Contacts of the helix formed by residues 318 - 328 (chain K) in PDB entry 4UJ3
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 CYS 318 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308K TRP* 4.0 11.0 - - + -
313K THR* 3.7 27.8 - - + -
315K ASP* 3.4 22.4 + - - +
317K THR* 1.3 79.5 + - - +
319K PRO* 1.3 78.5 - - + +
320K PHE* 4.1 1.8 - - - -
321K LEU* 3.6 24.5 - - - -
322K ASP* 2.9 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 319 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304K GLU* 3.1 31.0 - - + +
317K THR 4.6 0.4 - - - +
318K CYS* 1.3 92.2 - - + +
320K PHE* 1.3 64.9 + - - +
322K ASP* 4.0 3.4 - - + +
323K LYS* 3.4 15.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 320 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301K LEU 5.3 0.7 - - - -
304K GLU* 3.9 19.0 + - - +
305K PHE* 3.2 53.4 - + + -
308K TRP* 3.6 41.5 - + + -
318K CYS* 3.3 1.1 - - - -
319K PRO* 1.3 83.6 - - + +
321K LEU* 1.3 93.2 + - + +
323K LYS* 4.1 2.4 - - - +
324K ILE* 3.5 38.4 + - + +
421K ILE* 3.8 18.8 - - + -
441K VAL* 3.8 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 321 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308K TRP* 4.1 5.6 - - + +
313K THR 3.5 22.2 - - - +
314K MET* 3.7 18.2 - - + +
315K ASP 3.5 24.7 - - - +
316K ARG 4.8 0.4 - - - +
318K CYS* 3.6 11.1 + - - -
320K PHE* 1.3 107.6 - - + +
322K ASP* 1.3 60.3 + - - +
324K ILE* 3.4 3.0 + - - +
325K TYR* 2.9 51.5 + - + -
417K PHE* 3.8 25.1 - - + -
418K PHE* 6.1 3.1 - - + -
421K ILE* 4.8 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 322 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316K ARG* 3.3 17.7 + - - +
317K THR* 4.1 8.9 - - - +
318K CYS 2.9 23.3 + - - +
319K PRO* 4.0 3.6 - - + +
321K LEU* 1.3 76.9 - - - +
323K LYS* 1.3 64.4 + - - +
325K TYR* 3.2 5.2 + - - +
326K GLN* 3.1 43.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 323 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326E GLN* 6.3 0.2 - - - +
300K SER* 3.9 19.4 + - - -
301K LEU* 3.5 29.1 - - + +
304K GLU* 3.2 25.0 + - - +
319K PRO 3.4 12.1 + - - +
320K PHE 4.1 4.0 - - - +
321K LEU 3.3 0.4 - - - -
322K ASP* 1.3 80.3 - - - +
324K ILE* 1.3 58.9 + - + +
326K GLN* 3.1 6.3 + - - +
327K GLU* 2.9 59.5 + - - +
445K ARG* 5.0 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 324 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301K LEU* 6.1 0.4 - - + -
304K GLU* 6.0 0.4 - - - +
320K PHE* 3.5 38.5 + - + +
321K LEU 3.4 6.6 + - - +
322K ASP 3.3 0.2 - - - -
323K LYS* 1.3 74.5 - - + +
325K TYR* 1.3 60.4 + - - +
328K ASP* 3.0 37.6 + - - +
329K ILE* 3.0 12.5 + - + -
417K PHE* 3.8 37.5 - - + -
441K VAL* 4.6 0.7 - - + -
445K ARG* 3.7 34.8 - - - +
448K MET* 3.8 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 325 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314K MET 5.2 3.7 + - - -
316K ARG* 3.6 41.5 + - + +
321K LEU* 2.9 43.9 + - + +
322K ASP* 3.2 7.6 + - - +
324K ILE* 1.3 78.7 - - - +
326K GLN* 1.3 63.2 + - + +
329K ILE* 3.4 28.9 + - + -
330K PHE* 2.8 61.6 + + + +
345K LEU* 4.0 14.1 - - + -
349K GLU* 2.6 30.7 + - - +
417K PHE* 5.9 0.2 - + - -
418K PHE* 3.3 25.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 326 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326E GLN* 5.1 12.3 - - + +
327E GLU* 4.6 6.6 - - - +
316K ARG* 6.2 1.0 - - - +
322K ASP* 3.1 33.5 + - - +
323K LYS* 3.6 7.2 - - - +
325K TYR* 1.3 78.7 - - - +
327K GLU* 1.3 60.8 - - + +
330K PHE* 3.9 28.5 - - - +
331K PRO* 3.1 20.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 327 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326E GLN* 4.3 28.1 + - - +
327E GLU* 4.2 15.6 - - + +
331E PRO* 4.2 12.1 - - - +
452E LYS* 3.3 27.6 - - - +
301K LEU* 6.0 0.3 - - - +
323K LYS* 2.9 39.8 + - + +
326K GLN* 1.3 78.9 - - + +
328K ASP* 1.3 71.4 + - - +
331K PRO* 3.1 12.7 - - - +
445K ARG* 3.0 22.3 + - - +
452K LYS* 3.4 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 328 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452E LYS* 3.5 9.7 + - - -
324K ILE* 3.0 13.8 + - - +
326K GLN 3.5 0.4 - - - -
327K GLU* 1.3 94.5 - - - +
329K ILE* 1.3 64.6 + - - +
331K PRO* 3.4 4.5 - - - +
332K CYS* 3.2 28.6 + - - +
445K ARG* 2.3 51.8 + - - +
448K MET* 3.5 28.0 - - + +
449K SER* 3.6 11.6 + - - -
452K LYS* 5.0 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