Contacts of the helix formed by residues 413 - 434 (chain B) in PDB entry 2CEA
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 SER 413 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464A LYS* 4.1 9.7 + - - -
411B LEU* 3.8 3.7 + - - -
412B ILE* 1.3 77.9 - - - +
414B PRO* 1.3 71.1 - - - +
415B ALA* 3.7 7.0 + - - +
416B GLU* 2.7 49.6 + - - +
417B LYS* 2.8 23.9 + - - +
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Residues in contact with PRO 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B ILE 4.3 1.8 - - - +
413B SER* 1.3 87.5 - - - +
415B ALA* 1.3 65.3 + - - +
417B LYS* 3.4 14.4 - - + +
418B ARG* 3.1 23.0 + - - +
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Residues in contact with ALA 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B SER* 3.3 7.8 - - - +
414B PRO* 1.3 80.5 - - - +
416B GLU* 1.3 60.2 + - + +
418B ARG* 3.1 26.4 - - - +
419B ILE* 3.3 16.6 + - + +
490B PHE* 5.7 0.2 - - - -
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Residues in contact with GLU 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A LYS* 2.9 47.6 + - - +
465A TYR* 4.6 2.2 - - + +
466A LEU* 3.0 38.5 + - + +
411B LEU 4.3 1.2 - - - +
412B ILE* 3.9 11.0 - - + -
413B SER* 2.7 45.1 + - - +
415B ALA* 1.3 74.7 - - + +
417B LYS* 1.3 64.5 + - - +
418B ARG 3.1 1.8 - - - -
419B ILE* 3.1 13.5 + - + +
420B ILE* 2.9 28.8 + - + +
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Residues in contact with LYS 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B LYS* 4.8 9.8 + - - +
363B PRO* 4.6 15.7 - - + -
412B ILE* 3.8 13.6 - - + +
413B SER 2.8 16.6 + - - +
414B PRO* 3.4 15.5 - - + +
416B GLU* 1.3 75.8 - - - +
418B ARG* 1.3 63.8 + - - +
420B ILE* 3.5 5.9 + - - +
421B ALA* 2.9 24.6 + - - +
445B ILE* 4.0 29.1 - - + +
587B LEU* 3.4 34.6 + - + +
590B GLU* 4.1 21.7 + - - +
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Residues in contact with ARG 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B PRO 3.1 10.0 + - - +
415B ALA* 3.1 16.1 + - - +
416B GLU 3.1 0.2 - - - -
417B LYS* 1.3 81.7 - - - +
419B ILE* 1.3 62.9 + - - +
421B ALA* 3.1 10.4 + - - +
422B TYR* 3.1 31.7 + - + -
489B VAL* 5.6 3.6 - - - +
490B PHE* 3.3 37.9 - - + -
587B LEU* 4.3 22.0 - - + -
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Residues in contact with ILE 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A LEU* 3.8 17.7 - - + -
468A SER* 6.2 1.3 - - - -
415B ALA* 3.3 15.9 + - + +
416B GLU* 3.1 15.4 + - + +
418B ARG* 1.3 76.7 - - - +
420B ILE* 1.3 64.5 + - - +
422B TYR* 3.0 5.2 + - - +
423B HIS* 2.9 20.4 + - + +
486B GLU* 3.8 31.1 - - + +
490B PHE* 4.0 33.0 - - + -
494B THR* 4.1 20.6 - - + +
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Residues in contact with ILE 420 (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 TYR* 4.8 13.7 - - + -
466A LEU* 3.7 20.0 - - + -
412B ILE* 4.0 34.1 - - + -
416B GLU* 2.9 21.8 + - + +
417B LYS* 3.7 3.8 - - - +
419B ILE* 1.3 75.9 - - - +
421B ALA* 1.3 64.9 + - - +
423B HIS* 3.2 9.0 + - + +
424B GLU* 2.9 32.9 + - + +
445B ILE* 3.7 39.0 - - + +
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Residues in contact with ALA 421 (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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417B LYS 2.9 15.2 + - - +
