Contacts of the strand formed by residues 32 - 38 (chain C) in PDB entry 3ZXR
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 MET 32 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C ARG* 4.3 9.4 - - + +
25C PHE* 3.4 24.9 - - - +
26C CYS* 3.6 17.0 - - + +
30C GLY 4.0 0.6 + - - -
31C ILE* 1.3 76.0 - - - +
33C GLN* 1.3 60.2 - - - +
92C ASN* 3.8 35.0 - - + +
109C ARG* 5.1 1.3 - - - -
243C GLN* 3.4 50.0 - - + +
247C TYR* 6.5 0.9 - - + -
377C TYR* 4.2 5.2 - - - +
188D PRO* 3.4 5.9 - - - +
189D VAL* 2.9 47.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 33 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C ARG* 3.2 8.1 - - - +
25C PHE* 2.7 59.3 + - + +
27C ASP* 3.1 25.6 + - + -
31C ILE* 3.0 31.9 + - - +
32C MET* 1.3 82.8 + - - +
34C HIS* 1.3 64.2 + - - +
58C ILE* 3.6 13.7 - - + +
59C ARG* 5.2 0.2 - - - +
186D TYR 3.7 1.0 - - - +
187D PHE* 2.8 47.9 + - + -
188D PRO* 3.3 7.9 - - - +
189D VAL* 4.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 34 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C ASP* 2.8 39.3 + - - +
23C VAL 3.1 11.4 - - - +
24C ARG* 3.9 4.7 - - + -
25C PHE* 5.5 0.2 - - - -
33C GLN* 1.3 77.0 - - - +
35C PHE* 1.3 63.1 + - - +
36C THR* 4.4 3.1 + - - -
84C ARG* 4.5 4.9 - - - -
187D PHE* 2.9 48.5 + - + +
188D PRO 3.5 10.9 + - - -
189D VAL* 3.5 22.8 - - + -
190D ALA 5.0 0.9 - - - -
193D ASP* 3.0 28.3 + - - +
196D VAL* 4.0 15.2 - - + +
199D ARG* 4.2 8.4 + - - -
217D HIS* 4.4 1.9 - - - +
218D HIS* 5.5 0.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 35 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C ASP* 3.4 3.2 - - - +
23C VAL* 2.8 57.8 + - + +
25C PHE* 4.8 0.9 - + - -
34C HIS* 1.3 77.4 - - - +
36C THR* 1.3 65.0 + - - +
37C ILE* 3.9 21.3 - - + -
51C LEU* 4.0 18.6 - - + -
52C ALA 4.0 19.5 - - - -
53C PHE* 4.5 0.9 - - + -
71C LEU* 3.7 23.3 - - + -
187D PHE* 3.5 26.0 - + + -
215D LYS* 3.7 28.3 - - + -
216D GLY 3.8 3.6 - - - +
217D HIS* 3.5 24.2 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 36 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C TYR* 3.5 33.0 - - + -
21C VAL 3.5 7.6 - - - +
22C ASP* 2.9 17.2 + - - -
34C HIS* 4.4 4.3 + - - -
35C PHE* 1.3 73.2 - - - +
37C ILE* 1.3 66.0 + - - +
84C ARG* 2.9 29.8 + - - +
196D VAL* 5.5 0.2 - - - +
199D ARG* 5.4 2.9 + - - -
203D LEU* 4.4 12.5 - - + +
215D LYS* 3.1 7.4 - - - +
216D GLY 2.9 40.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 37 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C TYR* 3.5 4.3 - - - +
21C VAL* 2.8 52.0 + - + +
23C VAL* 4.5 6.5 - - + -
35C PHE* 3.9 24.5 - - + -
36C THR* 1.3 80.9 - - - +
38C PRO* 1.3 69.7 - - + +
41C ALA* 4.0 27.8 - - + +
42C PHE* 4.2 17.3 - - + -
46C VAL* 4.4 2.9 - - + -
51C LEU* 4.4 25.1 - - + -
203D LEU* 6.2 0.2 - - - -
214D GLU 3.3 19.7 - - - +
215D LYS* 4.0 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 38 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C GLU 4.5 0.2 - - - +
20C TYR* 3.7 14.3 - - + -
21C VAL 4.6 0.7 - - - -
37C ILE* 1.3 92.0 - - + +
39C ALA* 1.3 67.3 + - - +
40C SER* 3.6 18.6 - - - +
41C ALA* 2.9 17.8 + - + +
42C PHE* 3.5 6.8 + - - +
203D LEU* 5.8 2.9 - - + -
207D ILE* 4.4 16.8 - - + -
213D LEU* 3.2 37.7 - - + +
214D GLU 3.4 21.8 - - - +
215D LYS* 4.4 1.3 - - - +
----------------------------------------------------------
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