Contacts of the helix formed by residues 6 - 24 (chain H) in PDB entry 1XK4
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 6 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40F THR 3.5 21.1 - - - -
41F GLU* 2.7 34.9 + - - -
4H LYS 3.3 4.1 + - - -
5H MET* 1.3 75.8 - - - +
7H GLN* 1.3 65.3 + - - +
8H LEU 3.5 1.6 + - - -
9H GLU* 2.9 29.2 + - - +
10H ARG* 3.0 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 7 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F SER* 2.8 37.6 + - - +
14F ASP* 3.8 17.8 + - - +
15F VAL* 3.8 10.2 - - + +
18F LYS* 2.9 31.9 + - - +
41F GLU* 3.7 2.9 + - - +
6H SER* 1.3 73.8 - - - +
8H LEU* 1.3 62.7 + - - +
10H ARG* 3.2 31.6 + - - +
11H ASN* 3.0 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 8 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F ILE* 4.0 25.6 - - + -
15F VAL* 4.0 17.9 - - + +
37F LEU* 4.9 3.1 - - + -
41F GLU* 3.3 34.3 + - + +
71F PHE* 4.3 21.5 - - + -
75F VAL* 4.4 15.5 - - + -
78F MET* 3.7 35.4 - - + -
7H GLN* 1.3 77.5 - - - +
9H GLU* 1.3 57.1 + - - +
11H ASN* 3.2 8.1 + - - +
12H ILE* 2.9 35.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 9 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41F GLU 3.5 9.2 - - - +
42F SER 3.6 2.3 - - - -
43F PRO* 3.2 44.0 - - + +
78F MET* 4.8 3.6 - - + -
4H LYS 4.2 2.3 - - - +
5H MET* 3.5 25.2 - - + +
6H SER* 2.9 44.3 + - - +
8H LEU* 1.3 77.6 - - - +
10H ARG* 1.3 57.6 + - - +
12H ILE* 3.5 8.6 + - - +
13H GLU* 2.8 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 10 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H MET* 3.4 42.4 + - + -
6H SER 3.0 9.6 + - - +
7H GLN* 3.5 43.4 - - - +
9H GLU* 1.3 73.2 - - - +
11H ASN* 1.3 63.6 + - - +
13H GLU* 3.3 10.5 + - - +
14H THR* 2.9 32.4 + - - -
24L VAL* 3.6 44.8 + - + +
25L LYS* 4.5 17.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 11 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F ALA* 3.6 29.9 - - + +
11F SER* 2.7 47.0 + - - -
12F ILE* 3.6 13.5 - - + +
15F VAL* 4.1 1.4 - - - +
7H GLN* 3.0 23.5 + - - +
8H LEU* 3.2 10.8 + - - +
10H ARG* 1.3 76.6 + - - +
12H ILE* 1.3 65.9 + - - +
14H THR* 3.2 5.7 + - - -
15H ILE* 3.1 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 12 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F ILE* 5.5 0.9 - - + -
75F VAL* 4.4 13.2 - - + +
78F MET* 3.6 47.8 - - + +
79F GLY* 3.8 21.8 - - - +
82F ALA* 3.9 10.5 - - + -
8H LEU* 2.9 29.6 + - + +
9H GLU* 3.8 6.3 - - - +
11H ASN* 1.3 75.4 - - + +
13H GLU* 1.3 63.6 + - - +
15H ILE* 3.1 15.7 + - + +
16H ILE* 2.9 41.2 + - + +
76H PHE* 5.7 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 13 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H MET* 3.1 32.9 - - - +
9H GLU 2.8 21.6 + - - +
10H ARG* 3.4 10.4 - - - +
12H ILE* 1.3 74.5 - - - +
14H THR* 1.3 56.6 + - - +
16H ILE* 3.7 8.2 - - - +
17H ASN* 2.8 47.3 + - - +
20L HIS* 3.1 31.7 + - - -
21L GLN* 6.1 0.7 - - - +
24L VAL* 4.8 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 14 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4F GLU* 3.7 28.5 - - + +
5F LEU* 4.3 3.6 - - - -
8F ALA* 3.8 13.0 - - + +
10H ARG 2.9 17.6 + - - -
11H ASN* 3.2 9.5 + - - -
13H GLU* 1.3 73.3 - - - +
15H ILE* 1.3 57.9 + - - +
17H ASN* 3.4 4.5 + - - +
18H THR* 2.8 43.8 + - - +
21L GLN* 2.7 38.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 15 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F LEU* 4.2 22.2 - - + -
8F ALA* 4.8 3.6 - - + -
9F LEU* 4.0 14.8 - - + -
12F ILE* 4.0 26.5 - - + -
75F VAL* 5.8 1.3 - - + -
11H ASN 3.1 15.7 + - - +
12H ILE* 3.4 15.7 - - + +
14H THR* 1.3 74.1 - - - +
16H ILE* 1.3 59.1 + - - +
18H THR* 3.4 1.7 + - - -
19H PHE* 2.9 28.2 + - - +
76H PHE* 3.9 22.4 - - + -
79H PHE* 4.0 6.9 - - + -
80H ILE* 4.2 15.0 - - + -
