Contacts of the strand formed by residues 41 - 47 (chain F) in PDB entry 2ZHX
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 ILE 41 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22F ILE 3.5 1.2 - - - +
23F LEU* 3.2 6.1 - - - -
24F MET 2.8 36.7 + - - -
29F VAL* 4.1 16.6 - - + -
37F PRO* 3.6 23.6 - - + -
39F SER 3.9 3.8 - - - +
40F ASP* 1.3 81.1 - - - +
42F LEU* 1.3 65.8 + - - +
43F VAL* 3.8 2.7 + - + +
58F LEU* 3.6 33.7 - - + -
59F THR 3.4 13.0 - - - +
60F SER* 4.9 1.6 - - - +
68F TRP* 3.3 43.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 42 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137E PRO* 4.9 1.1 - - + +
138E ALA* 4.6 11.0 - - + -
141E ARG* 4.8 7.2 - - - +
21F SER* 3.7 19.7 - - - +
23F LEU* 3.4 41.3 - - + +
41F ILE* 1.3 73.9 - - - +
43F VAL* 1.3 60.8 + - - +
44F HIS* 3.1 27.7 + - + +
57F LEU 3.2 1.9 - - - +
58F LEU* 3.2 2.1 - - - -
59F THR* 3.0 31.0 + - - +
60F SER 3.8 17.0 + - - +
61F ASP* 4.0 1.3 - - - +
62F ALA* 3.9 18.6 - - - +
65F TYR* 4.2 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 43 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193E SER* 4.0 10.8 - - - +
195E LEU* 3.7 37.0 - - + -
20F GLU 3.6 1.4 - - - +
22F ILE* 2.5 41.7 + - + +
24F MET* 3.6 28.9 - - + -
29F VAL* 5.0 0.2 - - + -
41F ILE* 4.2 12.8 - - + +
42F LEU* 1.3 71.0 - - - +
44F HIS* 1.3 64.9 + - - +
45F THR* 3.2 13.0 + - - +
56F MET* 4.5 9.6 - - + -
57F LEU 4.0 2.0 - - - -
58F LEU* 4.4 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 44 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137E PRO* 3.9 12.5 - - + +
4F LEU* 3.9 16.4 - - + +
8F ILE* 5.4 0.7 - - - +
18F ILE* 3.7 35.1 - - + +
20F GLU 3.4 6.7 - - - -
21F SER* 2.7 26.9 + - - +
42F LEU* 3.1 23.6 + - + +
43F VAL* 1.3 69.4 - - - +
45F THR* 1.3 57.1 + - - +
46F ALA 4.1 0.6 + - - -
55F VAL 3.6 1.0 - - - +
56F MET* 3.1 5.2 - - - -
57F LEU* 2.7 54.8 + - + +
59F THR* 3.2 36.0 - - + +
65F TYR* 4.5 3.6 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 45 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92E ARG* 3.9 14.7 - - + +
193E SER* 3.4 9.2 + - - -
194E PRO* 3.7 26.9 - - + -
18F ILE* 4.6 1.5 - - - +
19F GLN* 3.2 24.2 + - - +
20F GLU* 3.1 36.0 + - - +
43F VAL* 3.2 13.2 + - - +
44F HIS* 1.3 70.7 - - - +
46F ALA* 1.3 69.1 + - - +
54F ASN* 4.5 3.6 - - + -
55F VAL 3.3 1.8 - - - -
56F MET* 3.8 19.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 46 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92E ARG* 5.1 0.4 - - - -
8F ILE* 4.6 6.7 - - + -
16F LEU* 3.9 22.4 - - + -
17F VAL 3.5 30.5 - - - +
18F ILE* 3.8 10.4 - - + +
19F GLN* 4.4 1.3 - - - +
44F HIS 4.1 1.0 + - - -
45F THR* 1.3 77.9 - - - +
47F TYR* 1.3 56.9 + - - +
54F ASN* 3.7 1.7 - - - -
55F VAL* 2.6 40.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 47 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89E PRO* 4.5 15.7 - - + +
92E ARG* 3.1 55.4 + - + +
16F LEU* 3.4 14.2 - - - +
17F VAL 4.7 2.3 + - - -
19F GLN* 4.3 13.2 + - - +
46F ALA* 1.3 76.8 - - - +
48F ASP* 1.3 68.0 + - - +
49F GLU* 3.3 51.7 + - + -
52F ASP* 2.9 32.8 + - - -
53F GLU 3.4 14.1 - - - -
54F ASN* 3.5 10.8 - - - -
----------------------------------------------------------
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