418B ARG 3.1 9.8 + - - +
420B ILE* 1.3 78.5 - - - +
422B TYR* 1.3 57.9 + - - +
424B GLU* 3.1 1.6 + - - +
425B ALA* 2.7 30.8 + - - +
445B ILE* 4.6 2.2 - - + +
583B VAL* 3.6 18.2 - - + -
586B LEU* 3.7 23.0 - - + +
587B LEU* 3.6 21.5 - - + -
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Residues in contact with TYR 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B ARG* 3.1 28.6 + - + -
419B ILE 3.0 7.8 + - - +
421B ALA* 1.3 78.3 - - - +
423B HIS* 1.3 54.4 + - - +
425B ALA* 3.6 0.5 - - - +
426B GLY 2.7 29.5 + - - -
485B ALA* 3.3 19.1 - - + +
486B GLU* 5.1 0.9 - - - +
489B VAL* 3.8 19.4 - - + +
490B PHE* 3.7 32.3 - + + -
576B ARG* 5.0 1.4 + - - -
579B LEU* 3.6 26.5 - - + +
580B ASP* 2.6 36.1 + - - +
583B VAL* 3.6 38.9 - - + +
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Residues in contact with HIS 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B ILE* 2.9 13.2 + - + +
420B ILE* 3.3 13.5 - - + +
422B TYR* 1.3 76.5 - - - +
424B GLU* 1.3 78.4 + - - +
426B GLY 3.0 9.5 + - - -
427B HIS* 3.0 16.2 + + - -
482B GLY* 3.2 35.8 - - - -
483B ARG 3.9 2.5 - - - -
486B GLU* 2.8 29.2 + - - +
496B GLY* 3.8 19.4 + - - -
497B ALA* 3.9 7.0 - - + -
500B ASP* 3.4 8.3 - - - -
1606B ZN 2.1 36.2 - - - -
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Residues in contact with GLU 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B ILE* 2.9 34.2 + - + +
421B ALA 3.8 2.2 - - - +
423B HIS* 1.3 92.5 + - + +
425B ALA* 1.3 62.8 + - - +
427B HIS* 3.4 13.3 + - - +
428B ALA* 3.1 20.8 + - - +
443B ILE* 3.6 26.0 - - + +
444B SER 3.7 24.7 + - - +
445B ILE* 4.9 1.1 - - - -
586B LEU* 4.5 4.3 - - + -
1606B ZN 4.3 4.3 - - - -
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Residues in contact with ALA 425 (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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421B ALA 2.7 20.6 + - - +
422B TYR 3.8 0.7 - - - +
424B GLU* 1.3 74.2 - - - +
426B GLY* 1.3 58.1 + - - +
428B ALA* 3.1 9.1 + - - +
429B VAL* 2.9 32.7 + - - +
443B ILE* 4.7 2.4 - - - +
579B LEU* 3.6 12.3 - - + -
582B ILE* 4.2 21.9 - - + +
583B VAL* 3.6 25.4 - - + +
586B LEU* 5.0 2.7 - - + +
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Residues in contact with GLY 426 (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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422B TYR 2.7 20.2 + - - -
423B HIS 3.0 5.5 + - - -
425B ALA* 1.3 69.2 - - - +
427B HIS* 1.3 65.7 + - - +
428B ALA 3.1 0.3 + - - -
429B VAL* 3.1 1.9 + - - +
430B VAL* 2.9 27.0 + - - +
481B GLY 3.9 10.1 - - - -
485B ALA* 3.9 17.0 - - - -
572B ILE* 4.3 4.7 - - - -
579B LEU* 3.8 6.5 - - - +
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Residues in contact with HIS 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B HIS* 3.0 29.6 + + - -
424B GLU* 3.4 14.3 + - - +
426B GLY* 1.3 73.6 - - - +
428B ALA* 1.3 57.4 + - - +
430B VAL* 4.9 0.2 - - - -
431B SER* 2.8 39.6 + - - +
440B VAL* 5.5 0.7 - - - -
478B ALA* 3.1 24.8 + - - +
479B LEU* 3.1 27.3 - - + +
482B GLY* 3.9 8.9 + - - +
500B ASP* 2.7 18.8 + - - -
1606B ZN 2.1 32.0 - - - -
