Contacts of the helix formed by residues 3 - 21 (chain B) in PDB entry 1K9K
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 CYS 3 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LYS 4.8 0.2 - - - -
41A GLU 3.1 23.8 - - - +
42A LEU 3.8 5.4 - - - -
43A THR* 3.1 38.9 + - - +
2B ALA* 1.3 73.7 - - - +
4B PRO* 1.3 71.2 - - + +
5B LEU 3.3 0.4 - - - -
6B ASP* 3.2 2.8 + - - +
7B GLN* 2.9 23.1 + - - +
200B BME 2.0 49.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 4 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 3.6 24.1 - - + +
15A ILE* 4.4 3.8 - - + -
40A LYS 4.8 0.9 - - - +
41A GLU* 3.5 24.9 - - - +
2B ALA 4.7 0.7 - - - +
3B CYS* 1.3 87.6 - - + +
5B LEU* 1.3 62.5 + - - +
7B GLN* 3.4 6.8 + - + +
8B ALA* 3.1 24.3 + - - +
200B BME 4.1 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 5 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 3.7 16.4 - - + -
15A ILE* 4.2 11.5 - - + +
37A LEU* 4.1 23.1 - - + -
38A ILE* 6.1 0.2 - - + -
41A GLU* 3.1 28.5 + - + +
42A LEU* 4.1 9.9 - - + +
73A TYR* 4.1 20.4 - - + +
76A PHE* 5.0 6.7 - - + -
77A LEU* 4.3 7.6 - - + -
80A LEU* 3.6 29.2 - - + -
4B PRO* 1.3 78.8 - - - +
6B ASP* 1.3 65.2 + - - +
8B ALA* 3.3 3.1 + - - +
9B ILE* 3.1 31.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 6 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A GLU 3.8 0.9 - - - +
42A LEU* 3.2 24.5 - - - +
43A THR* 2.7 48.6 + - - +
44A ILE* 5.3 0.9 + - - +
84A TYR* 4.8 9.4 - - + -
2B ALA* 4.0 9.0 - - + -
3B CYS* 3.2 5.2 + - - +
5B LEU* 1.3 77.0 - - - +
7B GLN* 1.3 58.3 + - - +
9B ILE* 3.5 5.3 + - - +
10B GLY* 2.9 26.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 7 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 6.0 0.7 - - + -
2B ALA* 3.1 41.4 + - + +
3B CYS 2.9 22.6 + - - +
4B PRO* 3.6 7.0 - - + +
5B LEU 3.2 0.2 - - - -
6B ASP* 1.3 77.6 - - - +
8B ALA* 1.3 56.6 + - - +
10B GLY* 3.1 3.7 + - - -
11B LEU* 2.9 28.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 8 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ALA* 3.8 31.0 - - + +
11A LEU* 4.0 13.2 - - + +
12A LEU* 3.9 14.8 - - + -
4B PRO 3.1 17.0 + - - +
5B LEU 3.3 4.2 + - - +
7B GLN* 1.3 76.3 - - - +
9B ILE* 1.3 65.0 + - - +
11B LEU* 3.1 8.8 + - - +
12B LEU* 3.0 26.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 9 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 3.8 22.9 - - + -
77A LEU* 3.9 29.8 - - + +
80A LEU* 4.0 13.7 - - + +
81A ALA* 3.6 34.1 - - + +
84A TYR* 4.3 8.3 - - + -
5B LEU* 3.1 32.1 + - + +
6B ASP* 3.8 6.1 - - - +
8B ALA* 1.3 74.1 - - - +
10B GLY* 1.3 63.8 + - - +
12B LEU* 3.1 12.1 + - + +
13B VAL* 3.0 24.7 + - + +
77B LEU* 6.4 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 10 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A TYR* 3.7 35.4 - - - -
6B ASP 2.9 16.2 + - - -
7B GLN* 3.1 5.1 + - - -
9B ILE* 1.3 78.2 - - - +
11B LEU* 1.3 55.2 + - - +
13B VAL* 3.4 2.3 + - - +
14B ALA* 2.9 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 11 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A PRO* 4.1 23.6 - - + +
7A GLN* 5.2 7.9 - - + +
8A ALA* 4.3 16.4 - - + +
7B GLN 2.9 12.7 + - - +
8B ALA* 3.1 12.5 + - - +
10B GLY* 1.3 76.8 - - - +
12B LEU* 1.3 57.5 + - - +
14B ALA* 3.3 7.4 + - - +
15B ILE* 3.0 50.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 12 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LEU* 3.6 37.5 - - + +
8A ALA* 3.6 20.2 - - + -
9A ILE* 3.7 23.6 - - + -
12A LEU* 3.9 22.0 - - + -
81A ALA* 6.3 1.1 - - + -
8B ALA 3.0 15.6 + - - +
9B ILE* 3.6 12.8 - - + +
11B LEU* 1.3 76.9 - - - +
