Contacts of the helix formed by residues 19 - 30 (chain B) in PDB entry 1D7K
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 19 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B LEU* 3.7 16.4 - - - +
17B GLY 5.3 2.2 - - - +
18B PHE* 1.3 76.0 - - - +
20B ALA* 1.3 63.6 + - - +
21B LYS* 3.4 13.2 + - + +
22B ASP* 2.8 33.4 + - - +
23B ILE* 3.3 15.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 20 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B LEU* 3.8 5.3 - - + +
19B THR* 1.3 74.2 - - - +
21B LYS* 1.3 61.5 + - + +
23B ILE* 3.1 9.7 + - - +
24B LEU* 3.4 11.1 + - - +
42B VAL* 3.7 23.0 - - + +
44B ASP* 3.8 37.8 + - + +
408B VAL* 4.1 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 21 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B THR* 3.3 10.9 + - + +
20B ALA* 1.3 73.6 - - + +
22B ASP* 1.3 66.5 + - - +
24B LEU* 3.2 24.5 + - + +
25B ASP* 3.3 20.2 + - - +
285B THR* 5.9 3.4 - - + +
341B GLN* 5.7 8.1 - - - +
384B GLU* 4.2 19.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 22 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B GLY 4.0 4.0 - - - +
18B PHE* 3.3 27.9 - - + -
19B THR* 2.8 38.8 + - - +
21B LYS* 1.3 77.0 - - - +
23B ILE* 1.3 66.5 + - - +
25B ASP* 3.4 12.7 + - - +
26B GLN* 3.1 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 23 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B HIS* 6.6 0.2 - - + -
14B LEU* 3.4 34.5 - - + -
18B PHE* 4.4 15.7 - - + -
19B THR 3.3 1.5 + - - +
20B ALA 3.1 10.4 + - - +
22B ASP* 1.3 80.0 - - - +
24B LEU* 1.3 62.8 + - - +
26B GLN* 3.2 23.7 + - + +
27B LYS* 3.1 42.2 + - + +
42B VAL* 4.1 20.9 - - + -
406B TYR* 5.5 2.2 - - + -
408B VAL* 4.5 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ALA 3.4 8.2 + - - +
21B LYS* 3.2 17.0 + - + +
23B ILE* 1.3 79.7 - - - +
25B ASP* 1.3 64.3 + - - +
27B LYS* 3.4 3.3 + - - +
28B ILE* 3.0 31.5 + - + +
40B PHE* 3.2 37.4 - - + -
42B VAL* 3.3 25.5 - - + +
285B THR* 3.6 35.9 - - + +
287B ALA* 4.1 7.9 - - + -
382B LEU* 4.3 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 25 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B LYS* 3.3 16.5 + - - +
22B ASP* 3.4 12.9 + - - +
24B LEU* 1.3 76.6 - - - +
26B GLN* 1.3 56.8 + - - +
28B ILE* 3.2 11.6 + - - +
29B ASN* 3.0 41.2 + - - +
341B GLN* 3.8 28.8 - - - +
382B LEU* 5.8 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ASP* 5.7 0.8 + - - -
18B PHE* 3.3 33.4 - - - -
22B ASP 3.1 13.0 + - - +
23B ILE* 3.2 24.0 + - + +
25B ASP* 1.3 76.7 - - - +
27B LYS* 1.3 61.2 + - + +
29B ASN* 3.4 8.3 + - + +
30B GLU* 3.0 40.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ILE* 3.1 34.5 + - + +
24B LEU 3.8 0.7 - - - +
26B GLN* 1.3 81.5 - - - +
28B ILE* 1.4 64.4 + - - +
30B GLU* 3.7 17.3 + - + +
31B VAL* 3.9 11.1 - - - +
40B PHE* 3.7 27.1 - - + -
42B VAL* 5.2 0.4 - - + -
406B TYR* 3.7 57.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU* 3.0 23.7 + - + +
25B ASP* 3.6 14.6 - - - +
26B GLN 3.2 0.2 - - - -
27B LYS* 1.4 80.1 - - - +
29B ASN* 1.3 70.7 + - - +
31B VAL* 3.2 19.1 + - - +
32B SER* 3.3 14.4 + - - +
37B LYS* 5.7 0.3 + - - -
40B PHE* 3.8 18.6 - - + -
287B ALA* 5.0 2.9 - - + -
380B TRP* 3.7 50.8 + - + +
382B LEU* 5.8 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ASP* 3.0 30.5 + - - +
26B GLN* 3.7 8.3 - - + +
28B ILE* 1.3 83.7 - - - +
30B GLU* 1.3 61.4 + - - +
32B SER* 3.0 28.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B GLN* 3.0 26.3 + - + +
27B LYS* 3.7 14.6 - - - +
28B ILE 3.4 0.2 - - - -
29B ASN* 1.3 74.2 - - - +
31B VAL* 1.3 60.6 + - + +
32B SER 3.3 0.8 + - - -
33B SER 5.1 0.9 + - - -
34B SER* 5.5 3.3 - - - -
----------------------------------------------------------
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