Contacts of the strand formed by residues 415 - 422 (chain D) in PDB entry 1ZMC
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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406D ILE* 4.5 7.4 - - + -
407D LEU 3.6 5.8 - - - +
408D GLY* 4.3 1.8 - - - -
414D ARG* 1.3 73.6 - - - +
416D LEU* 1.3 65.6 + - - +
417D GLY 3.8 22.9 - - - +
418D ALA* 5.2 5.2 - - + -
435D ALA* 5.6 3.8 - - + -
436D LEU* 2.9 35.3 - - + +
439D GLY* 6.2 0.2 - - - -
440D ALA* 3.0 13.0 + - + +
441D SER 3.8 2.7 - - - -
442D CYS* 3.7 20.4 - - - +
445D ILE* 3.6 19.5 - - + -
459D PHE* 6.1 1.6 - - + -
463D ASN* 3.5 22.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 416 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352D ASN* 4.6 3.0 + - - +
368D GLY* 3.4 6.6 - - - -
369D LYS* 2.8 27.9 + - + +
374D LEU* 4.0 36.8 - - + -
379D ILE* 4.2 18.2 - - + -
381D TYR* 4.4 0.9 - - + -
407D LEU 2.7 14.1 + - - +
408D GLY 3.9 4.0 - - - +
409D GLN* 3.6 35.4 - - + +
414D ARG* 3.5 18.6 - - + +
415D VAL* 1.3 77.1 - - - +
417D GLY* 1.3 54.8 + - - +
436D LEU* 4.2 9.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 417 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367D VAL 3.6 8.3 - - - -
368D GLY* 4.2 0.2 - - - -
369D LYS 3.5 19.1 - - - -
406D ILE* 3.7 3.8 - - - -
407D LEU* 3.0 29.4 + - - +
415D VAL* 3.7 10.2 - - - +
416D LEU* 1.3 81.7 - - - +
418D ALA* 1.3 61.5 + - - +
419D HIS* 4.0 5.8 - - - -
436D LEU* 4.9 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 418 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366D TRP* 3.1 27.5 - - - +
367D VAL* 3.1 15.1 + - + -
405D LYS 3.6 4.7 - - - -
406D ILE* 4.2 14.6 - - + -
415D VAL* 5.2 4.9 - - + -
417D GLY* 1.3 74.8 - - - +
419D HIS* 1.3 61.9 + - - +
420D ILE* 4.3 7.0 - - + -
429D VAL* 5.2 0.4 - - + +
432D ALA* 3.7 30.3 - - + -
436D LEU* 5.6 0.9 - - + -
459D PHE* 4.3 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 419 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219D ASP* 3.7 19.2 + - + +
222D ILE* 3.6 24.5 - - + +
365D ALA 3.6 3.6 - - - -
366D TRP* 3.5 29.3 - + + +
367D VAL 4.8 1.6 - - - -
368D GLY 5.2 0.2 - - - -
369D LYS 2.7 31.6 + - - -
370D SER* 3.6 16.8 - - - -
403D MET 3.7 1.6 - - - +
404D VAL* 3.5 1.9 - - - +
405D LYS* 2.8 56.7 + - + +
406D ILE* 5.2 0.2 - - - +
407D LEU* 3.5 18.0 - - + +
417D GLY 4.0 0.2 - - - -
418D ALA* 1.3 82.7 + - - +
420D ILE* 1.3 63.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 420 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222D ILE* 5.0 2.2 - - - +
364D VAL* 3.2 9.3 - - - +
365D ALA 2.8 41.2 + - - +
388D PHE* 4.0 15.0 - - + -
403D MET 3.5 1.6 - - - -
404D VAL* 4.0 30.3 - - + -
418D ALA* 4.9 3.1 - - + -
419D HIS* 1.3 81.2 - - - +
421D LEU* 1.3 61.3 + - - +
422D GLY 4.1 0.2 - - - -
425D ALA* 3.6 28.1 - - + +
428D MET* 4.0 20.0 - - + +
429D VAL* 3.8 37.2 - - + +
432D ALA* 5.3 3.4 - - + -
459D PHE* 5.2 5.8 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
222D ILE* 4.0 20.9 - - + +
225D ASN* 3.6 35.9 - - + +
226D PHE* 3.6 43.3 - - + +
229D ILE* 4.4 6.7 - - + -
362D PRO* 4.2 9.2 - - + -
363D GLU 3.6 2.7 - - - +
364D VAL* 3.8 12.6 - - + -
388D PHE* 3.2 6.1 - - - -
402D GLY* 3.0 17.2 - - - -
403D MET* 2.7 45.5 + - + +
419D HIS 4.2 0.2 + - - -
420D ILE* 1.3 73.0 - - - +
422D GLY* 1.3 61.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 422 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362D PRO* 3.5 15.6 - - - +
363D GLU* 2.8 37.0 + - - +
388D PHE* 3.9 1.6 - - - -
401D ASP 3.4 7.0 - - - -
420D ILE 4.1 0.6 - - - -
421D LEU* 1.3 75.5 - - - +
423D PRO* 1.3 77.5 - - - +
425D ALA* 3.5 4.4 + - - +
----------------------------------------------------------
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