Contacts of the helix formed by residues 16 - 28 (chain T) in PDB entry 2KFX
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 GLN 16 (chain T).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12T LEU* 3.7 42.2 - - + +
13T THR* 4.0 22.1 - - - +
15T GLU* 1.3 77.5 - - - +
17T LYS* 1.3 92.6 + - - +
19T GLU* 3.3 17.5 - - + +
20T PHE* 2.9 51.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 17 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13T THR 4.4 6.1 - - - +
14T GLU* 3.4 22.2 - - + +
15T GLU 3.1 0.2 - - - -
16T GLN* 1.3 90.1 + - - +
18T ASN* 1.3 61.0 + - - +
19T GLU 2.9 10.5 + - - -
20T PHE* 3.0 15.8 + - + +
21T LYS* 3.1 42.5 + - + +
74T PHE* 4.0 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 18 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14T GLU* 2.6 31.5 + - - +
15T GLU* 4.1 9.4 - - - +
16T GLN 3.5 0.4 - - - -
17T LYS* 1.3 75.5 - - - +
19T GLU* 1.3 66.1 + - - +
21T LYS* 3.9 26.4 + - - +
22T ALA* 3.2 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 19 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15T GLU 3.3 19.3 - - - +
16T GLN* 3.3 17.5 - - + +
17T LYS 2.9 0.6 - - - -
18T ASN* 1.3 86.1 - - - +
20T PHE* 1.3 69.0 + - + +
22T ALA* 3.6 5.2 - - - +
23T ALA* 3.6 12.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 20 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12T LEU* 6.1 0.7 - - + -
16T GLN* 2.9 50.9 - - + -
17T LYS* 3.0 7.7 + - - +
19T GLU* 1.3 77.0 - - + +
21T LYS* 1.3 57.2 + - - +
22T ALA 2.9 1.8 - - - -
23T ALA* 2.5 37.4 + - + +
24T PHE* 3.3 10.2 + - + -
74T PHE* 5.0 7.6 - - + -
77T PHE* 3.8 32.1 - + + -
78T LEU* 6.0 4.5 - - + -
81T MET* 4.3 24.0 - - + -
85T MET* 5.8 7.0 - - + -
91T WW7 4.3 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 21 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17T LYS* 3.1 41.6 + - + +
18T ASN* 3.9 33.9 + - - +
20T PHE* 1.3 75.8 - - - +
22T ALA* 1.3 60.9 + - - +
23T ALA 3.3 0.7 + - - -
24T PHE* 3.4 19.1 + - - +
25T ASP* 3.2 20.5 - - - +
74T PHE* 4.4 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 22 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18T ASN 3.2 20.3 + - - +
19T GLU* 3.6 8.5 - - - +
20T PHE 2.9 0.8 - - - -
21T LYS* 1.3 78.9 - - - +
23T ALA* 1.3 62.9 + - - +
25T ASP* 3.4 21.0 - - - +
26T ILE* 3.4 17.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 23 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19T GLU 3.6 5.9 + - - +
20T PHE* 2.5 25.1 + - - +
22T ALA* 1.3 70.3 - - - +
24T PHE* 1.3 66.0 + - - +
26T ILE* 2.8 23.4 + - - +
27T PHE* 3.1 16.0 + - + -
91T WW7 3.2 37.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 24 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20T PHE 3.4 20.2 - - - -
21T LYS* 3.4 11.6 + - - +
23T ALA* 1.3 77.8 - - - +
25T ASP* 1.3 67.8 + - - +
27T PHE* 2.8 10.9 + - - -
28T VAL* 2.7 33.3 + - + +
34T GLY 5.1 5.6 - - - -
36T ILE* 4.2 13.2 - - + -
72T VAL 3.8 15.0 - - - -
73T ASP* 4.7 0.2 - - - -
74T PHE* 3.7 46.9 - + + -
77T PHE* 3.5 42.8 - + - -
91T WW7 3.9 13.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 25 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21T LYS 3.2 17.8 - - - +
22T ALA* 3.4 16.7 - - - +
24T PHE* 1.3 73.9 - - - +
26T ILE* 1.3 61.6 + - + +
28T VAL* 2.8 7.7 - - - -
29T LEU* 2.6 41.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 26 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22T ALA 3.4 15.5 - - - +
23T ALA* 2.8 20.4 + - - +
25T ASP* 1.3 73.2 - - + +
27T PHE* 1.3 63.9 + - + +
28T VAL 3.0 5.3 + - - -
29T LEU* 3.4 28.4 - - + +
40T GLU* 5.8 0.2 - - - +
43T LYS* 4.9 10.5 - - + +
44T VAL* 3.8 23.2 - - + +
47T MET* 4.1 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 27 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23T ALA* 3.1 26.6 + - + -
24T PHE 2.8 9.7 + - - +
26T ILE* 1.3 74.7 - - + +
28T VAL* 1.3 65.3 + - - +
36T ILE* 3.7 34.4 - - + +
40T GLU* 2.8 41.8 - - - +
41T LEU* 3.9 22.7 - - + -
44T VAL* 3.1 47.8 - - + -
45T MET* 5.3 0.9 - - + -
91T WW7 3.2 63.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 28 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24T PHE* 2.7 31.8 + - + +
25T ASP* 2.8 10.4 - - - +
26T ILE 3.0 0.8 - - - -
27T PHE* 1.3 91.5 - - + +
29T LEU* 1.3 55.5 + - - +
30T GLY 3.2 9.2 + - - +
31T ALA* 3.7 26.3 + - + +
34T GLY* 3.8 27.6 - - - +
35T SER 3.7 25.4 - - - +
36T ILE* 4.1 6.5 - - + -
40T GLU* 4.9 5.2 - - + -
----------------------------------------------------------
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