Contacts of the helix formed by residues 6 - 24 (chain L) 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 L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40J THR* 3.5 21.1 - - - -
41J GLU* 2.7 35.1 + - - -
4L LYS 3.4 3.9 + - - -
5L MET* 1.3 77.2 - - - +
7L GLN* 1.3 65.3 + - - +
8L LEU 3.5 1.2 + - - -
9L GLU* 2.8 27.8 + - - +
10L ARG* 2.9 23.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 7 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11J SER* 2.8 36.4 + - - +
14J ASP* 2.8 26.3 + - - +
15J VAL* 3.4 10.9 - - + +
18J LYS* 2.7 44.6 + - - +
41J GLU* 3.5 2.5 + - - +
6L SER* 1.3 75.1 - - - +
8L LEU* 1.3 62.3 + - - +
10L ARG* 3.3 30.8 + - - +
11L ASN* 3.0 28.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 8 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12J ILE* 4.1 26.9 - - + -
15J VAL* 4.0 12.9 - - + +
37J LEU* 4.8 3.8 - - + -
41J GLU* 3.2 34.5 + - + +
71J PHE* 4.3 23.6 - - + -
75J VAL* 4.5 14.6 - - + -
78J MET* 3.7 35.4 - - + -
7L GLN* 1.3 77.6 - - - +
9L GLU* 1.3 58.4 + - - +
11L ASN* 3.2 8.4 + - - +
12L ILE* 3.0 38.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 9 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41J GLU 3.5 7.6 - - - +
42J SER 3.4 3.8 - - - +
43J PRO* 3.2 45.0 - - + +
78J MET* 4.9 3.4 - - + -
4L LYS 4.2 2.4 - - - +
5L MET* 3.4 23.5 - - + +
6L SER* 2.8 40.2 + - - +
8L LEU* 1.3 76.8 - - - +
10L ARG* 1.3 58.1 + - - +
12L ILE* 3.4 8.0 + - - +
13L GLU* 2.9 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 10 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21H GLN* 5.1 0.2 + - - -
24H VAL* 3.6 38.9 + - + -
25H LYS* 4.2 31.0 + - - +
5L MET* 4.1 32.9 + - + -
6L SER 2.9 16.6 + - - +
7L GLN* 3.5 39.7 + - - +
9L GLU* 1.3 77.3 - - - +
11L ASN* 1.3 62.4 + - - +
13L GLU* 3.3 6.3 + - - +
14L THR* 3.0 31.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 11 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8J ALA* 3.6 25.3 - - + +
11J SER* 2.7 53.2 + - - -
12J ILE* 3.4 16.3 - - + +
15J VAL* 4.1 0.6 - - - +
7L GLN* 3.0 22.1 + - - +
8L LEU* 3.2 9.6 + - - +
10L ARG* 1.3 79.7 + - - +
12L ILE* 1.3 64.2 - - - +
14L THR* 3.3 5.6 + - - -
15L ILE* 3.2 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 12 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12J ILE* 5.2 0.9 - - + -
75J VAL* 4.5 13.0 - - + +
78J MET* 3.5 49.1 - - + +
79J GLY* 4.0 15.0 - - - +
82J ALA* 3.7 29.2 - - + -
8L LEU* 3.0 29.9 + - + +
9L GLU* 3.8 6.3 - - + +
11L ASN* 1.3 75.7 - - + +
13L GLU* 1.3 58.0 + - - +
15L ILE* 3.3 13.9 + - + +
16L ILE* 2.9 34.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 13 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20H HIS* 3.0 36.0 + - + -
21H GLN* 5.8 3.5 + - - +
24H VAL* 4.5 4.3 - - - +
5L MET* 3.1 27.2 - - - +
9L GLU 2.9 18.2 + - - +
10L ARG* 3.4 7.7 - - - +
11L ASN 3.2 0.2 - - - -
12L ILE* 1.3 76.0 - - - +
14L THR* 1.3 61.1 + - - +
16L ILE* 3.4 7.6 + - + +
17L ASN* 2.9 47.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 14 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21H GLN* 2.7 39.5 + - - +
4J GLU* 3.7 30.7 - - + +
5J LEU* 4.2 3.4 - - - +
8J ALA* 3.9 11.7 - - + +
10L ARG 3.0 15.0 + - - -
11L ASN* 3.5 8.9 - - - -
13L GLU* 1.3 76.0 - - - +
15L ILE* 1.3 60.5 + - - +
17L ASN* 4.2 3.7 - - - +
18L THR* 2.6 42.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 15 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5J LEU* 4.0 22.0 - - + -
8J ALA* 4.8 2.2 - - + -
9J LEU* 3.7 24.7 - - + -
12J ILE* 3.8 20.0 - - + -
75J VAL* 5.7 2.5 - - + -
11L ASN 3.2 12.4 + - - +
12L ILE* 3.5 14.4 - - + +
14L THR* 1.3 78.7 - - - +
16L ILE* 1.3 63.6 + - - +
18L THR* 3.7 1.4 - - - -
19L PHE* 3.1 22.0 + - - +
76L PHE* 4.0 21.5 - - + -
79L PHE* 4.2 5.0 - - + -
80L ILE* 5.1 5.8 - - + -