13B VAL* 1.3 62.7 + - + +
15B ILE* 3.4 4.1 + - + -
16B PHE 3.4 8.1 + - - -
73B TYR* 2.8 25.1 + - - -
77B LEU* 3.9 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 13 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ALA* 3.8 22.9 - - + +
84A TYR* 3.7 23.8 - - + -
85A ASN* 3.7 26.5 - - + +
88A LEU* 3.7 18.8 - - + -
9B ILE* 3.0 20.2 + - + +
10B GLY 3.8 0.4 - - - +
12B LEU* 1.3 77.6 - - + +
14B ALA* 1.3 62.6 + - - +
16B PHE* 3.3 9.4 + - - +
17B HIS* 3.2 21.6 - - + -
70B PHE* 3.8 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 14 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A TYR* 6.0 0.2 - - + -
88A LEU* 4.3 14.1 - - + +
10B GLY 2.9 17.7 + - - +
11B LEU* 3.5 8.7 - - - +
13B VAL* 1.3 77.1 - - - +
15B ILE* 1.3 61.5 + - - +
17B HIS* 3.3 3.7 + - - +
18B LYS* 3.0 23.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 15 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A PRO* 3.8 18.8 - - + -
5A LEU* 3.7 25.1 - - + +
11B LEU* 3.0 40.7 + - + +
12B LEU* 3.6 10.1 - - + +
13B VAL 3.3 0.2 - - - -
14B ALA* 1.3 77.2 - - + +
16B PHE* 1.3 64.7 + - - +
18B LYS* 3.1 17.3 + - + +
19B TYR* 3.2 16.8 - - + -
37B LEU* 3.9 24.7 - - + -
41B GLU* 3.9 22.0 - - + +
73B TYR* 3.7 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 16 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LEU 3.4 2.4 + - - -
13B VAL 3.3 10.2 + - - +
14B ALA 3.3 0.6 - - - -
15B ILE* 1.3 81.3 - - - +
17B HIS* 1.3 76.6 + + - +
19B TYR* 3.2 1.2 + - - -
20B SER* 2.8 43.5 + - - -
27B HIS 3.2 30.3 - - - -
29B LEU* 3.5 29.7 - - + +
37B LEU* 4.3 8.1 - - - -
68B VAL 4.0 3.6 - - - -
69B ASN 3.7 19.5 - - - -
70B PHE* 3.5 34.5 - + + -
73B TYR* 3.4 38.5 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 17 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ASN* 2.6 34.1 + - - -
88A LEU* 3.6 37.3 + - + +
89A LYS* 4.6 5.4 - - + -
13B VAL* 3.2 23.2 + - + +
14B ALA* 3.3 6.1 + - - +
15B ILE 3.3 0.4 - - - -
16B PHE* 1.3 90.9 - + - +
18B LYS* 1.3 66.1 + - - +
19B TYR 3.1 2.8 + - - -
20B SER* 3.4 12.4 + - - -
21B GLY* 3.7 15.2 + - - -
26B LYS 4.8 0.6 + - - -
27B HIS* 4.2 25.7 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 18 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ALA 3.0 13.7 + - - +
15B ILE* 3.1 15.7 + - + +
17B HIS* 1.3 77.7 - - - +
19B TYR* 1.3 80.2 + - + +
21B GLY 4.9 0.3 + - - -
22B ARG* 3.2 28.9 + - - +
41B GLU* 3.0 23.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 19 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ILE* 3.2 16.4 - - + -
16B PHE 3.2 1.9 + - - +
18B LYS* 1.3 96.9 + - + +
20B SER* 1.3 63.9 + - - +
21B GLY 3.3 3.2 + - - -
22B ARG* 3.2 35.9 + - - +
29B LEU* 3.7 17.3 - - + -
33B GLU* 3.0 30.9 - - + +
36B GLU* 3.2 33.0 - - + -
37B LEU* 3.7 22.4 - - + -
40B LYS* 3.4 20.1 - - + +
41B GLU* 2.5 44.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 20 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B PHE* 2.8 40.5 + - - -
17B HIS* 3.4 20.6 + - - -
19B TYR* 1.3 73.2 - - - +
21B GLY* 1.3 58.4 + - - +
25B ASP 3.0 7.4 - - - +
26B LYS 2.8 19.9 + - - -
28B THR 3.7 15.3 - - - -
29B LEU* 3.4 12.2 - - - +
33B GLU* 2.9 1.4 - - - +
300B CA 2.3 28.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 21 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B HIS 3.7 9.8 + - - -
18B LYS 4.9 0.4 + - - -
19B TYR 3.3 1.2 - - - -
20B SER* 1.3 80.8 + - - +
22B ARG* 1.3 63.5 + - - +
23B GLU* 3.4 2.6 + - - -
24B GLY 5.5 0.5 - - - +
26B LYS* 3.5 29.5 - - - +
----------------------------------------------------------
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