Contacts of the helix formed by residues 399 - 408 (chain C) in PDB entry 2JIF
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 PRO 399 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311C TYR* 3.5 49.1 - - + +
397C ASP 4.9 0.4 - - - +
398C TYR* 1.3 89.1 - - + +
400C VAL* 1.3 64.6 + - + +
401C GLU 3.4 1.3 - - - -
402C LYS* 3.4 12.2 + - + +
403C TYR* 3.3 24.5 + - + -
1435C EDO 3.3 31.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 400 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308C CYS* 3.7 19.9 - - - +
311C TYR* 3.8 22.7 - - + -
312C THR* 3.7 20.0 - - - +
382C THR 4.1 1.3 - - - +
385C CYS* 3.8 2.2 - - + -
386C ILE* 3.5 38.4 - - + +
389C MET* 3.9 16.8 - - + -
393C GLY* 4.6 6.5 - - - +
398C TYR* 3.4 3.1 - - + -
399C PRO* 1.3 78.9 - - + +
401C GLU* 1.3 61.7 + - - +
403C TYR* 3.3 10.5 + - + +
404C PHE* 3.1 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 401 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A LEU* 3.5 29.3 - - + +
84C ASP* 4.7 0.2 - - - +
386C ILE* 4.0 10.1 - - - -
393C GLY 3.5 15.8 + - - +
394C TYR 4.7 0.2 - - - -
395C THR 3.5 26.0 - - - +
396C LYS* 2.8 43.5 + - + +
398C TYR 4.1 4.6 + - - +
400C VAL* 1.3 78.7 - - - +
402C LYS* 1.3 63.5 + - - +
404C PHE* 3.4 3.6 - - - +
405C ARG* 2.8 61.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 402 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C VAL* 3.4 31.7 - - + +
81C SER* 5.5 1.3 - - - -
84C ASP* 3.6 31.0 - - + +
131C VAL 4.8 1.0 + - - -
132C ASP* 2.9 33.2 + - - +
133C ALA 4.4 0.2 - - - +
134C SER* 4.7 2.6 + - - -
256C ARG 6.2 1.1 - - - +
257C ALA* 6.5 0.9 - - - -
399C PRO* 3.4 12.2 + - + +
400C VAL 3.3 0.4 - - - -
401C GLU* 1.3 82.9 + - - +
403C TYR* 1.3 69.3 + - + +
405C ARG* 3.2 25.0 + - - +
406C ASP* 2.6 60.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 403 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C ALA 4.1 9.0 - - - -
130C LYS 2.6 30.0 + - - -
131C VAL 4.3 7.9 - - - -
132C ASP* 5.7 0.7 - - - -
133C ALA 5.8 1.3 - - - -
304C LEU* 3.5 32.5 - - + +
307C GLY 3.8 6.5 + - - -
308C CYS* 3.6 33.7 - - + -
311C TYR* 5.1 2.5 - - + -
382C THR* 3.7 17.5 - - + -
399C PRO* 3.3 25.4 + - + -
400C VAL* 3.3 7.9 + - + +
402C LYS* 1.3 80.0 - - + +
404C PHE* 1.3 52.0 - - - +
406C ASP* 3.3 7.4 + - - +
407C ALA* 2.8 36.6 + - - +
1435C EDO 3.0 38.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 404 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A LEU* 3.9 23.3 - - + -
404A PHE* 3.3 47.9 - + - -
405A ARG* 5.1 0.4 - - - -
408A LYS* 3.6 31.0 - - + -
379C GLY* 4.7 1.8 - - - -
382C THR* 3.5 16.1 + - - -
383C SER* 3.7 34.3 - - - -
386C ILE* 3.4 24.0 - - + -
400C VAL 3.1 5.2 + - - +
401C GLU 3.4 7.9 - - - +
403C TYR* 1.3 76.0 - - - +
405C ARG* 1.3 70.1 + - + +
407C ALA* 3.5 8.8 + - - +
408C LYS* 3.6 12.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 405 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A LEU* 3.5 24.7 - - + -
394A TYR* 2.8 29.2 + - - -
396A LYS* 6.0 0.4 - - - +
404A PHE* 5.0 0.7 - - - -
405A ARG* 4.2 5.6 - - + +
84C ASP* 2.9 42.8 + - - -
253C LEU* 3.1 54.1 + - + +
254C GLY* 3.9 4.7 - - - -
256C ARG* 3.8 7.7 - - - +
396C LYS* 3.4 13.6 - - - +
401C GLU* 2.8 51.8 + - - +
402C LYS* 3.2 14.0 + - - +
404C PHE* 1.3 80.1 - - + +
406C ASP* 1.3 57.2 + - - +
408C LYS* 3.6 7.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 406 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A TYR* 3.6 4.9 + - - -
84C ASP* 4.8 0.9 - - - +
132C ASP* 4.3 0.3 - - - +
133C ALA* 3.9 16.4 + - + +
134C SER* 5.0 0.2 - - - -
254C GLY* 3.6 3.6 - - - -
255C LEU* 2.8 29.8 + - + +
256C ARG 4.7 0.2 + - - -
301C MET* 4.1 1.7 - - - +
304C LEU* 4.1 15.5 - - + -
402C LYS* 2.6 62.1 + - - +
403C TYR* 3.6 9.0 - - - +
405C ARG* 1.3 69.8 - - - +
407C ALA* 1.3 66.4 + - - +
408C LYS 3.2 0.3 + - - -
409C ILE* 3.1 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 407 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C MET* 3.6 9.7 - - - +
304C LEU* 3.8 20.4 - - + +
375C SER 4.7 4.3 - - - +
378C ALA* 3.6 33.2 - - + +
379C GLY* 4.0 5.3 - - - +
382C THR* 3.6 8.7 - - - +
403C TYR 2.8 20.5 + - - +
404C PHE 4.0 1.8 - - - +
405C ARG 3.4 0.8 - - - -
406C ASP* 1.3 72.6 - - - +
408C LYS* 1.3 63.6 + - - +
410C GLY* 2.9 14.9 + - - -
411C THR* 4.4 2.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 408 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A SER* 2.7 33.6 + - - +
386A ILE* 3.9 31.6 - - + -
387A GLU* 2.7 33.2 + - - -
394A TYR* 4.0 5.4 - - + -
404A PHE* 3.7 28.3 - - + -
253C LEU* 4.1 7.2 - - + -
379C GLY* 5.6 4.9 - - - -
404C PHE 3.6 9.9 + - - +
405C ARG 3.7 12.6 - - - +
406C ASP 3.2 1.0 - - - -
407C ALA* 1.3 77.5 - - - +
409C ILE* 1.3 60.3 + - - +
410C GLY 3.3 0.9 + - - -
411C THR* 3.5 18.6 + - - +
412C ILE* 4.1 5.7 - - - +
----------------------------------------------------------
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