83L MET* 3.8 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 16 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79J GLY 4.2 0.7 - - - +
82J ALA* 3.5 34.5 - - + +
83J HIS* 3.5 23.3 - - + +
86J SER* 3.7 24.7 - - - +
12L ILE* 2.9 30.4 + - + +
13L GLU* 3.8 7.2 - - - +
15L ILE* 1.3 72.4 - - - +
17L ASN* 1.3 67.5 + - - +
19L PHE* 3.3 5.7 + - - +
20L HIS* 2.9 30.0 + - + +
76L PHE* 3.8 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 17 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17H ASN* 4.3 36.8 + - + +
20H HIS* 4.8 7.9 - - - -
21H GLN* 5.8 3.7 - - - +
86J SER* 6.0 0.5 - - - -
13L GLU* 2.9 44.0 + - - +
14L THR* 4.2 3.8 - - - +
16L ILE* 1.3 81.3 - - - +
18L THR* 1.3 59.5 + - - +
20L HIS* 3.8 9.0 - - - +
21L GLN* 3.0 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 18 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5J LEU* 4.0 27.8 + - + +
14L THR* 2.6 32.1 + - - +
15L ILE 3.7 3.4 - - - -
17L ASN* 1.3 76.2 - - - +
19L PHE* 1.3 66.2 + - - +
21L GLN* 3.3 10.1 + - - +
22L TYR* 3.3 24.3 - - + -
40L LEU* 4.2 9.0 - - + -
44L ASP* 3.9 30.5 - - + +
79L PHE* 6.2 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 19 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83J HIS* 4.7 3.4 - + - -
15L ILE 3.1 13.9 + - - +
16L ILE 3.4 9.4 - - - +
18L THR* 1.3 77.2 - - - +
20L HIS* 1.3 60.9 + - + +
22L TYR 3.3 1.0 + - - -
23L SER* 2.9 40.6 + - - -
30L ASP* 3.4 37.9 - - - -
31L THR* 3.9 4.5 - - - -
32L LEU* 3.5 31.1 - - + +
40L LEU* 4.2 10.2 - - - +
74L LEU 3.6 18.6 - - - -
76L PHE* 3.6 33.2 - + + -
79L PHE* 3.6 36.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 20 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H MET* 4.1 10.0 - - + +
13H GLU* 3.1 39.4 + - - -
17H ASN* 4.8 8.7 - - - -
16L ILE* 2.9 20.3 + - + +
17L ASN* 3.9 10.3 - - - +
18L THR 3.3 0.2 - - - -
19L PHE* 1.3 77.7 - - + +
21L GLN* 1.3 69.9 + - - +
22L TYR 3.1 1.0 + - - -
23L SER* 3.3 18.1 + - - -
24L VAL* 3.3 32.1 + - + +
29L PRO 4.8 4.5 + - - -
30L ASP* 5.5 4.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 21 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4F GLU* 3.0 51.8 + - + +
8F ALA* 5.9 0.2 - - - +
13H GLU* 6.1 0.5 - - - +
14H THR* 2.7 41.6 + - - +
17H ASN* 6.2 0.2 - - - +
17L ASN 3.0 15.7 + - - +
18L THR* 3.3 13.9 + - - +
20L HIS* 1.3 81.2 - - - +
22L TYR* 1.3 66.9 + - + +
24L VAL* 3.9 8.1 - - - +
25L LYS* 3.5 21.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 22 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4F GLU* 3.3 34.9 + - + +
2008F FLC 4.1 0.2 - - - +
18L THR* 3.3 19.3 - - + -
19L PHE 3.3 2.4 + - - +
20L HIS 3.1 0.2 - - - -
21L GLN* 1.3 84.3 - - + +
23L SER* 1.3 66.1 + - - +
24L VAL 3.2 2.5 + - - -
25L LYS* 3.2 17.8 + - + +
32L LEU* 3.8 16.6 - - + -
36L GLU* 3.1 32.9 - - + +
39L GLU* 3.5 45.5 - - + -
40L LEU* 3.8 19.5 - - + -
43L LYS* 3.7 14.0 - - - +
44L ASP* 2.6 33.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 23 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19L PHE* 2.9 29.4 + - - -
20L HIS* 3.4 16.3 + - - -
22L TYR* 1.3 76.5 - - - +
24L VAL* 1.3 61.7 + - - +
25L LYS 3.2 1.4 + - - -
26L LEU 3.4 2.8 - - - +
28L HIS 3.2 4.2 - - - +
29L PRO* 2.7 22.1 + - - +
30L ASP* 4.0 2.8 + - - -
31L THR 3.3 29.8 - - - -
32L LEU* 3.6 4.2 - - - +
36L GLU* 3.7 1.8 - - - -
4522L CA 2.4 23.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 24 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H MET* 4.1 21.1 - - + -
10H ARG* 3.6 36.6 + - + +
13H GLU* 4.8 2.2 - - - +
20L HIS* 3.3 33.4 + - + +
21L GLN* 3.9 10.1 - - - +
23L SER* 1.3 78.4 + - - +
25L LYS* 1.3 68.3 + - + +
26L LEU* 3.3 1.9 + - - -
27L GLY 5.5 0.2 - - - +
29L PRO* 3.6 28.3 - - + +
----------------------------------------------------------
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