Contacts of the strand formed by residues 15 - 23 (chain E) in PDB entry 1S5E
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 THR 15 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E CYS* 2.8 27.4 + - - +
10E ALA* 4.9 0.7 - - - -
12E TYR* 2.8 31.8 + - + -
13E HIS 3.6 4.9 - - - +
14E ASN* 1.3 78.8 - - - +
16E GLN* 1.3 65.9 + - - +
86E CYS* 4.5 3.8 - - - -
87E VAL 3.1 12.8 - - - +
88E TRP* 3.5 35.0 - - + +
89E ASN* 3.7 8.5 + - - +
97E ALA* 5.4 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 16 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E CYS* 3.7 4.2 - - - -
15E THR* 1.3 77.7 - - - +
17E ILE* 1.3 67.4 + - - +
18E HIS* 3.4 25.6 + - + +
85E LEU 3.7 0.2 - - - +
86E CYS* 3.6 1.7 - - - -
87E VAL* 3.0 44.1 + - + +
89E ASN* 2.8 38.4 - - - +
94E HIS* 4.0 7.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 17 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5E ILE* 3.9 21.3 - - + +
6E THR* 4.1 21.5 - - + +
9E CYS* 3.7 31.6 - - + -
16E GLN* 1.3 80.7 - - - +
18E HIS* 1.3 76.1 + - - +
19E THR* 4.0 5.8 + - - +
84E LYS* 3.9 27.6 - - + -
85E LEU 3.4 2.2 - - - +
86E CYS* 3.9 14.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 18 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E GLN* 3.4 19.5 + - + -
17E ILE* 1.3 77.1 + - - +
19E THR* 1.3 61.8 + - - +
20E LEU* 3.6 22.8 + - + +
46E ALA* 5.6 2.9 - - + +
48E PHE* 3.6 30.1 - + + -
84E LYS* 3.3 5.0 - - - +
85E LEU* 2.9 34.0 + - + +
87E VAL* 3.6 19.7 - - + +
94E HIS* 3.1 30.6 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 19 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17E ILE* 4.0 6.0 + - - +
18E HIS* 1.3 72.3 - - - +
20E LEU* 1.3 62.9 + - - +
21E ASN* 3.6 26.0 - - - +
83E GLU* 3.7 7.4 - - + +
84E LYS* 3.5 32.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 20 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18E HIS* 3.6 28.2 + - + +
19E THR* 1.3 79.4 - - - +
21E ASN* 1.3 73.3 + - - +
22E ASP* 3.1 11.4 + - + +
42E PHE* 3.9 42.4 - - + -
44E ASN* 5.0 8.5 - - - +
46E ALA* 4.9 6.7 - - + -
48E PHE* 4.5 6.5 - - + -
82E VAL* 3.9 12.1 - - + +
83E GLU 2.9 5.8 + - - +
85E LEU* 3.8 32.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 21 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E THR* 3.6 24.4 - - - +
20E LEU* 1.3 76.8 - - - +
22E ASP* 1.3 56.6 - - - +
81E LYS* 4.6 8.3 - - - +
82E VAL 2.9 16.5 + - - -
83E GLU* 3.2 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 22 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E LEU* 3.2 11.3 - - + +
21E ASN* 1.3 77.9 - - - +
23E LYS* 1.3 92.0 + - - +
42E PHE* 3.6 13.5 - - + +
43E LYS* 3.1 49.6 + - - +
81E LYS* 3.9 4.7 - - - -
82E VAL* 2.9 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 23 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A ASP* 5.9 4.8 + - - +
216A SER* 4.4 7.4 + - - +
22E ASP* 1.3 100.4 + - - +
24E ILE* 1.3 71.4 + - - +
25E PHE* 3.6 2.7 + - - +
42E PHE* 3.3 13.2 - - - +
43E LYS* 5.2 2.9 + - - +
79E GLU* 3.8 51.8 - - + +
80E ALA 3.6 17.9 - - - +
81E LYS* 4.1 3.1 - - - +
----------------------------------------------------------
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