Contacts of the strand formed by residues 10 - 15 (chain E) in PDB entry 4FAO
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 GLU 10 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E ARG* 1.3 84.2 - - - +
11E CYS* 1.3 68.7 + - - +
28E LEU* 5.2 8.7 - - + +
29E GLU 3.4 8.3 - - - +
30E ARG* 3.7 30.6 + - + +
41E CYS* 3.7 1.2 - - - -
89E ASN* 3.5 22.1 + - - +
90E PHE* 3.2 56.0 + - + -
59J GLU* 5.6 8.0 - - - +
60J GLY* 5.6 5.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 11 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E ARG* 5.1 0.7 - - - -
10E GLU* 1.3 75.3 - - - +
12E ILE* 1.3 60.8 + - - +
28E LEU* 3.2 9.2 - - - +
29E GLU* 2.9 30.2 + - + +
31E CYS* 3.7 12.1 - - - -
40E HIS 3.4 9.9 - - - -
41E CYS* 2.0 57.2 - - + -
58E GLY* 3.9 12.6 - - - -
59E CYS* 3.8 12.6 - - - -
90E PHE* 3.7 9.6 - - - +
92E ASN* 4.2 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 12 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E CYS* 1.3 73.1 - - - +
13E TYR* 1.3 67.7 + - - +
14E TYR* 5.0 1.8 - - + -
27E GLY 3.8 10.8 - - - +
28E LEU* 5.0 0.7 - - + -
29E GLU 5.0 0.2 - - - -
57E LYS* 3.2 31.0 - - + +
58E GLY* 3.1 25.0 + - - -
90E PHE* 3.8 12.5 - - + -
92E ASN* 3.0 25.1 + - - +
93E GLU* 3.8 25.4 - - + +
67H THR* 3.6 37.7 - - + +
68H LYS* 6.1 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 13 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A LEU* 6.4 1.8 - - + -
11E CYS 3.6 2.2 + - - -
12E ILE* 1.3 76.5 - - - +
14E TYR* 1.3 66.6 + - - +
15E ASN* 3.9 19.2 + - + +
23E THR* 3.1 23.4 + - - +
24E ASN* 3.5 35.9 - - + -
25E GLN 4.4 3.8 - - - -
26E SER* 3.4 1.8 - - - -
27E GLY* 2.9 46.7 + - - +
28E LEU 3.8 15.5 - - - +
29E GLU* 4.1 30.7 - - + +
42E TYR* 5.6 3.4 - - - -
56E LYS* 6.0 0.2 - - - -
57E LYS 3.4 13.7 - - - -
58E GLY* 4.4 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 14 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E ILE* 5.0 1.3 - - + -
13E TYR* 1.3 81.0 - - - +
15E ASN* 1.3 73.3 + - - +
16E ALA* 3.2 38.6 - - + +
25E GLN* 3.2 35.0 + - + -
26E SER* 3.8 17.3 - - - -
42E TYR* 5.1 0.2 + - - -
54E LEU* 4.0 36.2 + - + +
56E LYS* 3.2 12.4 - - - +
57E LYS* 2.7 51.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 15 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13E TYR* 3.9 16.7 + - + +
14E TYR* 1.3 79.5 - - - +
16E ALA* 1.3 63.8 + - - +
17E ASN* 3.0 10.2 + - - -
18E TRP* 2.9 31.2 + - - +
21E GLU* 3.1 21.0 + - - -
23E THR* 3.2 24.9 + - - +
24E ASN 4.0 8.3 - - - +
25E GLN 2.9 11.8 + - - +
55E VAL 4.0 2.7 - - - -
56E LYS* 2.8 31.0 + - + +
----------------------------------------------------------
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