Contacts of the strand formed by residues 40 - 46 (chain C) in PDB entry 3ZO7
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 TRP 40 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B ARG* 4.0 0.2 + - - -
7C MET* 4.0 22.2 - - + -
31C SER* 3.5 31.4 - - - -
34C LEU* 3.2 22.0 + - + -
35C GLN* 3.5 43.3 - - + +
38C GLY 4.0 1.6 - - - -
39C GLN* 1.3 74.8 - - - +
41C ARG* 1.3 66.7 + - - +
42C TYR 3.2 22.7 + - - -
43C LEU* 3.6 28.0 - - + +
52C ASN* 4.5 4.5 - - - -
54C SER* 3.0 30.2 + - - -
55C VAL 4.3 1.3 - - - -
56C PHE* 3.4 24.7 - + + -
71C LEU* 3.9 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 41 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B ARG* 3.1 23.6 + - - -
2C LEU* 3.7 24.9 - - - +
38C GLY* 4.0 12.8 + - - +
39C GLN 3.4 2.2 + - - -
40C TRP* 1.3 74.0 - - - +
42C TYR* 1.3 99.0 + - + +
55C VAL* 2.9 19.3 + - - +
57C ASP* 3.3 28.9 + - + -
93C LYS* 5.9 1.8 - - - +
94C ASP* 3.3 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 42 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B TYR* 3.2 42.9 + + - -
44B TRP* 4.2 14.1 - + - -
90B ARG* 4.0 12.6 - - - +
93B LYS 4.7 4.7 - - - -
94B ASP 4.6 4.0 - - - -
40C TRP* 3.2 13.5 - - - -
41C ARG* 1.3 127.0 + - + +
43C LEU* 1.3 61.6 + - - +
44C TRP* 3.5 37.5 - + + -
53C ILE 4.7 0.4 - - - -
54C SER* 3.3 2.4 - - - -
55C VAL* 3.1 40.2 + - + -
94C ASP* 3.7 6.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 43 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B HIS* 3.6 39.7 + - + +
89B ALA* 4.1 10.5 - - + +
90B ARG* 3.8 28.3 + - - +
94B ASP* 4.4 1.4 - - - +
31C SER* 4.9 2.0 - - - +
35C GLN* 3.7 26.7 - - - +
40C TRP* 3.6 22.2 - - + +
42C TYR* 1.3 77.3 - - - +
44C TRP* 1.3 70.0 + - - +
52C ASN* 3.6 27.8 - - + +
53C ILE 3.8 2.0 - - - -
54C SER* 3.3 18.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 44 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B LEU* 3.6 21.4 - - + +
4B LEU* 5.6 0.7 - - + -
42B TYR* 3.9 13.5 - + - -
44B TRP* 4.6 2.5 - + - -
55B VAL* 4.0 25.4 - - + -
84B LEU* 3.9 34.1 - - + -
85B SER 3.6 11.0 - - - +
87B HIS* 4.0 5.6 - - - -
94B ASP* 3.3 43.7 + - + +
4C LEU* 5.4 1.1 - - + -
42C TYR* 3.5 42.4 - + + -
43C LEU* 1.3 80.9 + - - +
45C ARG* 1.3 59.8 + - - +
52C ASN* 3.1 8.7 - - - +
53C ILE* 3.0 57.2 + - + +
55C VAL* 4.3 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 45 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A HIS* 3.3 42.7 + - + +
69A TRP* 4.1 21.6 - - - -
84B LEU* 3.5 7.2 - - - +
85B SER* 2.8 46.4 + - - +
86B HIS 3.8 14.1 - - - +
87B HIS* 3.5 31.1 + - - +
88B PRO* 3.5 30.7 - - - +
44C TRP* 1.3 74.0 - - - +
46C THR* 1.3 63.5 + - - +
47C THR 3.3 0.5 + - - -
49C LYS 3.5 8.3 + - - -
50C TYR* 4.4 11.5 - - - -
51C GLY* 3.1 34.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 46 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B GLU* 3.7 16.8 - - - +
83B PRO 4.5 4.3 - - - -
84B LEU* 4.9 1.6 - - + -
6C ARG* 4.2 9.0 - - + +
7C MET 5.6 0.4 - - - +
44C TRP 3.8 0.4 + - - -
45C ARG* 1.3 75.6 - - - +
47C THR* 1.3 67.3 + - - +
48C GLY 3.3 0.3 + - - -
49C LYS* 2.9 43.7 + - + +
51C GLY* 3.2 21.1 + - - -
52C ASN* 4.0 11.4 - - - +
53C ILE* 3.6 31.4 - - + -
----------------------------------------------------------
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