Contacts of the helix formed by residues 397 - 407 (chain C) in PDB entry 1KRB
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 ASN 397 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C ILE* 3.3 7.4 - - - -
31C GLU* 2.9 45.9 + - - +
33C GLU* 3.2 29.2 + - - +
81C ILE* 3.7 18.6 - - + +
395C ASN* 3.1 28.7 + - - +
396C ASP* 1.3 76.9 - - - +
398C PHE* 1.3 62.7 + - - +
400C VAL* 3.3 4.8 + - - +
401C LYS* 3.0 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 398 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388C LEU* 3.8 11.7 - - + -
390C GLU* 3.5 45.1 - - + +
391C GLU* 3.0 19.8 + - - +
397C ASN* 1.3 75.3 - - - +
399C ARG* 1.3 68.8 + - - +
401C LYS* 3.0 17.6 + - + +
402C ARG* 2.9 56.3 + - + -
527C HIS* 3.8 39.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 399 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C LEU* 4.3 12.8 - - + -
350C ASP* 3.0 36.7 + - - -
378C ALA* 3.7 23.9 + - + -
381C MET 4.0 6.7 + - - -
382C LYS* 3.5 23.5 - - - +
385C ARG* 4.8 2.4 - - - +
386C GLY 2.7 31.9 + - - -
387C ALA* 4.2 5.1 - - - +
388C LEU* 3.3 35.6 - - + +
391C GLU* 2.8 17.2 + - - +
396C ASP* 3.1 18.9 + - + +
398C PHE* 1.3 72.0 - - - +
400C VAL* 1.3 58.7 + - - +
402C ARG* 3.3 1.9 + - - -
403C TYR* 3.0 53.2 + - + -
----------------------------------------------------------
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
----------------------------------------------------------
23C LEU* 4.0 16.4 - - + -
28C LEU* 4.9 8.5 - - + -
30C ILE* 3.7 28.7 - - + -
76C VAL* 3.8 28.3 - - + -
81C ILE* 4.3 4.5 - - + -
375C TRP* 3.4 22.2 - - + -
396C ASP* 2.9 24.2 + - + +
397C ASN* 3.6 8.3 - - - +
399C ARG* 1.3 77.4 - - + +
401C LYS* 1.3 56.2 + - - +
403C TYR 3.4 0.2 + - - -
404C ILE* 2.9 29.3 + - - +
440C PHE* 6.0 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 401 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C GLU* 3.2 33.0 + - - -
77C ASP 3.8 8.7 - - - +
78C HIS* 3.7 17.4 - - - +
79C TRP 4.4 4.8 + - - -
80C GLY* 3.9 22.2 - - - +
81C ILE* 4.3 10.3 - - + -
397C ASN* 3.0 23.1 + - - +
398C PHE* 3.0 18.1 + - + +
400C VAL* 1.3 73.0 - - + +
402C ARG* 1.3 65.4 + - - +
404C ILE* 3.5 10.2 - - - +
405C ALA* 3.3 23.9 + - - +
527C HIS* 3.5 22.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 402 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349C HIS 4.0 9.4 - - - -
350C ASP 2.7 36.6 + - - -
351C LEU* 3.6 21.4 + - - +
352C GLY* 4.1 1.8 - - - -
388C LEU* 3.6 21.0 - - - +
390C GLU* 3.4 26.5 + - - -
398C PHE* 2.9 33.2 + - + +
399C ARG* 3.7 4.7 - - - +
401C LYS* 1.3 79.0 - - - +
403C TYR* 1.3 71.8 + - + +
405C ALA 3.7 3.1 + - - -
406C LYS* 3.6 8.8 - - - +
527C HIS* 2.8 39.5 + - + +
528C ASN* 3.1 33.1 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
349C HIS* 4.5 3.4 - + + -
350C ASP* 2.9 54.5 + - - +
374C THR* 3.5 38.5 - - + +
375C TRP* 3.8 18.4 - - + -
377C VAL* 3.8 12.0 - - + +
378C ALA* 3.7 23.3 - - + -
381C MET* 3.7 11.3 - - - +
399C ARG* 3.0 42.3 + - + +
402C ARG* 1.3 88.1 - - + +
404C ILE* 1.3 64.7 + - - +
405C ALA 3.1 1.6 - - - -
406C LYS* 3.1 35.8 + - + +
407C TYR* 3.9 1.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 404 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C VAL* 3.5 38.1 - - + +
77C ASP* 4.1 6.1 - - - +
78C HIS* 4.1 17.5 - - + +
127C THR* 3.9 20.4 - - + -
128C ALA 5.6 0.7 - - - +
375C TRP* 3.8 15.2 - - + -
400C VAL 2.9 22.0 + - - +
401C LYS* 3.5 13.9 - - - +
403C TYR* 1.3 76.1 - - - +
405C ALA* 1.3 60.1 + - - +
406C LYS 3.2 0.9 + - - -
407C TYR* 3.3 33.4 + - + +
408C THR* 2.8 30.9 + - + +
440C PHE* 5.0 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 405 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C HIS* 4.3 9.9 - - + -
401C LYS 3.3 15.0 + - - +
402C ARG 3.8 5.2 - - - +
403C TYR 3.1 0.6 - - - -
404C ILE* 1.3 82.9 - - - +
406C LYS* 1.3 59.3 + - - +
407C TYR 3.2 1.4 + - - -
408C THR* 3.4 10.7 + - - -
409C ILE* 3.5 17.7 + - + -
410C ASN* 3.0 32.0 + - - +
526C VAL* 3.7 24.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 406 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349C HIS* 3.0 41.7 + - + -
354C PHE 2.8 20.6 + - - -
355C SER 3.5 20.2 - - - +
356C LEU* 3.4 6.1 - - - -
357C THR* 3.3 33.7 + - + +
374C THR* 4.4 1.6 - - + -
402C ARG* 3.6 15.9 - - - +
403C TYR* 3.2 41.7 - - + +
404C ILE 3.1 0.4 - - - -
405C ALA* 1.3 77.6 - - - +
407C TYR* 1.3 57.2 + - - +
411C PRO* 3.3 14.4 - - - +
528C ASN* 2.6 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 407 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127C THR* 5.3 3.8 + - - -
128C ALA 5.3 3.6 - - - -
130C GLY* 3.4 11.7 - - - -
131C ILE 2.8 31.9 + - - +
151C VAL* 5.9 1.1 - - + -
357C THR* 3.9 11.2 - - - +
370C VAL* 4.2 13.9 - - + -
371C ILE* 3.5 35.7 - - + +
374C THR* 4.0 21.5 - - + -
375C TRP* 3.0 41.2 + + - -
403C TYR 3.9 9.4 - - - -
404C ILE* 3.3 23.6 + - + +
405C ALA 3.2 0.6 - - - -
406C LYS* 1.3 76.3 - - - +
408C THR* 1.3 72.9 + - + +
411C PRO* 3.7 11.4 - - - -
435C TRP* 5.5 2.3 - + - -
440C PHE* 4.6 4.0 - - - -
----------------------------------------------------------
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