Contacts of the helix formed by residues 375 - 395 (chain B) in PDB entry 2CT8
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 375 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B ALA 3.9 0.8 + - - -
374B ARG* 1.3 71.0 - - - +
376B GLU* 1.3 60.5 + - - +
377B GLU* 3.1 11.7 - - + +
378B TYR* 2.8 41.2 + - - +
379B ALA* 3.5 3.7 + - - -
415B TYR* 3.0 31.2 + - - +
419B LYS* 4.2 6.5 + - - +
435B LYS* 3.2 33.4 - - + +
439B ALA* 3.4 10.8 - - - +
478B TYR* 3.3 11.1 + - - -
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Residues in contact with GLU 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B ARG* 3.7 28.0 + - - +
375B ASP* 1.3 70.8 - - - +
377B GLU* 1.3 64.0 + - + +
379B ALA* 3.8 17.7 - - - +
380B LYS* 2.9 30.3 + - - +
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Residues in contact with GLU 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B ASP* 2.9 12.4 + - + +
376B GLU* 1.3 77.8 - - + +
378B TYR* 1.3 62.5 + - - +
380B LYS* 3.7 5.0 + - - +
381B ILE* 3.3 26.6 + - + +
411B TYR* 4.1 7.6 - - - +
415B TYR* 6.1 0.2 - - + -
419B LYS* 5.0 8.7 + - - -
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Residues in contact with TYR 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B ASP* 2.8 23.8 + - - +
377B GLU* 1.3 75.1 - - - +
379B ALA* 1.3 60.6 + - - +
381B ILE* 2.7 9.0 + - - +
382B ALA* 2.6 58.1 + - + +
408B PHE* 3.7 15.3 - + - -
411B TYR* 3.5 30.2 + + + +
412B LEU* 4.3 5.6 - - + -
415B TYR* 4.7 3.1 - + + -
439B ALA* 3.7 22.2 - - + -
442B ASP* 2.5 32.1 + - - -
443B GLY* 3.2 20.7 - - - -
446B VAL* 4.2 5.9 - - - +
477B PRO 3.9 1.7 + - - -
478B TYR* 3.2 32.8 - + - -
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Residues in contact with ALA 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B ASP 3.5 1.2 + - - -
376B GLU* 3.4 24.8 + - - +
378B TYR* 1.3 82.7 - - - +
380B LYS* 1.3 58.6 + - - +
382B ALA* 4.2 0.7 - - - -
383B GLN* 2.8 36.7 + - - +
477B PRO* 3.6 21.3 - - + +
478B TYR* 3.8 22.7 - - + -
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Residues in contact with LYS 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B GLU* 2.9 21.1 + - - +
377B GLU* 3.9 5.8 - - - +
379B ALA* 1.3 76.7 - - - +
381B ILE* 1.3 60.5 + - + +
383B GLN* 3.9 10.7 + - - +
384B GLU* 3.3 23.9 + - - +
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Residues in contact with ILE 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B GLU* 3.3 15.9 + - + +
378B TYR 2.7 13.9 + - - +
380B LYS* 1.3 74.3 - - + +
382B ALA* 1.3 67.0 + - - +
383B GLN 3.0 1.3 - - - -
384B GLU* 3.2 6.3 + - + +
385B SER* 2.9 36.5 + - - +
408B PHE* 4.3 4.7 - - + -
411B TYR* 3.2 54.7 - - + +
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Residues in contact with ALA 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B TYR* 2.6 50.2 + - + +
379B ALA* 3.7 4.3 - - - +
381B ILE* 1.3 73.0 - - - +
383B GLN* 1.3 58.5 + - - +
385B SER* 3.3 3.3 + - - -
386B ILE* 3.0 33.1 + - - +
408B PHE* 3.5 19.6 - - + -
446B VAL* 5.0 5.0 - - + +
477B PRO* 4.1 13.5 - - + -
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Residues in contact with GLN 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B ALA* 2.8 20.8 + - - +
380B LYS* 3.9 9.5 + - - +
382B ALA* 1.3 74.7 - - - +
384B GLU* 1.3 63.8 + - - +
385B SER 3.0 1.8 - - - -
386B ILE* 2.8 40.5 - - + +
387B LYS* 3.1 6.9 + - + +
477B PRO* 3.8 17.9 - - + +
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Residues in contact with GLU 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B LYS 3.3 16.5 + - - +
381B ILE* 3.2 7.9 + - + +
383B GLN* 1.3 80.3 - - - +
385B SER* 1.3 62.7 + - - +
387B LYS* 3.4 21.7 + - - +
388B ASN* 3.0 53.7 + - - +
404B GLU* 5.4 0.7 - - - +
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Residues in contact with SER 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B ILE* 2.9 24.5 + - - +
382B ALA 3.4 5.4 - - - -
384B GLU* 1.3 76.8 - - - +
386B ILE* 1.3 65.5 + - - +
387B LYS 3.1 0.2 + - - -
388B ASN* 3.3 1.2 + - - +
389B TYR* 2.9 27.4 + - - +
404B GLU* 3.8 20.5 + - - +
407B LYS* 6.1 0.2 - - - +
408B PHE* 3.6 35.4 + - - +
450B LEU* 5.2 7.2 - - - -
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Residues in contact with ILE 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B ALA 3.0 17.6 + - - +
