Contacts of the helix formed by residues 323 - 334 (chain D) in PDB entry 1NDD
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 323 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322D LYS* 1.3 72.3 - - - +
324D GLU* 1.3 62.1 + - - +
326D ILE* 3.1 11.2 + - + +
327D LYS* 3.0 36.1 + - - +
343D LEU* 4.2 9.2 - - + -
350D MET* 3.6 45.8 - - + +
351D ASN 3.1 25.8 - - - +
352D ASP* 3.5 15.0 + - - +
354D LYS 2.8 15.4 + - - +
355D THR 4.7 3.8 - - - -
359D TYR* 4.0 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 324 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322D LYS* 3.1 7.3 - - + -
323D VAL* 1.3 77.6 - - - +
325D ARG* 1.3 55.5 - - - +
327D LYS* 3.3 5.4 + - - +
328D GLU* 3.0 49.4 + - - +
338D PRO* 3.3 35.7 - - - +
352D ASP* 3.2 46.1 + - + +
353D GLU* 5.5 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 325 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321D ASP* 3.6 25.0 + - + +
322D LYS* 2.9 22.6 + - + +
324D GLU* 1.3 77.6 - - - +
326D ILE* 1.3 65.1 + - - +
328D GLU* 3.1 28.8 + - - +
329D ARG* 3.0 65.5 + - - +
332D GLU* 4.3 17.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 326 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305D VAL* 5.3 0.4 - - + -
315D ILE* 3.7 23.8 - - + -
317D ILE* 4.0 31.4 - - + -
321D ASP* 4.5 9.0 - - + +
322D LYS 3.6 9.6 - - - +
323D VAL* 3.1 19.2 + - + +
325D ARG* 1.3 75.6 - - - +
327D LYS* 1.3 62.9 + - - +
329D ARG* 3.1 12.4 + - - +
330D VAL* 3.1 23.4 + - + +
343D LEU* 3.9 16.8 - - + -
350D MET* 4.4 18.8 - - + -
356D ALA* 4.5 11.7 - - + -
361D ILE* 4.8 0.7 - - + -
367D LEU* 4.3 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 327 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323D VAL* 3.0 24.9 + - - +
324D GLU* 3.5 10.1 - - - +
325D ARG 3.2 0.2 - - - -
326D ILE* 1.3 76.7 - - - +
328D GLU* 1.3 56.7 + - - +
330D VAL* 3.2 1.5 + - - -
331D GLU* 2.9 24.3 + - - +
338D PRO* 3.6 32.5 + - + +
341D GLN* 2.9 54.4 + - + +
342D ARG* 4.3 0.4 - - - +
343D LEU* 3.7 22.0 - - + +
350D MET 4.4 4.2 + - - -
352D ASP* 2.9 26.6 + - - +
3001D SO4 2.8 31.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 328 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324D GLU* 3.0 41.7 + - - +
325D ARG* 3.1 34.5 + - - +
327D LYS* 1.3 75.8 - - - +
329D ARG* 1.3 59.6 + - - +
331D GLU* 3.3 18.2 + - - +
332D GLU* 3.0 32.3 + - - +
338D PRO* 4.6 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 329 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315D ILE* 4.6 18.5 - - + +
316D ASP 3.5 25.3 + - - -
317D ILE* 3.9 16.2 - - - +
318D GLU* 4.7 7.5 - - - +
321D ASP* 2.9 32.8 + - - -
325D ARG* 3.0 60.7 + - - +
326D ILE* 3.1 9.6 + - - +
328D GLU* 1.3 74.2 - - - +
330D VAL* 1.3 65.8 + - - +
332D GLU* 3.2 32.1 + - - +
333D LYS* 3.3 12.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 330 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305D VAL* 4.5 17.0 - - + -
313D ILE* 4.6 11.2 - - + -
315D ILE* 4.2 17.5 - - + -
326D ILE* 3.1 17.3 + - + +
327D LYS* 3.2 1.8 + - - +
329D ARG* 1.3 78.1 - - - +
331D GLU* 1.3 51.7 + - - +
333D LYS* 3.3 3.0 + - - -
334D GLU* 2.7 50.5 + - + +
336D ILE* 4.6 3.8 - - + -
341D GLN* 3.5 30.3 - - - +
343D LEU* 5.4 3.4 - - + -
369D LEU* 4.1 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 331 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327D LYS 2.9 15.8 + - - +
328D GLU* 3.5 14.0 - - - +
329D ARG 3.2 0.2 - - - -
330D VAL* 1.3 74.7 - - - +
332D GLU* 1.3 61.2 + - - +
335D GLY* 2.7 34.9 + - - +
336D ILE 3.2 26.2 - - - +
337D PRO* 3.8 9.9 - - + +
338D PRO* 3.2 28.9 - - + +
341D GLN* 3.8 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 332 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325D ARG* 4.3 14.5 + - - -
328D GLU* 3.0 14.8 + - - +
329D ARG* 3.2 35.4 + - - +
331D GLU* 1.3 77.6 - - - +
333D LYS* 1.3 60.8 + - + +
335D GLY 4.9 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 333 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313D ILE* 4.1 20.4 - - + +
314D GLU 3.3 25.1 + - - +
315D ILE* 4.2 9.3 - - + +
329D ARG 3.3 15.8 + - - +
330D VAL* 3.9 4.0 - - - +
331D GLU 3.2 0.2 - - - -
332D GLU* 1.3 82.1 - - + +
334D GLU* 1.3 78.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 334 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PRO* 3.9 1.7 - - - +
40A GLN* 3.0 47.6 + - + +
73A LEU* 3.6 23.9 - - + -
74A ARG* 3.1 27.4 + - - +
313D ILE* 3.4 31.9 - - + +
330D VAL* 2.7 22.3 + - + +
333D LYS* 1.3 87.4 - - - +
335D GLY* 1.3 59.7 + - - +
336D ILE* 3.5 19.1 + - + -
----------------------------------------------------------
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