Contacts of the helix formed by residues 415 - 434 (chain C) 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 ALA 415 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413C SER* 3.1 5.1 - - - +
414C PRO* 1.3 80.6 - - + +
416C GLU* 1.3 66.0 + - + +
417C LYS 3.5 0.4 - - - -
418C ARG* 3.2 21.7 - - - +
419C ILE* 3.4 15.9 - - + +
490C PHE* 5.5 0.7 - - - -
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Residues in contact with GLU 416 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466B LEU* 3.6 32.4 + - + +
471B GLU* 5.1 5.2 - - - +
411C LEU 5.1 1.6 - - - +
412C ILE* 4.2 10.6 - - + -
413C SER* 2.3 50.1 + - - +
415C ALA* 1.3 70.7 - - + +
417C LYS* 1.3 65.1 + - - +
418C ARG 3.1 1.1 - - - -
419C ILE* 2.9 26.6 + - + +
420C ILE* 3.0 20.7 + - + +
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Residues in contact with LYS 417 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412C ILE* 3.6 16.4 - - + +
413C SER 2.5 19.1 + - - +
414C PRO* 4.0 14.1 - - + +
416C GLU* 1.3 72.7 - - - +
418C ARG* 1.3 63.6 - - + +
420C ILE* 3.3 8.3 + - - +
421C ALA* 2.9 21.5 + - - +
445C ILE* 4.5 13.1 - - + +
587C LEU* 3.2 46.2 + - + +
590C GLU* 5.5 9.9 - - - -
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Residues in contact with ARG 418 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414C PRO 3.5 18.6 - - - +
415C ALA* 3.2 14.3 + - - +
416C GLU 3.1 0.2 - - - -
417C LYS* 1.3 79.7 - - + +
419C ILE* 1.3 58.7 + - - +
421C ALA* 2.9 10.5 + - - +
422C TYR* 2.8 63.0 + - - -
489C VAL* 5.2 3.4 - - - +
490C PHE* 4.5 21.9 - - + -
583C VAL* 5.6 0.8 - - - +
587C LEU* 4.2 25.6 - - + +
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Residues in contact with ILE 419 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466B LEU* 4.8 9.2 - - + -
415C ALA* 3.4 18.6 - - + +
416C GLU* 2.9 20.5 + - + +
418C ARG* 1.3 74.7 - - - +
420C ILE* 1.3 65.9 + - - +
422C TYR* 2.8 3.8 + - - +
423C HIS* 2.7 22.8 + - + +
486C GLU* 3.6 35.9 - - + +
490C PHE* 4.0 33.2 - - + -
494C THR* 4.3 20.4 - - + +
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Residues in contact with ILE 420 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466B LEU* 4.8 14.6 - - + -
412C ILE* 3.4 35.0 - - + -
416C GLU* 3.0 17.9 + - + +
417C LYS* 3.5 7.9 - - - +
419C ILE* 1.3 75.2 - - - +
421C ALA* 1.3 62.4 + - - +
423C HIS* 3.6 8.0 - - + +
424C GLU* 2.9 25.0 + - + +
444C SER 5.2 0.4 - - - +
445C ILE* 3.1 35.4 - - + +
447C PRO* 5.8 2.9 - - + +
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Residues in contact with ALA 421 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417C LYS 2.9 12.6 + - - +
418C ARG 2.9 13.3 + - - +
420C ILE* 1.3 78.2 - - - +
422C TYR* 1.3 56.2 + - - +
424C GLU* 3.8 1.2 - - - +
425C ALA* 2.9 31.1 + - - +
445C ILE* 4.1 14.6 - - + +
583C VAL* 3.5 26.9 - - + -
586C LEU* 4.0 9.2 - - + +
587C LEU* 3.5 15.9 - - + -
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Residues in contact with TYR 422 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418C ARG* 2.8 50.6 + - - +
419C ILE* 2.8 6.3 + - + +
421C ALA* 1.3 74.9 - - - +
423C HIS* 1.3 59.2 + - - +
425C ALA* 3.7 1.3 - - - +
426C GLY 2.9 22.7 + - - -
485C ALA* 3.2 21.4 - - + +
486C GLU* 5.4 1.1 - - - +
489C VAL* 3.5 39.8 - - + +
490C PHE* 4.0 25.1 - + + -
576C ARG* 4.5 2.3 + - - -
579C LEU* 3.8 16.2 - - + +
580C ASP* 2.8 31.3 + - - +
583C VAL* 3.7 34.2 - - + +
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Residues in contact with HIS 423 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419C ILE* 2.7 19.7 + - + +
420C ILE* 3.6 9.9 - - + +
422C TYR* 1.3 73.6 - - - +
424C GLU* 1.3 64.8 - - + +
426C GLY 3.1 8.7 + - - -
427C HIS* 3.0 17.7 + + - -
454C GLY* 5.6 0.7 - - - -
482C GLY* 3.2 38.7 - - - +
486C GLU* 3.3 24.3 + - + +
496C GLY* 4.3 7.2 + - - -
497C ALA* 4.1 20.9 - - + -
500C ASP* 3.3 8.5 - - - -
1607C ZN 2.1 37.3 - - - -
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Residues in contact with GLU 424 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420C ILE* 2.9 17.0 + - + +
421C ALA 4.0 0.4 - - - +
423C HIS* 1.3 77.8 - - + +
425C ALA* 1.3 65.3 + - - +
427C HIS* 3.1 10.9 + - - -
428C ALA* 3.0 20.5 + - - +
443C ILE* 3.7 18.2 - - + -
444C SER 3.5 15.6 + - - +
445C ILE* 3.7 16.4 - - + -
452C ALA* 3.2 14.1 - - - +
453C LEU* 2.5 39.8 + - - +
454C GLY* 3.1 18.0 + - - -
586C LEU* 4.3 1.8 - - + -