383B GLN* 2.8 34.3 - - + +
385B SER* 1.3 76.1 - - - +
387B LYS* 1.3 58.6 + - + +
389B TYR* 4.0 1.2 - - - +
390B GLU* 3.1 39.2 + - - +
446B VAL* 4.5 21.1 - - + -
450B LEU* 4.5 12.1 - - + +
475B LEU* 2.8 52.5 - - + +
477B PRO* 4.6 7.0 - - + -
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Residues in contact with LYS 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B GLN* 3.1 9.4 + - + +
384B GLU* 3.5 25.8 - - - +
385B SER 3.1 0.4 - - - -
386B ILE* 1.3 81.4 - - + +
388B ASN* 1.3 68.1 + - - +
390B GLU* 3.4 5.9 + - - +
391B ASN* 2.9 48.2 + - - +
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Residues in contact with ASN 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B GLU* 3.0 46.8 + - - +
387B LYS* 1.3 82.6 - - - +
389B TYR* 1.3 68.0 + - - +
391B ASN* 3.1 11.2 + - - +
392B TYR* 2.9 38.9 + - + -
404B GLU* 3.5 33.6 + - + +
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Residues in contact with TYR 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B TYR* 4.1 6.6 - + - -
41B ARG* 3.7 24.1 + - - -
385B SER 2.9 17.7 + - - +
386B ILE 4.0 4.0 - - - +
388B ASN* 1.3 76.5 - - - +
390B GLU* 1.3 64.6 + - + +
392B TYR* 3.2 6.0 + - - +
393B MET* 2.9 52.5 + - - +
401B ALA* 3.6 22.6 - - + +
404B GLU* 4.1 14.3 - - + +
405B ILE* 3.8 17.7 - - + -
449B HIS 4.3 0.8 + - - -
450B LEU* 2.5 61.0 + - + -
453B PRO* 3.6 20.8 - - - +
454B ILE* 5.0 2.1 - - + +
475B LEU* 4.9 0.7 - - + -
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Residues in contact with GLU 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B TYR* 2.9 25.2 + - - +
41B ARG* 3.1 33.8 + - - +
386B ILE* 3.1 22.4 + - - +
387B LYS* 3.8 5.4 - - - +
389B TYR* 1.3 82.1 - - + +
391B ASN* 1.3 66.0 + - - +
393B MET* 4.4 1.6 - - - -
394B GLU* 3.0 34.4 + - - +
475B LEU* 4.1 19.8 + - - +
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Residues in contact with ASN 391 (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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387B LYS* 2.9 47.6 + - - +
388B ASN* 3.1 11.1 + - - +
390B GLU* 1.3 75.8 - - - +
392B TYR* 1.3 65.9 + - + +
394B GLU* 3.4 16.2 - - - +
395B LYS* 3.1 29.0 + - + +
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Residues in contact with TYR 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B ASN* 2.9 33.0 + - + -
389B TYR 3.5 5.2 - - - +
391B ASN* 1.3 78.1 - - + +
393B MET* 1.3 61.6 + - - +
395B LYS* 2.9 11.6 + - + -
397B ASN* 2.7 51.6 + - + +
400B LYS* 3.3 56.6 + - + +
401B ALA* 3.8 5.2 - - - +
403B GLU* 5.4 0.9 - - - -
404B GLU* 3.8 22.0 + - + -
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Residues in contact with MET 393 (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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33B THR* 5.4 0.9 - - - -
34B ILE* 3.9 15.1 - - + +
37B TYR* 3.3 46.0 - - + -
389B TYR* 2.9 36.9 + - + +
390B GLU 4.0 0.4 - - - +
392B TYR* 1.3 72.1 - - - +
394B GLU* 1.3 56.5 + - - +
396B VAL* 2.6 25.8 + - - -
397B ASN 4.1 0.4 - - - +
398B PHE* 3.1 45.8 - - + +
401B ALA* 3.3 27.1 - - + -
402B ILE* 6.1 1.1 - - + -
453B PRO* 5.4 3.4 - - - -
454B ILE* 5.2 9.4 - - - -
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Residues in contact with GLU 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B TYR* 3.3 21.0 + - - +
38B TYR* 3.8 29.0 + - + +
282B LYS* 4.5 5.9 + - - -
390B GLU* 3.0 24.9 + - - +
391B ASN* 3.4 19.8 - - - +
393B MET* 1.3 77.7 - - - +
395B LYS* 1.3 63.3 + - + +
396B VAL* 3.4 6.6 + - - +
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Residues in contact with LYS 395 (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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182B GLU* 3.5 27.9 + - - +
185B GLN* 4.1 19.3 + - - +
282B LYS* 4.5 8.3 + - - +
284B PHE* 4.1 10.2 - - - -
391B ASN* 3.1 17.7 - - + +
392B TYR* 2.9 9.7 + - + +
394B GLU* 1.3 81.0 - - + +
396B VAL* 1.3 71.6 + - - +
397B ASN* 3.0 10.5 + - + +
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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
------------------------------------------------------------
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