Contacts of the helix formed by residues 480 - 491 (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 LEU 480 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523B PRO* 4.8 11.2 - - + +
476C LEU* 3.3 21.1 + - + +
477C THR 3.4 5.8 + - - +
478C ALA 3.1 0.6 - - - -
479C LEU* 1.3 76.0 - - - +
481C GLY* 1.3 58.6 + - - +
482C GLY 3.3 2.0 - - - -
483C ARG* 3.4 11.9 + - + +
484C ALA* 2.9 27.8 + - - +
500C ASP* 4.9 2.5 - - + +
501C ILE* 4.8 15.7 - - + +
504C ALA* 4.2 17.9 - - + -
561C VAL* 3.7 24.0 - - + +
564C CYS* 4.1 7.9 - - + -
565C TYR* 3.6 49.0 - - + +
568C ALA* 4.4 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 481 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426C GLY* 3.5 13.2 - - - -
430C VAL* 3.8 26.0 - - - -
477C THR 3.3 2.9 + - - -
478C ALA 2.8 14.1 + - - -
479C LEU 3.2 0.2 - - - -
480C LEU* 1.3 75.8 - - - +
482C GLY* 1.3 65.2 + - - +
484C ALA* 3.6 5.3 - - - +
485C ALA* 3.0 24.8 + - - +
568C ALA* 4.3 0.4 - - - -
572C ILE* 4.5 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 482 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423C HIS* 3.2 47.6 + - - -
427C HIS* 3.3 15.3 + - - -
480C LEU 3.3 0.4 - - - -
481C GLY* 1.3 78.6 - - - +
483C ARG* 1.3 59.0 + - - +
485C ALA* 3.5 3.6 + - - +
486C GLU* 3.3 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 483 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515B LEU 3.0 20.8 + - - -
516B GLY* 2.6 32.5 + - - -
517B MET* 4.4 0.2 - - - +
523B PRO* 4.1 15.9 - - - +
423C HIS* 4.0 3.0 + - - -
479C LEU 5.1 0.6 + - - -
480C LEU* 3.4 15.2 + - + +
481C GLY 3.2 0.4 - - - -
482C GLY* 1.3 73.1 - - - +
484C ALA* 1.3 66.2 + - - +
486C GLU* 3.1 17.0 + - + +
487C GLU* 3.1 13.7 + - - +
493C VAL* 3.0 45.5 - - + +
494C THR 3.8 8.9 + - - -
497C ALA* 3.8 25.5 - - + +
500C ASP* 5.3 1.1 + - + -
501C ILE* 3.7 19.7 - - - +
565C TYR* 4.0 19.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 484 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480C LEU 2.9 17.7 + - - +
481C GLY* 3.6 6.5 - - - +
483C ARG* 1.3 77.0 - - - +
485C ALA* 1.3 62.1 + - - +
487C GLU* 3.4 1.2 + - - +
488C VAL* 3.1 30.6 + - - +
565C TYR* 3.9 8.2 - - + -
568C ALA* 3.6 30.5 - - + +
569C LYS* 3.7 20.9 - - + -
572C ILE* 4.1 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 485 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422C TYR* 3.2 31.9 - - + +
426C GLY* 3.9 8.7 - - - -
481C GLY 3.0 17.2 + - - +
482C GLY 3.5 3.6 - - - +
484C ALA* 1.3 78.0 - - - +
486C GLU* 1.3 61.0 + - - +
488C VAL* 3.9 0.3 - - - +
489C VAL* 3.0 30.1 + - - +
572C ILE* 4.0 13.4 - - + +
579C LEU* 4.3 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 486 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419C ILE* 3.6 24.2 - - + +
422C TYR* 5.5 0.2 - - - -
423C HIS* 3.3 31.2 + - + +
482C GLY 3.3 12.0 + - - +
483C ARG* 3.1 12.2 + - - +
485C ALA* 1.3 77.0 - - - +
487C GLU* 1.3 58.1 + - - +
490C PHE* 2.9 38.2 + - + +
492C ASP 3.0 14.3 - - - +
493C VAL* 3.9 5.2 - - + -
494C THR* 2.6 45.1 + - - +
496C GLY* 4.6 2.4 - - - -
497C ALA* 4.6 7.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 487 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483C ARG 3.1 11.6 + - - +
484C ALA 3.9 2.9 - - - +
486C GLU* 1.3 78.2 - - - +
488C VAL* 1.3 62.2 + - - +
491C GLY* 2.8 37.8 + - - +
492C ASP 3.4 12.3 - - - +
493C VAL* 4.3 9.4 - - + +
565C TYR* 2.0 40.3 + - - +
569C LYS* 3.6 23.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 488 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484C ALA 3.1 18.0 + - - +
485C ALA 4.0 0.2 - - - +
487C GLU* 1.3 80.9 - - - +
489C VAL* 1.3 60.4 + - + +
491C GLY* 4.4 1.4 + - - -
569C LYS* 3.9 30.3 - - + -
572C ILE* 3.8 23.8 - - + -
573C ARG* 3.5 38.6 - - + +
576C ARG* 4.2 17.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 489 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418C ARG* 5.2 3.8 - - - +
422C TYR* 3.5 35.7 - - + -
485C ALA 3.0 18.1 + - - +
488C VAL* 1.3 80.4 - - + +
490C PHE* 1.3 81.2 + - + +
491C GLY 3.7 0.2 - - - -
576C ARG* 3.3 45.8 + - - +
579C LEU* 4.0 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 490 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415C ALA 5.7 0.2 - - - -
418C ARG* 4.5 20.6 - - + -
419C ILE* 4.0 38.6 - - + -
422C TYR* 4.0 35.2 - + + -
486C GLU* 2.9 27.8 + - + +
489C VAL* 1.3 94.4 - - + +
491C GLY* 1.3 59.0 + - - +
492C ASP 3.0 14.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 491 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486C GLU 3.7 0.2 + - - -
487C GLU* 2.8 27.8 + - - +
488C VAL 4.4 0.8 + - - -
489C VAL 3.7 0.8 - - - -
490C PHE* 1.3 77.1 - - - +
492C ASP* 1.3 61.7 + - - +
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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