Contacts of the helix formed by residues 398 - 407 (chain P) in PDB entry 1ZD2
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 ASN 398 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394P GLU 4.2 1.8 + - - -
395P LEU 4.1 1.6 + - - -
396P GLU 3.2 0.4 - - - -
397P GLN* 1.3 87.0 + - + +
399P LEU* 1.3 63.8 + - - +
400P SER* 3.4 10.4 + - - -
401P ARG* 2.8 40.0 + - + +
402P THR* 2.7 23.1 + - - +
433P GLU* 4.3 14.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 399 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395P LEU 3.9 6.3 - - - +
396P GLU* 3.9 16.5 + - + +
398P ASN* 1.3 70.8 - - - +
400P SER* 1.3 64.3 + - - +
402P THR* 3.1 4.5 + - - -
403P PHE* 2.9 42.3 + - + -
450P VAL* 3.7 29.4 - - + +
453P PHE* 4.1 7.4 - - + +
454P LYS* 3.6 40.8 - - + +
458P PHE* 3.6 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 400 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398P ASN* 3.2 7.9 + - - -
399P LEU* 1.3 78.2 - - - +
401P ARG* 1.3 63.3 + - - +
403P PHE* 4.0 1.2 - - - +
404P LYS* 3.0 46.2 + - - +
443P GLU* 4.6 0.2 + - - -
446P ILE* 4.2 1.1 - - - +
447P GLN* 3.4 24.0 + - - +
450P VAL* 4.0 15.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 401 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394P GLU* 5.9 0.8 + - - +
397P GLN* 5.9 5.9 - - - +
398P ASN* 2.8 35.8 + - - +
400P SER* 1.3 73.5 - - - +
402P THR* 1.3 56.2 + - - +
404P LYS* 4.5 1.6 - - - -
405P SER* 2.6 43.8 + - - +
428P PHE* 3.5 46.6 + - - +
429P VAL 5.6 0.4 + - - -
431P SER* 3.0 27.5 + - - -
432P PRO 2.9 14.3 + - - -
433P GLU* 3.6 44.2 + - - +
435P PRO* 3.7 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 402 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394P GLU 4.1 1.0 + - - -
395P LEU* 2.6 55.2 + - + +
398P ASN* 2.7 16.8 + - - +
399P LEU* 3.3 10.8 - - - +
401P ARG* 1.3 74.1 - - - +
403P PHE* 1.3 59.9 + - + +
405P SER* 3.7 2.1 - - - -
406P LEU* 3.1 40.9 + - + +
428P PHE* 3.5 20.8 - - + -
458P PHE* 3.9 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 403 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266P PRO* 3.6 24.5 - - + -
399P LEU* 2.9 48.2 + - + +
400P SER 4.1 2.0 - - - +
402P THR* 1.3 75.0 - - + +
404P LYS* 1.3 61.7 + - - +
405P SER 3.2 1.3 - - - -
406P LEU* 4.4 4.7 - - + +
407P PHE* 2.9 59.6 + + + +
446P ILE* 3.9 21.7 - - + +
449P TYR* 4.0 21.1 - - + -
450P VAL* 4.2 11.9 - - + -
453P PHE* 3.4 31.0 - + - -
458P PHE* 3.5 19.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 404 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400P SER* 3.0 36.5 + - - +
401P ARG* 4.0 3.6 - - - +
403P PHE* 1.3 76.7 - - - +
405P SER* 1.3 58.7 + - - +
407P PHE 4.1 2.1 - - - +
408P ARG* 3.0 30.3 + - - +
435P PRO* 4.1 32.8 + - + +
436P SER 4.4 6.8 - - - +
437P LEU* 4.4 15.4 - - + +
438P SER* 5.2 2.6 - - - +
441P VAL* 5.9 1.3 - - + -
443P GLU* 2.9 42.3 + - - -
446P ILE* 3.8 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 405 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401P ARG* 2.6 31.5 + - - +
402P THR 3.7 4.3 - - - -
404P LYS* 1.3 78.5 - - - +
406P LEU* 1.3 62.6 + - - +
408P ARG* 3.3 17.6 - - - +
413P SER 4.7 0.7 - - - +
415P VAL* 3.8 8.3 - - - +
416P LEU* 3.6 25.2 - - - +
428P PHE* 4.2 20.0 - - - -
431P SER* 4.9 3.5 - - - -
432P PRO 4.7 0.5 + - - -
435P PRO* 3.2 19.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 406 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265P PHE* 5.6 1.6 - - + -
266P PRO* 3.4 37.9 - - + -
395P LEU* 5.1 4.5 - - + -
402P THR* 3.1 38.8 + - + +
403P PHE* 3.4 7.6 + - + +
405P SER* 1.3 78.8 - - - +
407P PHE* 1.3 59.0 + - + +
408P ARG* 2.7 19.9 + - - +
416P LEU* 3.7 22.4 - - + -
418P MET* 5.9 0.2 - - + -
427P LEU* 4.3 15.5 - - + -
428P PHE* 4.8 1.1 - - + -
524P TRP* 2.9 22.3 + - + -
700P NC3 4.2 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 407 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266P PRO* 3.8 11.2 - - + -
267P GLU* 4.2 5.8 - - + -
403P PHE* 2.9 38.6 + + + +
404P LYS* 4.1 2.9 - - - +
406P LEU* 1.3 75.3 - - + +
408P ARG* 1.3 65.8 + - - +
438P SER* 3.3 17.2 + - - -
440P MET* 3.7 5.1 - - + +
441P VAL* 4.3 9.8 - - + +
446P ILE* 3.7 18.8 - - + -
449P TYR* 3.6 48.2 - + - -
524P TRP* 3.5 47.6 - + - +
527P MET* 3.8 24.7 - - + -
----------------------------------------------------------
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