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Residues in contact with ALA 428 (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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424B GLU 3.1 6.7 + - - +
425B ALA* 3.1 11.2 + - - +
426B GLY 3.0 0.4 - - - -
427B HIS* 1.3 81.1 - - - +
429B VAL* 1.3 60.2 + - - +
431B SER* 3.8 3.8 - - - -
432B THR* 3.0 30.1 + - - -
440B VAL* 4.6 14.7 - - + +
443B ILE* 3.4 34.8 - - + -
582B ILE* 4.9 7.9 - - + -
601B LEU* 4.9 6.7 - - + +
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Residues in contact with VAL 429 (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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425B ALA 2.9 17.9 + - - +
426B GLY 3.7 2.7 - - - +
428B ALA* 1.3 74.6 - - - +
430B VAL* 1.3 68.3 + - - +
432B THR* 3.1 5.8 + - - -
433B VAL* 2.9 31.8 + - + +
571B ILE* 4.0 15.9 - - + +
572B ILE* 3.9 21.3 - - + -
575B TYR* 4.4 14.6 - - + +
579B LEU* 4.1 30.7 - - + +
582B ILE* 4.4 12.1 - - + -
605B PHE* 4.2 17.9 - - + -
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Residues in contact with VAL 430 (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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426B GLY 2.9 18.1 + - - +
427B HIS 4.1 0.9 - - - +
429B VAL* 1.3 75.4 - - - +
431B SER* 1.3 63.0 + - - +
433B VAL* 3.1 1.9 + - - +
434B VAL* 3.0 28.4 + - + +
477B THR* 3.7 19.1 - - + +
478B ALA* 3.3 35.0 - - + +
481B GLY* 3.9 18.4 - - - -
568B ALA* 4.3 10.1 - - + +
571B ILE* 4.3 17.9 - - + -
572B ILE* 3.9 16.8 - - + -
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Residues in contact with SER 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B HIS* 2.8 26.3 + - - +
428B ALA 3.8 0.7 - - - -
430B VAL* 1.3 77.7 - - - +
432B THR* 1.3 62.0 + - - +
433B VAL 3.5 0.2 + - - -
434B VAL* 3.6 4.4 - - - +
437B GLY* 3.4 26.2 - - - -
438B GLU* 4.0 12.6 + - - +
440B VAL* 3.7 25.6 - - - +
478B ALA* 3.4 22.5 - - - +
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Residues in contact with THR 432 (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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428B ALA 3.0 18.7 + - - -
429B VAL 3.1 4.9 + - - -
431B SER* 1.3 80.6 - - - +
433B VAL* 1.3 64.2 + - - +
434B VAL 3.8 4.3 - - - +
440B VAL* 5.1 3.5 - - - +
601B LEU* 3.8 28.3 - - + +
605B PHE* 3.8 37.7 - - + -
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Residues in contact with VAL 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429B VAL* 2.9 21.5 + - + +
430B VAL 3.1 3.3 + - - +
432B THR* 1.3 77.2 - - - +
434B VAL* 1.3 67.9 - - - +
435B PRO* 3.5 5.2 - - - +
571B ILE* 3.7 32.5 - - + -
575B TYR* 3.9 26.0 - - + +
605B PHE* 4.1 24.0 - - + -
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Residues in contact with VAL 434 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430B VAL* 3.0 29.9 + - + +
431B SER* 3.6 8.0 - - - +
432B THR 3.8 4.5 - - - +
433B VAL* 1.3 80.9 - - - +
435B PRO* 1.3 67.6 - - - +
437B GLY* 3.1 21.2 + - - +
474B ASP* 3.0 42.8 - - + +
477B THR* 4.2 6.5 - - + -
478B ALA* 5.8 0.4 - - + -
567B ARG* 4.0 28.0 - - - +
571B ILE* 4.3 8.3 - - + -
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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
------------------------------------------------------------
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