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Residues in contact with ALA 425 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421C ALA 2.9 17.9 + - - +
422C TYR 3.7 1.8 - - - +
424C GLU* 1.3 75.3 - - - +
426C GLY* 1.3 52.8 + - - +
428C ALA* 3.0 9.8 + - - +
429C VAL* 2.8 36.9 + - - +
579C LEU* 3.2 23.6 - - + +
582C ILE* 4.1 20.6 - - + -
583C VAL* 3.8 16.2 - - + +
586C LEU* 4.2 3.4 - - + +
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Residues in contact with GLY 426 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422C TYR 2.9 16.5 + - - -
423C HIS 3.4 4.9 - - - -
424C GLU 3.0 0.6 - - - -
425C ALA* 1.3 74.4 - - - +
427C HIS* 1.3 67.0 + - - +
429C VAL* 3.9 0.5 - - - +
430C VAL* 3.1 26.5 + - - +
481C GLY 3.5 20.0 - - - -
485C ALA* 3.9 7.2 - - - -
572C ILE* 4.2 4.7 - - - -
579C LEU* 4.1 6.3 - - - -
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Residues in contact with HIS 427 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423C HIS* 3.0 18.9 + + - -
424C GLU* 3.1 15.0 + - - +
426C GLY* 1.3 72.9 - - - +
428C ALA* 1.3 59.1 + - - +
430C VAL* 4.1 1.2 - - - +
431C SER* 2.4 34.9 + - - -
453C LEU* 3.5 13.7 - - + -
454C GLY* 3.4 22.2 + - - -
457C LEU* 3.8 13.0 - - + +
478C ALA 3.1 19.0 + - - +
479C LEU* 3.0 27.8 - - + -
482C GLY* 3.3 14.2 + - - -
500C ASP* 3.0 11.6 - - - -
1607C ZN 2.1 30.5 - - - -
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Residues in contact with ALA 428 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424C GLU 3.0 12.0 + - - +
425C ALA* 3.2 13.2 - - - +
427C HIS* 1.3 78.9 - - - +
429C VAL* 1.3 62.8 + - - +
431C SER* 3.7 1.7 - - - -
432C THR* 2.9 28.8 + - - -
440C VAL* 4.3 6.6 - - + +
443C ILE* 4.0 16.8 - - + -
453C LEU* 3.2 18.1 - - + +
582C ILE* 4.9 12.1 - - + -
601C LEU* 5.4 6.5 - - + -
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Residues in contact with VAL 429 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425C ALA 2.8 23.1 + - - +
426C GLY 3.2 2.9 + - - +
428C ALA* 1.3 72.0 - - - +
430C VAL* 1.3 64.7 + - - +
432C THR* 3.2 3.0 + - - -
433C VAL* 3.0 23.9 + - - +
571C ILE* 4.3 11.2 - - + -
572C ILE* 4.4 13.5 - - + -
575C TYR* 3.9 28.9 - - + +
579C LEU* 3.8 26.7 - - + +
582C ILE* 4.0 22.2 - - + -
605C PHE* 4.1 16.6 - - + -
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Residues in contact with VAL 430 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426C GLY 3.1 15.5 + - - +
427C HIS 4.1 0.7 - - - +
429C VAL* 1.3 75.1 - - - +
431C SER* 1.3 57.5 + - - +
434C VAL* 2.9 32.5 + - + +
477C THR* 3.3 42.0 - - + +
478C ALA* 3.6 12.6 - - + +
481C GLY* 3.8 17.5 - - - -
568C ALA* 4.2 14.4 - - + +
571C ILE* 4.2 18.8 - - + -
572C ILE* 4.2 15.5 - - + -
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Residues in contact with SER 431 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427C HIS 2.4 29.0 + - - -
428C ALA 3.7 3.6 - - - -
430C VAL* 1.3 76.2 - - - +
432C THR* 1.3 62.8 + - - +
434C VAL* 3.5 13.4 - - - +
437C GLY* 3.5 16.9 - - - -
438C GLU 4.2 13.3 - - - +
440C VAL* 3.9 19.1 - - - -
453C LEU* 4.1 5.8 - - - +
457C LEU* 4.2 8.9 - - - +
478C ALA* 3.6 21.1 - - - +
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Residues in contact with THR 432 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428C ALA 2.9 18.7 + - - -
429C VAL 3.7 4.0 - - - -
431C SER* 1.3 80.5 - - - +
433C VAL* 1.3 64.4 + - - +
434C VAL 3.7 3.8 - - - +
440C VAL* 4.2 6.4 - - - +
601C LEU* 3.5 29.0 - - + +
605C PHE* 3.7 42.0 - - + -
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Residues in contact with VAL 433 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429C VAL 3.0 19.5 + - - +
430C VAL 4.0 0.2 - - - +
432C THR* 1.3 77.2 - - - +
434C VAL* 1.3 68.4 + - - +
435C PRO* 3.3 6.2 - - - +
571C ILE* 3.9 28.5 - - + -
575C TYR* 3.6 43.3 - - + +
605C PHE* 3.8 20.9 - - + -
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Residues in contact with VAL 434 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430C VAL* 2.9 17.8 + - + +
431C SER* 3.5 9.6 - - - +
432C THR 3.7 3.3 - - - +
433C VAL* 1.3 78.7 - - - +
435C PRO* 1.3 65.1 - - - +
437C GLY* 3.2 23.8 + - - +
474C ASP* 3.3 35.4 - - + +
477C THR* 4.1 18.4 - - + -
478C ALA* 5.5 0.9 - - + -
567C ARG* 2.9 38.1 - - - +
571C ILE* 4.3 7.6 - - + -
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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