Contacts of the helix formed by residues 414 - 425 (chain D) in PDB entry 3CB4
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 TYR 414 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410D LEU* 4.4 2.7 - - + -
411D PRO* 3.2 37.5 + - + +
412D GLN 3.0 1.0 - - - -
413D ALA* 1.3 93.1 - - + +
415D LEU* 1.3 64.5 + - - +
416D GLY 3.2 3.1 - - - -
417D ASN* 2.8 25.7 + - - +
418D VAL* 3.2 22.9 + - + +
461D THR 3.8 9.0 - - - +
462D SER* 3.2 42.7 + - - -
463D ARG* 3.9 35.3 + - - +
465D TYR* 4.3 14.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 415 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419C ILE* 4.1 22.7 - - + -
420C THR* 5.5 1.1 - - - +
423C VAL* 4.9 20.2 - - + -
443C TYR* 5.2 0.4 - - - +
410D LEU* 3.7 21.6 - - + +
411D PRO 3.9 0.2 + - - -
412D GLN* 3.1 26.6 + - + +
413D ALA 5.2 0.7 - - - -
414D TYR* 1.3 76.5 - - - +
416D GLY* 1.3 78.3 + - - +
418D VAL* 3.3 0.6 + - - -
419D ILE* 3.1 34.0 + - + +
432D MET* 3.8 21.3 - - + -
434D TYR* 3.2 27.6 - - + +
439D VAL* 3.7 21.3 - - + -
441D LEU* 5.3 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 416 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416C GLY* 4.5 3.3 - - - +
419C ILE* 4.2 7.4 - - - -
420C THR* 4.2 18.6 - - - -
413D ALA 5.2 0.6 + - - -
414D TYR 3.2 1.2 - - - -
415D LEU* 1.3 89.2 - - - +
417D ASN* 1.3 63.8 + - - +
419D ILE* 3.2 24.5 - - - +
420D THR* 3.4 13.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 417 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420C THR* 5.3 3.1 + - - -
413D ALA 5.8 1.5 + - - -
414D TYR* 2.8 18.5 + - - +
416D GLY* 1.3 77.3 - - - +
418D VAL* 1.3 59.5 + - - +
420D THR* 3.1 21.5 - - - +
421D LEU* 4.0 2.9 + - - +
461D THR* 3.3 43.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 418 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408D MET* 3.3 34.3 - - + -
410D LEU* 3.7 21.3 - - + -
414D TYR* 3.2 23.4 + - + +
415D LEU 3.9 4.3 - - - +
416D GLY 3.2 0.4 - - - -
417D ASN* 1.3 79.8 - - + +
419D ILE* 1.3 62.0 + - - +
420D THR 3.1 1.1 - - - -
421D LEU* 2.9 24.4 + - + +
422D CYS* 3.1 12.7 + - - -
441D LEU* 4.2 4.9 - - + -
458D LEU* 4.3 14.1 - - + -
461D THR* 4.5 8.1 - - + -
462D SER* 4.3 15.7 - - - -
466D ALA* 4.8 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 419 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415C LEU* 4.0 11.4 - - + +
416C GLY* 3.4 30.5 - - - -
419C ILE* 3.8 9.4 - - + -
415D LEU* 3.1 18.4 + - - +
416D GLY* 3.2 33.7 - - - +
418D VAL* 1.3 74.9 - - - +
420D THR* 1.3 62.1 + - - +
422D CYS* 3.7 7.7 - - - +
423D VAL* 3.1 29.3 + - + +
429D GLN* 4.6 4.5 - - - +
432D MET* 5.1 7.9 - - + -
441D LEU* 3.7 26.9 - - + -
443D TYR* 3.2 25.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 420 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416C GLY* 5.5 5.2 - - - -
417C ASN* 5.2 5.3 + - - -
416D GLY 3.4 11.4 + - - +
417D ASN* 3.1 30.1 - - - +
418D VAL 3.1 0.8 - - - -
419D ILE* 1.3 85.3 - - - +
421D LEU* 1.3 64.4 + - + +
423D VAL* 3.5 10.3 - - - +
424D GLU* 3.2 23.0 + - - +
461D THR* 5.6 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 421 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417D ASN 4.2 7.0 - - - +
418D VAL* 2.9 10.9 + - + +
420D THR* 1.3 81.4 - - + +
422D CYS* 1.3 59.1 + - - +
424D GLU* 3.1 8.3 + - - +
425D LYS* 2.8 46.2 + - + +
454D PHE* 3.9 13.5 - - + -
457D ARG* 3.6 43.3 - - + +
458D LEU* 3.4 44.2 - - + +
461D THR* 3.9 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 422 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408D MET* 4.3 21.3 - - - -
418D VAL* 3.1 17.3 + - - -
419D ILE* 3.7 6.1 - - - +
421D LEU* 1.3 76.0 - - - +
423D VAL* 1.3 53.5 + - - +
425D LYS* 3.0 18.9 + - - +
427D GLY* 2.8 28.2 + - - -
441D LEU* 5.4 0.2 - - - -
443D TYR* 3.6 44.4 - - + -
445D ILE* 4.0 20.0 - - + +
454D PHE* 4.6 9.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 423 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412C GLN* 4.2 20.4 - - + +
413C ALA* 5.0 13.2 - - - +
415C LEU* 4.7 3.8 - - + -
416C GLY* 6.4 1.6 - - - -
419D ILE* 3.1 19.7 + - + +
420D THR* 3.5 13.7 - - - +
422D CYS* 1.3 73.4 - - - +
424D GLU* 1.3 67.2 + - + +
426D ARG* 3.2 12.6 + - - +
427D GLY 3.8 20.0 - - - +
443D TYR* 3.8 16.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 424 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420D THR 3.2 20.9 + - - +
421D LEU* 3.1 9.2 + - - +
423D VAL* 1.3 78.1 - - - +
425D LYS* 1.3 70.5 + - - +
426D ARG* 3.2 9.0 + - - +
449D GLU* 5.2 0.9 - - - +
457D ARG* 3.5 24.9 + - - +
503D ASN* 6.2 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 425 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421D LEU* 2.8 31.2 + - + +
422D CYS* 3.1 6.7 - - - +
424D GLU* 1.3 84.8 + - - +
426D ARG* 1.3 67.5 + - - +
427D GLY 3.1 1.9 + - - -
445D ILE* 3.4 21.6 - - + +
446D PRO* 3.9 1.2 - - - +
449D GLU* 3.6 47.4 - - + +
452D LEU* 4.4 8.7 - - - -
453D ASP 3.9 6.1 + - - -
454D PHE* 4.2 16.1 - - + +
457D ARG* 3.2 36.8 - - - +
507D ARG* 6.0 2.7 - - - +
----------------------------------------------------------
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