Contacts of the strand formed by residues 375 - 382 (chain C) in PDB entry 3RIK
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 375 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C GLN* 3.0 18.0 + - - +
310C VAL* 5.3 2.7 - - + -
324C LEU* 4.2 15.3 - - + -
336C LEU* 3.3 24.9 - - + +
337C PHE* 4.0 0.7 - - - -
338C ALA* 3.7 11.4 - - + +
370C ASN* 3.2 40.4 + - + +
371C LEU* 4.1 1.2 - - - +
373C TYR 3.9 7.6 - - - +
374C HIS* 1.3 75.5 - - - +
376C VAL* 1.3 62.5 + - - +
377C GLY 3.5 22.2 - - - +
378C TRP* 3.4 24.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 376 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C GLN* 4.1 11.0 - - + -
77C LYS 3.4 23.8 - - - +
78C VAL* 3.3 8.9 - - - +
79C LYS* 2.6 37.3 + - + +
80C GLY 3.6 1.7 + - - -
335C MET* 3.7 46.2 - - + -
336C LEU 2.8 23.4 + - - +
337C PHE* 4.1 6.7 - - + -
374C HIS 3.8 12.6 - - - +
375C VAL* 1.3 72.1 - - - +
377C GLY* 1.3 54.6 + - - +
378C TRP* 3.8 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 377 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C GLY 3.2 9.6 - - - -
337C PHE* 3.6 20.4 - - - -
338C ALA 2.8 28.6 + - - -
375C VAL* 3.5 2.5 - - - +
376C VAL* 1.3 82.9 - - - +
378C TRP* 1.3 76.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 378 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C VAL* 4.9 2.9 - - + -
80C GLY 3.0 8.4 + - - +
81C PHE* 3.3 50.0 - + + -
82C GLY 3.0 24.8 + - - +
118C ILE* 4.3 1.7 - - - +
312C TRP* 3.2 31.2 - + + -
337C PHE* 4.0 3.4 - - - -
338C ALA* 3.4 15.3 - - + +
341C ALA* 4.1 6.1 - - + -
367C ILE* 3.8 17.4 - - + +
370C ASN* 2.9 42.0 + - + +
371C LEU* 3.5 24.7 - - + -
375C VAL* 3.4 25.8 - - + -
376C VAL 3.8 4.3 - - - -
377C GLY* 1.3 102.1 - - - -
379C THR* 1.3 62.9 + - - +
380C ASP 4.0 0.9 - - - +
420C LEU* 5.8 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 379 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C GLY 3.6 2.2 - - - -
83C GLY* 3.7 16.8 - - - +
118C ILE* 3.6 12.2 - - + +
120C ARG* 3.5 31.0 - - + +
175C LEU* 3.9 3.1 - - - +
337C PHE* 3.5 20.6 - - - -
338C ALA 2.8 8.1 + - - -
339C SER* 3.2 17.7 - - - +
340C GLU* 3.3 4.5 + - - -
341C ALA* 2.6 32.1 + - - -
378C TRP* 1.3 71.9 - - - +
380C ASP* 1.3 69.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 380 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C GLY 2.9 17.8 + - - +
83C GLY* 4.0 3.0 - - - -
84C ALA* 3.3 6.1 + - - +
108C TYR* 5.0 1.0 + - - -
116C TYR* 4.6 4.0 + - + +
120C ARG* 5.4 0.2 - - - -
339C SER 4.6 1.0 - - - +
340C GLU* 5.0 0.2 - - - -
341C ALA* 3.2 14.2 - - - +
363C TYR* 2.4 39.1 + - + -
378C TRP* 4.0 1.8 - - - +
379C THR* 1.3 91.3 - - - +
381C TRP* 1.3 91.6 + - - +
382C ASN 4.0 1.7 - - - +
383C LEU* 5.4 0.9 - - - +
399C ASP 5.8 0.2 - - - +
401C PRO* 3.2 32.6 - - - +
420C LEU* 4.2 12.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 381 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C GLY* 3.9 1.9 - - - -
84C ALA* 2.9 51.8 + - + -
86C THR* 3.5 23.8 - - + -
120C ARG* 3.6 23.1 - - + -
122C PRO* 4.8 2.0 - - + -
126C CYS* 3.9 8.3 - - - -
127C ASP* 4.2 6.8 + - - -
128C PHE* 3.3 33.4 - + - -
179C TRP* 3.2 35.2 - + - -
340C GLU* 4.0 20.8 + - + -
341C ALA 4.3 2.4 + - - +
342C CYS* 3.8 34.8 - - + -
380C ASP* 1.3 84.5 + - - +
382C ASN* 1.3 85.2 + - - +
383C LEU 3.3 0.2 + - - -
397C PHE* 6.1 1.2 - - - -
398C VAL* 4.2 7.0 - - + -
399C ASP 5.9 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 382 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C ALA* 3.7 7.6 - - - -
86C THR* 2.7 27.7 + - - +
88C ALA* 4.1 0.2 - - - +
128C PHE* 3.4 36.8 - - - +
380C ASP* 4.0 0.5 - - - +
381C TRP* 1.3 105.8 - - - +
383C LEU* 1.3 56.6 + - - +
384C ALA 3.8 16.2 - - - +
385C LEU* 3.7 23.7 - - + +
398C VAL* 4.2 1.4 - - - +
399C ASP 5.4 2.4 + - - +
400C SER* 2.8 24.9 + - - +
401C PRO* 3.9 8.0 - - - +
----------------------------------------------------------
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