Contacts of the strand formed by residues 415 - 422 (chain E) in PDB entry 1ZMD
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 VAL 415 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406E ILE* 4.3 9.4 - - + -
407E LEU 3.9 4.9 - - - +
413E ASP 4.4 0.2 - - - -
414E ARG* 1.3 82.8 + - - +
416E LEU* 1.3 61.4 + - - +
417E GLY 3.8 20.6 - - - +
418E ALA* 4.8 5.4 - - + +
435E ALA* 5.2 2.2 - - + -
436E LEU* 3.6 36.6 - - + +
439E GLY* 5.8 0.9 - - - -
440E ALA 2.9 20.2 + - - +
441E SER 3.6 20.2 - - - +
442E CYS* 3.6 7.4 - - - +
445E ILE* 3.9 12.3 - - + -
459E PHE* 6.1 0.9 - - + -
463E ASN* 3.7 16.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 416 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352E ASN* 4.7 3.5 + - - -
368E GLY* 3.4 7.6 - - - -
369E LYS* 2.8 26.2 + - + +
374E LEU* 4.0 27.1 - - + -
379E ILE* 3.8 29.4 - - + -
381E TYR* 4.6 1.1 - - + -
407E LEU 2.8 10.3 + - - +
408E GLY 4.2 3.4 - - - +
409E GLN* 3.7 40.4 - - + +
414E ARG* 3.7 19.1 - - + +
415E VAL* 1.3 79.6 - - - +
417E GLY* 1.3 59.3 + - - +
436E LEU* 4.5 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 417 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367E VAL 3.5 10.1 - - - -
369E LYS 3.5 17.7 - - - -
406E ILE* 3.5 2.8 - - - -
407E LEU* 2.9 32.9 + - - +
415E VAL* 3.7 8.8 - - - +
416E LEU* 1.3 80.9 - - - +
418E ALA* 1.3 61.6 + - - +
419E HIS* 4.1 4.5 - - - -
436E LEU* 5.2 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 418 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365E ALA 4.0 0.2 - - - +
366E TRP* 3.1 6.6 - - - +
367E VAL* 2.9 36.8 + - + +
405E LYS 3.7 4.5 - - - -
406E ILE* 3.7 18.2 - - + -
415E VAL* 4.9 5.6 - - + -
417E GLY* 1.3 75.4 - - - +
419E HIS* 1.3 63.6 + - - +
420E ILE* 5.0 4.7 - - + -
429E VAL* 5.1 0.7 - - + +
432E ALA* 3.7 29.4 - - + -
436E LEU* 5.6 1.3 - - + +
459E PHE* 4.0 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 419 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219E ASP* 3.6 23.3 + - + +
222E ILE* 3.7 24.5 - - + +
365E ALA 3.6 3.1 - - - -
366E TRP* 3.3 33.9 - + + +
367E VAL 5.0 0.7 - - - -
368E GLY 4.9 1.6 - - - -
369E LYS 2.7 31.2 + - - -
370E SER* 3.4 19.9 - - - -
403E MET 3.9 0.9 - - - +
404E VAL* 3.5 2.6 - - - -
405E LYS* 2.8 51.8 + - + +
406E ILE* 4.9 0.6 - - - +
407E LEU* 3.8 14.8 - - + +
417E GLY 4.1 0.4 - - - -
418E ALA* 1.3 82.8 + - - +
420E ILE* 1.3 63.7 + - - +
421E LEU 4.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 420 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222E ILE* 4.7 1.9 - - - +
364E VAL* 3.1 9.2 - - - +
365E ALA 2.7 42.3 + - - +
388E PHE* 4.1 12.3 - - + -
403E MET 3.7 1.6 - - - -
404E VAL* 4.1 24.5 - - + -
418E ALA 5.0 1.6 - - - -
419E HIS* 1.3 81.3 - - - +
421E LEU* 1.3 63.1 + - - +
425E ALA* 3.5 27.0 - - + +
428E MET* 4.0 27.1 - - + +
429E VAL* 3.9 38.6 - - + +
432E ALA* 5.3 1.1 - - + -
459E PHE* 4.7 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 421 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222E ILE* 4.0 21.0 - - + +
225E ASN* 3.4 37.0 - - + +
226E PHE* 3.6 41.5 - - + +
229E ILE* 4.0 13.5 - - + -
362E PRO* 4.0 10.5 - - + -
363E GLU 3.6 4.7 - - - +
364E VAL* 3.8 14.1 - - + -
388E PHE* 3.5 3.8 - - - -
402E GLY* 3.1 14.9 - - - -
403E MET* 2.8 41.5 + - + +
419E HIS 4.3 0.2 - - - -
420E ILE* 1.3 71.9 - - - +
422E GLY* 1.3 58.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 422 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362E PRO* 3.6 17.7 - - - +
363E GLU* 2.9 27.4 + - - +
388E PHE* 3.9 4.0 - - - -
401E ASP 3.6 3.8 - - - -
420E ILE 4.0 1.0 - - - -
421E LEU* 1.3 78.1 - - - +
423E PRO* 1.3 78.2 - - - +
424E GLY 3.5 0.3 + - - -
425E ALA* 3.5 11.3 + - - +
----------------------------------------------------------
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