83H MET* 3.8 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 16 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79F GLY 4.2 0.7 - - - +
82F ALA* 3.8 9.0 - - + +
83F HIS* 3.6 36.8 - - + +
86F SER* 3.8 23.6 - - - +
12H ILE* 2.9 37.2 + - + +
13H GLU* 3.7 7.2 - - - +
15H ILE* 1.3 77.1 - - - +
17H ASN* 1.3 68.7 + - - +
19H PHE* 3.5 3.5 + - - +
20H HIS* 3.0 29.0 + - + +
76H PHE* 3.7 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 17 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13H GLU* 2.8 42.1 + - - +
14H THR* 4.1 3.8 - - - +
16H ILE* 1.3 84.6 - - - +
18H THR* 1.3 61.4 + - - +
20H HIS* 3.8 7.6 - - - +
21H GLN* 3.0 29.1 + - - +
17L ASN* 4.3 36.4 + - + +
20L HIS* 4.8 8.5 - - - -
21L GLN* 6.0 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 18 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F LEU* 4.0 25.5 + - + +
14H THR* 2.8 30.9 + - - +
15H ILE 3.7 3.8 - - - -
17H ASN* 1.3 73.8 - - - +
19H PHE* 1.3 66.9 + - - +
20H HIS 3.2 0.3 + - - -
21H GLN* 3.3 12.3 + - - +
22H TYR* 3.3 22.5 - - + -
40H LEU* 4.1 11.9 - - + -
44H ASP* 3.8 32.5 - - + +
79H PHE* 5.8 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 19 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83F HIS* 4.1 11.7 - + - -
15H ILE 2.9 19.1 + - - +
16H ILE 3.6 4.9 - - - +
18H THR* 1.3 76.4 - - - +
20H HIS* 1.3 62.7 + - + +
22H TYR 3.3 0.7 + - - -
23H SER* 2.9 41.8 + - - -
30H ASP* 3.4 31.9 - - - -
31H THR* 4.0 4.3 - - - -
32H LEU* 3.7 31.8 - - + +
40H LEU* 4.3 9.6 - - - +
74H LEU 3.6 13.0 - - - -
75H SER 3.9 3.1 - - - -
76H PHE* 3.4 45.8 - + + -
79H PHE* 3.7 25.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 20 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83F HIS* 6.5 0.4 - - + -
16H ILE* 3.0 21.1 + - + +
17H ASN* 3.8 8.5 - - - +
18H THR 3.2 0.2 - - - -
19H PHE* 1.3 79.8 - - + +
21H GLN* 1.3 70.8 + - - +
22H TYR 3.0 0.5 + - - -
23H SER* 3.5 12.5 + - - -
24H VAL* 3.1 51.9 + - + +
29H PRO* 4.6 3.8 + - + -
30H ASP* 5.4 4.8 + - - +
5L MET* 3.9 7.3 - - + +
13L GLU* 3.0 40.3 + - - -
17L ASN* 4.8 9.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 21 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17H ASN 3.0 17.2 + - - +
18H THR* 3.3 10.3 + - - +
20H HIS* 1.3 81.4 - - - +
22H TYR* 1.3 68.0 + - + +
24H VAL* 3.9 7.9 - - - +
25H LYS* 3.5 20.6 + - - +
4J GLU* 2.8 44.7 - - + +
13L GLU* 5.4 3.2 + - - +
14L THR* 2.7 44.0 + - - +
17L ASN* 5.8 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 22 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2008F FLC 3.4 5.2 + - - -
18H THR* 3.3 18.4 - - + -
19H PHE 3.3 1.3 + - - +
20H HIS 3.0 0.4 - - - -
21H GLN* 1.3 86.2 - - + +
23H SER* 1.3 66.3 + - - +
24H VAL 3.1 2.9 + - - -
25H LYS* 3.2 16.3 + - - +
32H LEU* 3.7 18.4 - - + -
36H GLU* 3.1 28.2 - - + +
39H GLU* 3.5 41.7 - - + -
40H LEU* 3.7 22.4 - - + -
43H LYS* 3.6 10.2 - - - +
44H ASP* 2.6 30.9 + - - -
4J GLU* 3.3 39.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 23 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19H PHE* 2.9 35.9 + - - -
20H HIS* 3.3 13.5 + - - -
22H TYR* 1.3 77.2 - - - +
24H VAL* 1.3 61.0 + - - +
25H LYS 3.4 1.2 + - - -
26H LEU 3.4 1.2 - - - +
28H HIS 3.1 6.9 - - - +
29H PRO 2.7 21.1 + - - -
30H ASP* 3.9 1.0 + - - -
31H THR 3.3 27.1 - - - -
32H LEU* 3.6 5.5 - - - +
36H GLU* 3.8 2.2 - - - -
4512H CA 2.3 26.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 24 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20H HIS* 3.1 39.7 + - + +
21H GLN* 3.9 10.5 - - - +
23H SER* 1.3 78.4 + - - +
25H LYS* 1.3 65.6 + - - +
26H LEU* 3.3 2.8 + - - -
29H PRO* 3.5 25.5 - - + +
5L MET* 3.5 29.6 - - + +
10L ARG* 3.6 27.9 + - + -
13L GLU* 4.5 3.1 - - - +
----------------------------------------------------------
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