Contacts of the helix formed by residues 389 - 400 (chain C) in PDB entry 4HH3
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 LEU 389 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226C ARG* 6.1 2.0 - - - +
384C PHE* 3.7 12.1 - - + +
385C ALA* 4.2 13.0 - - + +
386C HIS* 2.9 47.6 + - + +
388C ALA* 1.3 81.8 - - + +
390C LEU* 1.3 63.4 + - - +
391C PRO* 3.4 2.7 - - - -
392C ALA* 3.3 16.4 + - + +
393C ALA* 3.2 17.2 + - - +
396C ARG* 5.3 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 390 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293C ALA* 3.6 38.1 - - + +
296C MET* 4.5 4.5 - - + -
297C LEU* 4.0 27.4 - - + -
328C VAL* 3.9 23.6 - - + -
362C LEU* 4.1 9.9 - - + -
384C PHE* 3.7 42.0 - - + +
387C LEU* 3.1 16.2 + - + +
389C LEU* 1.3 74.6 - - - +
391C PRO* 1.3 72.6 - - + +
393C ALA* 3.1 1.9 + - - +
394C LEU* 2.9 21.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 391 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222C ALA* 5.8 2.7 - - + -
296C MET* 4.1 33.7 - - + +
297C LEU* 4.7 7.0 - - + -
300C VAL* 5.0 18.2 - - + -
388C ALA 3.5 16.2 - - - +
389C LEU 3.7 0.4 - - - -
390C LEU* 1.3 93.8 - - + +
392C ALA* 1.3 62.3 - - - +
394C LEU* 3.3 5.9 + - + +
395C ALA* 2.9 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 392 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389C LEU* 3.3 20.0 + - + +
390C LEU 3.2 0.6 - - - -
391C PRO* 1.3 79.8 - - - +
393C ALA* 1.3 62.6 + - - +
395C ALA* 3.3 6.8 + - - +
396C ARG* 3.1 41.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 393 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362C LEU* 3.7 15.7 - - + -
382C ALA* 4.1 3.9 - - + +
383C GLY 3.6 14.8 - - - +
384C PHE* 4.1 8.5 - - + +
389C LEU 3.2 8.7 + - - +
390C LEU 3.1 8.1 + - - +
392C ALA* 1.3 79.9 - - - +
394C LEU* 1.3 62.3 + - - +
396C ARG* 3.2 29.5 + - - +
397C VAL* 3.1 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 394 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276C VAL* 4.6 4.5 - - + -
297C LEU* 3.5 34.3 - - + -
302C TRP* 3.4 48.0 - - + +
326C THR* 3.7 29.4 - - + -
328C VAL* 5.2 1.1 - - + -
362C LEU* 3.6 18.3 - - + +
390C LEU* 2.9 16.3 + - + +
391C PRO* 3.8 6.3 - - + +
393C ALA* 1.3 75.7 - - - +
395C ALA* 1.3 57.4 + - - +
397C VAL* 3.3 5.6 + - + +
398C ALA* 2.8 34.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 395 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302C TRP* 6.0 0.9 - - - -
391C PRO 2.9 17.2 + - - +
392C ALA* 3.6 7.6 - - - +
394C LEU* 1.3 78.0 - - - +
396C ARG* 1.3 62.2 + - + +
398C ALA* 3.5 5.6 + - - +
399C SER* 3.1 27.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 396 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382C ALA* 4.5 7.1 - - + +
383C GLY 3.1 30.5 + - - +
389C LEU 5.3 0.6 + - - -
392C ALA* 3.1 36.8 + - - +
393C ALA* 3.5 21.6 - - - +
394C LEU 3.2 0.2 - - - -
395C ALA* 1.3 77.6 - - + +
397C VAL* 1.3 61.7 + - + +
399C SER* 3.3 15.0 + - - -
400C SER* 3.4 15.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 397 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326C THR* 5.3 1.3 - - + +
360C SER* 3.5 35.6 + - - +
362C LEU* 4.1 17.3 - - + -
381C ASP* 4.4 15.0 - - + +
382C ALA* 3.4 26.2 - - + -
393C ALA 3.1 14.3 + - - +
394C LEU* 3.7 12.3 - - + +
396C ARG* 1.3 75.4 - - - +
398C ALA* 1.3 65.3 + - - +
399C SER 3.3 0.7 + - - -
400C SER* 3.3 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 398 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302C TRP* 4.1 27.4 - - + -
394C LEU* 2.8 18.8 + - + +
395C ALA* 3.9 6.3 - - - +
397C VAL* 1.3 78.7 - - - +
399C SER* 1.3 61.0 - - - +
400C SER 3.8 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 399 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395C ALA 3.1 14.4 + - - -
396C ARG* 3.5 11.4 - - - -
397C VAL 3.2 0.2 - - - -
398C ALA* 1.3 79.6 - - - +
400C SER* 1.3 62.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 400 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396C ARG 3.4 12.5 + - - -
397C VAL* 3.3 18.7 + - - +
398C ALA 3.8 4.0 - - - +
399C SER* 1.3 83.9 - - - +
----------------------------------------------------------
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