Contacts of the helix formed by residues 13 - 24 (chain B) in PDB entry 1KXJ
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 ILE 13 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ASN* 3.0 43.4 + - + +
5B ILE* 4.8 5.8 - - + +
6B ILE 4.4 4.5 - - - +
7B SER* 3.6 39.3 - - - +
9B GLY 4.7 6.3 - - - +
10B PRO 5.5 1.1 - - - +
11B GLY 3.4 16.1 + - - +
12B ASN* 1.3 73.0 - - - +
14B MET* 1.3 61.0 - - - +
15B ASN 3.3 2.5 - - - -
16B LEU* 3.3 8.8 + - + +
17B TYR* 2.9 25.6 + - - +
34B LEU* 4.6 13.9 - - + -
49B PRO* 4.5 17.7 - - + -
50B GLY* 5.6 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 14 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A GLU* 3.7 32.5 - - + +
94A SER 4.1 2.2 - - - -
95A GLU* 3.7 19.7 - - - +
109A ASN* 3.7 27.6 - - + +
110A VAL 3.5 24.9 - - - +
111A VAL* 4.0 9.6 - - + -
12B ASN* 3.3 7.0 + - - +
13B ILE* 1.3 79.5 - - - +
15B ASN* 1.3 60.4 + - - +
17B TYR* 3.3 21.7 + - + +
18B ARG* 2.9 50.3 + - - +
34B LEU* 5.1 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 15 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A GLU* 4.9 1.4 - - - +
98A PRO 4.8 4.3 - - - +
12B ASN* 3.0 30.4 + - - +
14B MET* 1.3 77.0 - - - +
16B LEU* 1.3 59.5 + - - +
18B ARG* 3.5 21.3 + - - +
19B GLY* 2.8 26.7 + - - -
180B GLU* 3.9 27.6 + - + +
181B LYS* 5.0 15.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 16 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ILE* 4.3 13.7 - - + -
12B ASN* 4.4 2.6 + - - +
13B ILE* 3.3 12.1 + - - +
14B MET 3.3 0.2 - - - -
15B ASN* 1.3 75.8 - - - +
17B TYR* 1.3 70.5 + - - +
19B GLY 4.3 0.2 - - - +
20B VAL* 2.9 38.0 + - + +
47B PHE* 4.5 15.7 - - + -
49B PRO* 3.7 34.3 - - + -
83B VAL* 4.8 13.2 - - + -
179B PRO* 4.7 12.3 - - + -
180B GLU* 3.6 29.3 - - + +
190B LEU* 4.8 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 17 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A GLU* 3.5 28.2 + - + -
111A VAL* 3.4 30.8 - - + +
112A LYS* 4.8 1.7 + - - +
5B ILE* 3.9 10.3 - - + +
13B ILE* 2.9 15.5 + - + +
14B MET* 3.4 27.4 - - - +
16B LEU* 1.3 78.0 - - - +
18B ARG* 1.3 69.8 + - + +
20B VAL* 3.1 2.1 + - - +
21B LYS* 2.9 47.4 + - + +
32B ILE* 3.7 43.5 + - + -
34B LEU* 3.3 33.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 18 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A SER 4.0 1.2 + - - -
95A GLU* 3.8 27.4 + - + +
98A PRO* 3.3 47.3 + - - +
14B MET* 2.9 42.7 + - - +
15B ASN* 3.6 27.2 + - - +
17B TYR* 1.3 81.7 - - + +
19B GLY* 1.3 53.5 + - - +
21B LYS* 2.9 10.2 + - - +
22B ARG* 2.8 49.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 19 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ASN 2.8 21.0 + - - -
16B LEU* 3.7 1.6 - - - -
18B ARG* 1.3 74.6 - - - +
20B VAL* 1.3 56.2 + - - +
22B ARG* 3.4 7.6 + - - +
23B ALA* 3.0 26.0 + - - +
180B GLU* 4.9 7.0 - - - -
187B ARG* 5.2 7.0 - - - +
190B LEU* 3.7 15.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 20 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B ILE* 4.1 28.5 - - + -
5B ILE* 4.4 6.1 - - + -
16B LEU* 2.9 40.4 + - + +
17B TYR 3.7 2.2 - - - +
19B GLY* 1.3 69.0 - - - -
21B LYS* 1.3 61.3 + - - +
23B ALA* 3.1 8.3 + - - +
24B SER* 2.8 27.7 + - - -
32B ILE* 4.4 9.4 - - + -
47B PHE* 3.7 38.4 - - + -
190B LEU* 3.9 11.6 - - + +
194B ILE* 4.6 5.3 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
95A GLU* 2.9 26.1 + - - +
112A LYS* 4.7 14.6 - - - +
17B TYR* 2.9 43.5 + - + +
18B ARG* 3.2 14.1 - - - +
20B VAL* 1.3 78.2 - - - +
22B ARG* 1.3 60.4 + - - +
24B SER* 3.1 15.0 + - - +
25B GLU* 3.5 13.6 + - + +
32B ILE* 3.2 25.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 22 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ARG* 2.8 29.8 + - + +
19B GLY* 3.7 10.5 - - - +
21B LYS* 1.3 71.6 - - - +
23B ALA* 1.3 64.2 + - - +
25B GLU* 3.3 53.7 + - - +
26B ASN* 4.4 0.5 + - - +
187B ARG* 4.2 27.1 - - - +
191B GLU* 5.0 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 23 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B GLY 3.0 15.0 + - - +
20B VAL* 3.1 8.9 + - - +
22B ARG* 1.3 77.3 - - - +
24B SER* 1.3 57.9 + - - +
25B GLU 3.2 4.2 + - - -
26B ASN* 3.4 21.1 + - - +
27B PHE* 3.7 8.3 - - - -
187B ARG* 4.3 6.7 - - + +
190B LEU* 3.7 29.8 - - + +
191B GLU* 3.8 23.7 - - - +
194B ILE* 4.7 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B ILE* 4.6 6.3 - - - -
20B VAL 2.8 11.2 + - - -
21B LYS* 3.1 12.7 + - - +
23B ALA* 1.3 73.0 - - - +
25B GLU* 1.3 62.4 + - - +
26B ASN 3.1 2.7 - - - -
27B PHE* 3.2 28.7 + - - +
30B VAL* 3.8 33.6 + - - +
32B ILE* 3.2 20.7 - - - +
194B ILE* 4.6 6.0 - - - +
----------------------------------------------------------
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