Contacts of the strand formed by residues 3 - 8 (chain A) in PDB entry 5HKE
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 3 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A OCS 1.3 73.6 - - - +
4A ALA* 1.3 62.6 + - - +
5A ILE* 4.0 14.1 - - + -
16A ARG* 3.1 5.0 - - - +
17A ASN* 2.8 42.1 + - - +
19A ASP* 4.6 1.0 + - - -
78A LEU* 4.1 0.9 - - - -
168A ILE* 5.1 1.1 - - + -
169A LEU 3.4 9.2 - - - +
170A THR* 3.8 7.5 - - + +
224A ARG* 3.1 22.0 + - - +
228A ALA* 3.9 27.6 - - + -
252A LEU* 4.1 4.3 - - + +
255A VAL* 3.6 26.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 4 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A THR* 1.3 73.8 - - - +
5A ILE* 1.3 67.8 + - - +
14A PHE* 5.2 1.1 - - + -
15A GLY 3.3 10.3 - - - +
16A ARG* 3.9 9.2 - - + -
76A ALA* 4.7 4.7 - - + -
78A LEU* 3.7 25.9 - - + +
142A LEU* 3.7 23.4 - - + +
168A ILE* 3.5 1.0 - - - -
169A LEU* 2.8 36.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 5 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A THR* 4.0 16.8 - - + -
4A ALA* 1.3 80.8 - - - +
6A THR* 1.3 71.1 + - - +
7A LEU* 5.4 0.4 - - + -
14A PHE* 3.4 4.3 - - - -
15A GLY 2.9 31.9 + - - +
142A LEU* 4.6 2.2 - - - -
167A GLY 3.1 10.8 - - - +
168A ILE* 3.7 19.3 - - + -
228A ALA* 4.8 4.3 - - + -
232A LYS* 4.7 3.1 - - + -
248A PHE* 3.4 35.4 - - + -
251A ILE* 3.6 36.8 - - + -
252A LEU* 4.0 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 6 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE* 1.3 82.5 - - - +
7A LEU* 1.3 64.7 + - - +
8A ASN* 4.8 8.2 + - - -
13A TYR 3.2 13.5 - - - +
14A PHE* 4.3 4.7 - - + -
142A LEU* 4.5 4.0 - - + -
144A ALA* 3.7 30.7 - - + -
145A ASP 5.6 2.2 - - - +
148A LYS 5.6 1.1 - - - +
149A SER* 4.3 13.7 + - - +
167A GLY* 3.0 22.7 + - - -
232A LYS* 2.8 33.3 + - - +
248A PHE* 4.4 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 7 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE* 5.4 0.7 - - + -
6A THR* 1.3 75.5 - - - +
8A ASN* 1.3 74.6 + - - +
9A GLY* 6.0 0.2 - - - -
12A ASN* 3.6 0.7 - - - -
13A TYR* 2.8 48.4 + - + +
232A LYS* 4.1 29.6 - - + +
235A SER* 4.3 8.7 - - - +
244A ASP* 4.1 22.2 - - + +
247A GLN* 5.1 4.9 - - + -
248A PHE* 3.8 30.1 - - + +
251A ILE* 4.2 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 8 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A THR* 4.8 8.7 + - - -
7A LEU* 1.3 90.1 + - - +
9A GLY* 1.3 59.1 + - - +
12A ASN* 2.7 31.7 + - - +
13A TYR 5.5 0.8 + - - -
145A ASP 5.3 0.8 + - - -
146A ARG* 3.3 17.6 + - - +
147A GLU 5.2 6.5 + - - +
232A LYS* 5.4 2.8 + - - +
237A LYS* 4.0 19.1 + - - +
----------------------------------------------------------
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