Contacts of the helix formed by residues 36 - 45 (chain B) in PDB entry 1KFV
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 GLY 36 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B VAL* 3.0 12.1 + - - -
34B LEU 3.3 2.6 + - - -
35B THR* 1.3 81.2 - - - +
37B PHE* 1.3 61.0 + - - -
38B GLU* 3.2 3.8 - - - -
39B GLN* 3.3 6.4 + - - -
40B LEU* 2.9 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 37 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ILE* 2.9 51.4 - - + -
26B GLU* 4.1 0.2 - - - -
27B ALA* 3.5 39.9 - - + -
30B PRO* 3.8 32.4 + - + +
33B VAL* 3.4 26.5 + - + +
36B GLY* 1.3 69.1 - - - +
38B GLU* 1.3 67.6 + - - +
40B LEU* 3.0 8.8 + - + +
41B LYS* 2.6 58.8 + - + +
94B LEU* 4.4 1.8 - - + -
114B TRP* 5.8 0.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 38 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B GLY* 3.2 1.8 - - - -
37B PHE* 1.3 89.0 - - - +
39B GLN* 1.3 63.7 + - - +
41B LYS* 2.9 48.2 + - - +
42B LYS* 3.0 15.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 39 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B THR* 2.8 27.7 - - - +
36B GLY* 3.3 9.2 + - - +
38B GLU* 1.3 80.5 - - - +
40B LEU* 1.3 61.1 - - - +
41B LYS 3.4 0.2 + - - -
42B LYS* 3.4 19.9 + - - +
43B GLU* 3.0 44.7 + - - +
67B PHE* 5.3 2.6 - - - -
116B LEU* 3.3 31.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 40 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ILE* 3.8 18.4 - - + -
33B VAL* 3.9 20.2 - - + -
36B GLY 2.9 15.3 + - - +
37B PHE* 3.0 14.6 + - + +
39B GLN* 1.3 77.3 - - - +
41B LYS* 1.3 60.9 + - - +
43B GLU 4.0 0.2 - - - -
44B LEU* 3.2 41.8 + - + +
69B LEU* 3.5 31.0 - - + -
114B TRP* 3.9 17.7 - - + -
116B LEU* 3.6 28.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 41 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B SER* 5.9 2.2 - - - -
25B ILE* 3.5 27.6 - - + +
37B PHE* 2.6 41.8 + - + +
38B GLU* 2.9 27.8 + - - +
40B LEU* 1.3 73.1 - - - +
42B LYS* 1.3 66.6 + - - +
43B GLU 3.1 3.1 + - - -
45B THR* 2.4 44.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B GLU 3.0 10.2 + - - +
39B GLN* 3.4 15.4 + - - +
41B LYS* 1.3 78.4 - - - +
43B GLU* 1.3 82.8 + - - +
45B THR* 4.8 5.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 43 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B GLN* 3.0 44.4 + - - +
40B LEU 4.4 0.2 - - - +
41B LYS 3.1 0.4 - - - -
42B LYS* 1.3 100.8 + - - +
44B LEU* 1.3 59.5 + - + +
45B THR 3.5 1.9 + - - +
47B LYS* 2.6 37.2 + - - +
67B PHE* 3.0 42.0 - - + -
116B LEU* 3.3 15.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 44 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ILE* 3.3 13.5 - - + +
25B ILE* 3.4 15.5 - - + -
40B LEU* 3.2 41.0 + - + +
43B GLU* 1.3 79.1 - - - +
45B THR* 1.3 62.0 + - - +
47B LYS* 3.0 26.5 + - + +
63B ILE* 3.3 43.5 - - + +
67B PHE* 4.9 6.1 - - + +
69B LEU* 4.5 8.7 - - + -
96B MSE 4.0 20.2 - - + -
116B LEU* 4.4 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 45 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ILE* 3.8 7.2 - - - -
23B ILE 2.8 27.8 - - - +
24B SER* 3.6 14.2 - - - -
25B ILE* 4.4 3.1 + - - +
41B LYS* 2.4 44.4 + - + +
42B LYS 5.1 4.1 - - - +
43B GLU 3.5 3.2 - - - +
44B LEU* 1.3 77.3 - - - +
46B GLY* 1.3 62.5 + - - +
47B LYS* 4.1 6.2 - - - +
----------------------------------------------------------
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