Contacts of the strand formed by residues 27 - 31 (chain K) in PDB entry 1DM0
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 LYS 27 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4K CYS* 4.4 9.4 + - - -
5K VAL* 4.1 14.8 - - + +
22K VAL 4.0 0.9 - - - +
23K LYS* 3.6 5.9 - - - +
24K VAL 3.2 28.4 + - - +
25K GLY 3.4 0.6 - - - -
26K ASP* 1.3 113.1 + - - +
28K GLU* 1.3 60.4 + - - +
29K LEU* 3.9 20.8 + - + +
57K CYS* 4.0 23.8 + - - +
58K HIS* 3.7 28.5 - - - +
59K ASN* 3.6 10.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 28 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11K TYR* 2.3 37.2 + - + +
13K LYS* 3.3 22.3 + - - +
21K THR* 4.0 19.3 - - + +
22K VAL 3.5 4.7 - - - -
23K LYS* 4.2 8.0 - - + +
27K LYS* 1.3 72.9 - - - +
29K LEU* 1.3 58.8 + - - +
59K ASN* 3.1 16.4 + - + +
60K GLY* 2.9 23.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 29 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4K CYS* 4.4 10.5 - - - -
5K VAL* 4.4 13.5 - - + -
21K THR* 3.4 4.8 - - - +
22K VAL* 2.8 31.1 + - + +
24K VAL* 6.3 0.4 - - + -
27K LYS* 3.9 14.8 - - + +
28K GLU* 1.3 72.6 - - - +
30K PHE* 1.3 60.7 + - - +
52K ILE* 3.8 37.7 - - + -
54K THR* 4.6 4.0 - - + -
56K ALA 3.9 8.7 - - - +
58K HIS 2.9 41.1 - - - +
60K GLY 4.4 0.7 - - - +
61K GLY* 3.4 16.2 - - - +
63K PHE* 3.8 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 30 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15K ASN* 4.7 0.2 - - - +
19K THR* 3.7 33.9 - - + +
20K PHE 3.0 15.9 - - - +
21K THR* 3.5 14.8 - - - +
29K LEU* 1.3 76.3 - - - +
31K THR* 1.3 67.2 + - - +
32K ASN* 4.8 7.2 - - + -
60K GLY* 3.2 26.2 - - - -
61K GLY 3.1 15.8 + - - -
62K GLY* 3.2 13.3 - - - -
63K PHE* 3.1 26.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 31 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19K THR* 3.4 4.9 - - - -
20K PHE* 2.9 38.6 + - + +
30K PHE* 1.3 77.4 - - - +
32K ASN* 1.3 67.6 + - - +
33K ARG* 3.0 28.2 - - - +
36K LEU* 3.7 14.9 - - + +
40K LEU* 4.4 9.0 - - + -
63K PHE* 2.9 50.2 + - + -
----------------------------------------------------------
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