Contacts of the helix formed by residues 24 - 37 (chain B) in PDB entry 1LJF
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 SER 24 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ASP* 4.6 0.4 - - - -
19B ASN* 3.5 18.8 + - - -
22B GLY 3.6 4.6 + - - -
23B TYR* 1.3 76.7 - - - +
25B LEU* 1.3 67.0 + - - +
26B GLY* 3.9 6.7 + - - -
27B ASN* 2.9 36.3 + - - +
28B TRP* 3.5 3.7 - - - -
120B VAL* 3.9 10.0 - - - +
121B GLN* 5.0 10.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 25 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ALA* 3.7 28.3 - - + +
12B MET* 3.8 23.1 - - + -
13B LYS* 4.1 19.5 - - + +
17B LEU 5.0 1.6 - - - -
18B ASP* 2.9 34.7 + - + +
23B TYR 3.9 0.4 + - - -
24B SER* 1.3 72.8 - - - +
26B GLY* 1.3 63.2 + - - +
28B TRP* 3.1 18.8 + - + +
29B VAL* 3.2 16.1 + - + +
124B ILE* 4.1 25.8 - - + -
129B LEU* 3.8 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B SER* 3.1 6.2 + - - -
25B LEU* 1.3 79.7 - - - +
27B ASN* 1.3 55.7 + - - +
29B VAL* 3.5 0.4 + - - -
30B CYS* 3.0 31.0 + - - +
120B VAL* 3.3 31.1 - - - +
121B GLN* 4.8 3.9 - - - +
123B TRP* 3.9 4.3 - - - +
124B ILE* 4.1 18.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B GLY 5.4 0.2 + - - -
23B TYR* 4.1 15.9 - - + +
24B SER* 2.9 41.2 + - - +
26B GLY* 1.3 77.3 - - - +
28B TRP* 1.3 57.9 + - - +
30B CYS* 3.4 2.6 + - - +
31B ALA* 2.9 28.9 + - - +
105B MET* 3.7 19.1 - - - -
111B TRP* 3.1 31.4 + - - +
115B CYS 5.3 0.2 - - - +
120B VAL* 3.6 25.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B MET* 3.7 25.2 - - + +
17B LEU* 3.2 56.2 + - + -
20B TYR* 4.5 7.2 + + - -
23B TYR* 3.4 25.2 + - + +
24B SER 3.5 16.6 - - - -
25B LEU* 3.1 9.1 + - + +
27B ASN* 1.3 74.0 - - - +
29B VAL* 1.3 60.6 + - - +
31B ALA* 3.3 4.2 + - - +
32B ALA* 3.0 29.1 + - - +
56B LEU* 4.5 14.4 - - + +
95B ALA* 4.1 15.0 - - + -
99B VAL* 3.8 38.8 - - + -
105B MET* 3.9 16.8 - - + -
108B TRP* 3.9 25.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ARG* 4.3 11.4 - - + +
8B LEU* 4.9 2.0 - - + -
9B ALA* 3.9 33.7 - - + +
12B MET* 4.3 12.1 - - - -
25B LEU* 3.2 15.0 + - + +
26B GLY 3.9 6.3 - - - +
28B TRP* 1.3 75.5 - - - +
30B CYS* 1.3 63.1 + - - +
32B ALA* 3.2 5.5 + - - -
33B LYS* 2.9 19.6 + - - +
38B PHE* 3.5 25.8 - - + -
123B TRP* 3.8 28.5 - - + +
124B ILE* 4.3 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B GLY 3.0 18.7 + - - +
27B ASN 3.6 4.3 - - - +
29B VAL* 1.3 77.9 - - - +
31B ALA* 1.3 61.2 + - - +
33B LYS* 3.2 10.6 + - - +
34B PHE* 3.2 33.4 + - - +
114B ARG 4.1 1.8 - - - -
115B CYS* 2.0 51.1 - - + -
118B THR* 5.1 0.2 - - - -
120B VAL* 4.3 4.3 - - + -
123B TRP* 3.3 37.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ASN 2.9 17.4 + - - +
28B TRP* 3.5 6.1 - - - +
30B CYS* 1.3 77.7 - - - +
32B ALA* 1.3 58.3 + - - +
34B PHE* 4.1 0.7 - - - +
35B GLU* 2.9 40.3 + - + +
56B LEU* 4.4 11.9 - - + -
105B MET* 3.8 20.2 - - + -
108B TRP* 5.0 4.3 - - + -
110B ALA* 4.7 0.2 - - - +
111B TRP* 4.1 15.7 - - + +
115B CYS* 3.8 6.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 32 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LEU* 3.5 29.2 - - + -
12B MET* 4.7 2.9 - - + -
28B TRP 3.0 13.3 + - - +
29B VAL 3.5 7.9 - - - +
31B ALA* 1.3 76.9 - - - +
33B LYS* 1.3 64.0 + - - +
36B SER* 3.1 24.4 + - - -
37B ASN 3.2 4.9 + - - -
38B PHE* 3.5 4.5 + - + -
55B ILE* 3.7 23.6 - - + +
56B LEU* 4.1 7.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B VAL 2.9 13.2 + - - +
30B CYS 3.2 10.5 + - - +
32B ALA* 1.3 76.5 - - - +
34B PHE* 1.3 79.7 + - + +
37B ASN* 2.8 52.3 + - - +
38B PHE* 3.6 34.8 - - + -
123B TRP* 3.6 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 34 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B CYS* 3.2 33.0 + - - +
33B LYS* 1.3 93.2 - - + +
35B GLU* 1.3 63.3 + - - +
37B ASN 4.6 0.2 - - - -
110B ALA* 3.6 24.6 - - + +
114B ARG* 3.2 73.6 - - + -
115B CYS* 3.9 1.1 - - - -
123B TRP* 3.6 32.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 35 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ALA* 2.9 26.5 + - - +
34B PHE* 1.3 80.3 - - - +
36B SER* 1.3 59.8 + - - +
42B ALA* 5.3 0.5 - - - +
55B ILE 4.0 11.0 - - - +
56B LEU* 4.3 2.9 - - - +
57B GLN* 3.3 42.9 - - + +
108B TRP* 3.6 30.7 - - + +
109B VAL* 3.5 12.0 + - - +
110B ALA* 3.0 33.6 + - + +
111B TRP 5.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 36 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ALA 3.1 6.9 + - - -
35B GLU* 1.3 78.2 - - - +
37B ASN* 1.3 71.9 + - - +
38B PHE 3.5 1.0 + - - -
39B ASN* 3.1 38.3 + - - +
42B ALA* 3.7 14.3 - - - +
54B GLY 3.6 12.1 - - - -
55B ILE* 2.8 32.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 37 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B VAL* 4.3 8.7 - - - +
32B ALA 3.2 0.2 + - - -
33B LYS* 2.8 52.7 + - - +
34B PHE 4.6 0.2 - - - -
35B GLU 3.9 0.2 - - - -
36B SER* 1.3 80.4 - - - +
38B PHE* 1.3 71.1 - - - +
39B ASN* 3.2 4.3 + - + +
----------------------------------------------------------
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