Contacts of the strand formed by residues 47 - 53 (chain E) in PDB entry 3VZC
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 47 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E CYS* 3.6 11.9 - - - -
17E VAL* 3.6 33.0 - - + -
42E LEU* 3.0 52.2 + - + +
43E ALA* 5.1 1.2 - - - +
45E ALA* 3.7 9.4 - - + +
46E GLU* 1.3 75.3 - - - +
48E SER* 1.3 66.4 + - - +
49E PHE* 3.8 5.5 + - - -
142E LEU* 3.9 31.4 - - + +
143E CYS* 4.0 12.3 - - - -
145E ARG* 3.4 24.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 48 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14E PRO* 5.8 1.7 - - - +
15E CYS 2.9 13.4 + - - -
16E ARG* 3.3 21.3 + - - -
17E VAL* 2.9 29.8 + - - +
46E GLU 3.9 2.2 + - - -
47E ILE* 1.3 75.0 - - - +
49E PHE* 1.3 59.9 + - - +
56F ARG* 4.0 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 49 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17E VAL* 3.2 11.7 - - + +
19E VAL* 4.0 15.7 - - + -
34E PHE* 3.6 29.2 - + - -
35E ARG* 3.9 1.1 - - - -
39E GLN* 3.7 35.4 - - + -
42E LEU* 4.2 18.6 - - + -
43E ALA* 6.0 1.8 - - + -
47E ILE* 4.0 10.8 - - + +
48E SER* 1.3 80.2 - - - +
50E THR* 1.3 69.6 + - - +
51E LEU* 4.0 9.0 - - + -
55F GLU* 3.5 42.1 - - + +
56F ARG* 3.2 21.1 + - - +
59F HIS* 3.7 3.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 50 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E ARG* 6.4 0.2 - - + -
17E VAL 3.1 5.5 + - - -
18E LEU* 3.8 10.7 - - - +
19E VAL* 3.0 23.2 + - - -
49E PHE* 1.3 76.1 - - - +
51E LEU* 1.3 62.9 + - - +
72E TRP* 3.4 37.1 - - + -
52F MET* 4.1 15.4 - - - +
53F LEU 4.3 3.4 - - - -
55F GLU* 5.5 0.4 - - - -
56F ARG* 5.0 0.9 - - - +
59F HIS* 2.9 38.4 - - + +
63F LEU* 4.0 10.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 51 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E VAL* 3.4 28.0 - - + -
21E LEU* 3.7 30.3 - - + -
31E LEU* 4.2 10.8 - - + -
34E PHE* 3.8 28.3 - - + -
35E ARG* 3.9 24.7 - - - +
49E PHE* 4.0 15.3 - - + -
50E THR* 1.3 76.0 - - - +
52E MET* 1.3 59.9 + - - +
53E LEU* 4.2 3.6 - - + -
52F MET* 3.3 8.0 - - - +
53F LEU* 3.1 47.6 + - + -
55F GLU* 4.1 4.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 52 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18E LEU* 3.7 19.7 - - + -
19E VAL 2.8 9.2 + - - +
20E LEU* 3.4 28.8 - - + +
21E LEU 3.1 22.7 + - - -
51E LEU* 1.3 74.5 - - - +
53E LEU* 1.3 67.1 + - - +
54E THR* 4.4 0.2 - - - +
63E LEU* 3.5 45.3 - - + -
67E GLU* 3.9 17.0 - - - +
71E ARG* 5.5 0.4 - - - +
50F THR* 4.4 4.3 - - - +
51F LEU 3.5 11.4 - - - +
52F MET* 2.7 40.6 - - + -
71F ARG* 4.9 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 53 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E LEU* 3.3 31.4 - - + +
23E PRO* 4.2 14.8 - - + -
31E LEU* 4.5 12.3 - - + -
51E LEU* 4.7 10.1 - - + -
52E MET* 1.3 85.9 - - - +
54E THR* 1.3 62.2 + - - +
55E GLU* 5.8 0.9 - - + -
59E HIS* 3.6 15.4 - - - -
31F LEU* 4.2 29.6 - - + -
35F ARG* 3.9 22.7 - - - +
51F LEU* 3.1 32.5 + - + +
53F LEU* 4.8 12.1 - - + -
----------------------------------------------------------
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