Contacts of the helix formed by residues 26 - 40 (chain A) in PDB entry 5JKC
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 ASP 26 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A VAL 3.1 9.2 + - - +
24A ILE 3.0 2.5 - - - +
25A CYS* 1.3 76.9 - - - +
27A PRO* 1.3 72.7 - - - +
28A SER* 2.8 36.3 + - - -
29A VAL* 3.0 22.0 + - + +
30A VAL* 3.3 12.5 + - - +
83A LEU* 4.2 8.9 - - + +
84A GLN* 2.8 28.4 + - - +
87A SER* 3.2 32.0 + - - +
91A LEU* 4.3 1.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A CYS 3.8 7.4 - - - +
26A ASP* 1.3 89.6 - - - +
28A SER* 1.3 60.4 + - - +
30A VAL* 3.3 11.1 + - + +
31A LEU* 3.0 42.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ASP* 2.8 17.6 + - - -
27A PRO* 1.3 77.8 - - - +
29A VAL* 1.3 51.9 + - - +
31A LEU* 3.4 8.9 + - - +
32A ALA* 2.8 35.2 + - - +
91A LEU* 3.7 20.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A VAL* 3.5 44.6 - - + +
24A ILE* 4.3 8.5 - - + -
26A ASP* 3.0 21.8 + - - +
28A SER* 1.3 74.9 - - - +
30A VAL* 1.3 61.7 + - - +
32A ALA* 3.1 6.8 + - + +
33A LEU* 2.8 46.3 + - + +
87A SER* 3.9 14.8 - - - -
90A LEU* 4.1 14.4 - - + -
91A LEU* 4.1 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ILE* 3.4 30.3 - - + +
26A ASP 3.4 8.5 - - - +
27A PRO* 3.3 11.4 + - + +
29A VAL* 1.3 79.7 - - + +
31A LEU* 1.3 68.4 + - + +
33A LEU* 3.2 10.0 + - + +
34A LYS* 2.9 30.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A PRO* 3.0 30.0 + - + +
28A SER* 3.9 6.3 - - - +
30A VAL* 1.3 85.4 - - + +
32A ALA* 1.3 54.0 + - - +
34A LYS* 3.1 17.3 + - + +
35A SER* 2.7 36.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A SER 2.8 21.6 + - - +
29A VAL* 3.5 5.2 - - - +
31A LEU* 1.3 72.2 - - - +
33A LEU* 1.3 58.1 + - - +
35A SER* 3.2 7.4 + - - -
36A LEU* 2.8 28.8 + - - +
91A LEU* 3.5 23.6 - - + -
94A LEU* 4.0 20.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ILE* 4.6 7.6 - - + -
29A VAL* 2.8 35.4 + - + +
30A VAL* 3.6 7.4 - - + +
32A ALA* 1.3 75.3 - - - +
34A LYS* 1.3 63.9 + - - +
36A LEU* 3.4 14.5 + - + +
37A GLU* 3.1 20.8 + - - +
54A MET* 4.4 12.1 - - + +
57A VAL* 4.5 19.7 - - + -
58A GLU* 6.5 0.2 - - - -
61A VAL* 4.2 24.9 - - + -
90A LEU* 5.8 5.6 - - + -
94A LEU* 4.2 20.4 - - + -
111A LEU* 6.2 1.1 - - + -
115A LEU* 5.8 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A VAL* 2.9 20.1 + - + +
31A LEU* 3.7 16.6 - - + +
33A LEU* 1.3 76.6 - - - +
35A SER* 1.3 63.6 + - - +
37A GLU* 3.1 10.3 + - - +
38A LYS* 3.0 40.9 + - + +
54A MET* 5.9 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LEU 2.7 17.2 + - - -
32A ALA* 3.6 7.6 - - - -
34A LYS* 1.3 75.1 - - - +
36A LEU* 1.3 60.0 + - - +
38A LYS* 5.2 0.9 - - - -
39A ASP* 2.6 60.1 + - - +
40A TYR* 3.3 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ALA 2.8 13.9 + - - +
33A LEU* 3.4 23.8 - - + +
35A SER* 1.3 75.6 - - - +
37A GLU* 1.3 62.8 + - - +
40A TYR* 3.0 25.8 + - + +
41A LEU* 3.0 31.6 + - + +
53A MET* 6.0 0.7 - - + -
54A MET* 5.1 9.4 - - + -
57A VAL* 5.2 4.9 - - + -
94A LEU* 4.3 17.3 - - + -
98A THR* 3.6 30.5 - - + -
107A PHE* 4.4 9.0 - - + -
111A LEU* 4.4 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU 3.1 8.9 + - - +
34A LYS* 3.1 13.8 + - - +
36A LEU* 1.3 79.7 - - - +
38A LYS* 1.3 83.3 + - + +
41A LEU* 3.4 27.4 - - + +
42A PRO* 3.8 2.8 - - - +
50A HIS* 5.2 4.5 + - + +
51A LYS* 5.9 1.0 - - - -
54A MET* 3.5 51.8 - - + +
58A GLU* 5.0 4.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LYS* 3.0 31.8 + - + +
35A SER* 5.2 0.2 - - - -
37A GLU* 1.3 106.6 - - + +
39A ASP* 1.3 69.4 + - - +
42A PRO* 3.2 22.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A SER* 2.6 45.9 + - - +
38A LYS* 1.3 81.8 - - - +
40A TYR* 1.3 60.1 + - + +
42A PRO* 3.9 4.4 - - - +
43A GLY 4.9 2.4 + - - -
44A HIS* 5.0 3.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A SER 3.3 1.0 + - - +
36A LEU* 3.0 28.1 + - + +
39A ASP* 1.3 80.6 - - + +
41A LEU* 1.3 65.2 - - - +
42A PRO 3.4 0.7 - - - -
43A GLY 3.5 1.2 + - - -
44A HIS* 2.7 67.8 + + + +
97A ILE* 3.8 3.9 + - + -
98A THR* 3.4 43.9 + - + -
101A ASP* 3.1 6.9 + - - -
102A VAL* 2.6 38.7 + - - +
107A PHE* 3.8 35.4 - + - -
----------------------------------------------------------
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