377 (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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373B LEU* 3.1 39.6 + - + -
374B ILE 3.7 6.7 - - - +
376B ALA* 1.4 75.5 - - + +
378B ARG* 1.3 61.2 + - - +
381B GLY* 2.8 28.1 + - - +
382B HIS 4.6 0.2 + - - -
436B LEU* 4.0 24.9 - - + +
439B LEU* 3.8 38.6 - - + -
440B ARG* 3.7 31.2 + - + +
443B TYR* 3.6 13.8 - - + -
444B CYS* 3.5 32.5 - - - -
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Residues in contact with ARG 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A GLU* 5.8 2.4 + - - -
374B ILE* 3.1 44.0 + - + +
375B ALA* 3.7 7.6 - - - +
377B TYR* 1.3 78.2 - - - +
379B ASN* 1.3 59.4 + - - +
381B GLY 5.0 0.2 + - - -
439B LEU* 4.7 0.2 - - + -
443B TYR* 3.7 14.4 - - + +
449B VAL 4.3 8.5 - - - +
450B GLU* 5.8 0.2 - - - -
451B TYR* 3.3 31.5 + - - +
452B THR* 3.6 19.2 + - + +
464B GLN* 3.2 31.4 + - - +
468B GLU* 2.6 40.0 + - - +
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Residues in contact with ASN 379 (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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379A ASN* 5.6 7.6 + - - +
375B ALA* 2.9 34.6 + - - +
376B ALA* 4.2 3.0 - - - +
378B ARG* 1.3 78.4 - - - +
380B ARG* 1.3 91.7 + - + +
381B GLY 3.9 0.2 - - - -
382B HIS* 3.1 14.5 + - - -
452B THR* 3.1 37.3 + - - +
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Residues in contact with ARG 380 (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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452A THR 2.6 29.7 + - - -
453A HIS* 3.7 5.5 + - - +
454A ILE 2.8 25.2 + - - -
455A LEU* 3.8 27.2 + - - +
460A GLN* 3.0 7.1 - - - +
376B ALA* 2.8 20.3 + - + +
379B ASN* 1.3 103.9 + - + +
381B GLY* 1.3 64.0 + - - +
382B HIS* 3.1 8.8 + - - -
383B LEU* 3.0 46.3 + - + +
384B MET* 4.1 3.8 + - - +
452B THR* 4.8 4.9 + - - -
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Residues in contact with GLY 381 (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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376B ALA 3.4 2.2 + - - -
377B TYR* 2.8 25.9 + - - -
379B ASN 3.9 0.2 - - - -
380B ARG* 1.3 77.0 - - - +
382B HIS* 1.4 52.6 + - - +
384B MET* 2.9 24.5 + - - -
385B ALA 3.2 8.5 + - - -
443B TYR* 3.2 13.3 - - - +
444B CYS* 3.4 23.0 - - - -
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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