Contacts of the helix formed by residues 6 - 24 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B THR* 3.5 22.2 - - - -
41B GLU* 2.8 35.0 + - - -
4D LYS 3.4 3.8 + - - -
5D MET* 1.3 76.7 - - - +
7D GLN* 1.3 64.9 + - - +
8D LEU 3.7 0.5 + - - -
9D GLU* 2.8 29.9 + - - -
10D ARG* 2.9 23.0 + - - +
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Residues in contact with GLN 7 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B SER* 2.8 36.7 + - - +
14B ASP* 2.9 27.1 + - - +
15B VAL* 3.6 11.0 - - + +
18B LYS* 2.7 42.9 + - - +
41B GLU* 3.6 2.3 + - - +
6D SER* 1.3 73.2 - - - +
8D LEU* 1.3 63.5 + - - +
10D ARG* 3.2 10.3 + - - +
11D ASN* 3.0 27.5 + - - +
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Residues in contact with LEU 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ILE* 4.2 25.8 - - + -
15B VAL* 3.9 13.1 - - + +
37B LEU* 4.6 7.0 - - + -
41B GLU* 3.2 34.5 + - + +
71B PHE* 4.4 20.0 - - + -
75B VAL* 4.5 14.8 - - + -
78B MET* 3.9 35.2 - - + -
7D GLN* 1.3 79.5 - - - +
9D GLU* 1.3 62.6 + - - +
11D ASN* 3.1 8.6 + - - +
12D ILE* 3.0 37.4 + - + +
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Residues in contact with GLU 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B GLU 3.6 8.5 - - - +
42B SER 3.3 3.6 - - - +
43B PRO* 3.0 45.7 - - + +
78B MET* 4.9 3.6 - - + -
4D LYS 4.3 2.3 - - - +
5D MET* 3.7 21.7 - - + +
6D SER* 2.8 42.4 + - - +
8D LEU* 1.3 76.3 - - - +
10D ARG* 1.3 58.3 + - - +
12D ILE* 3.4 8.3 + - - +
13D GLU* 2.9 28.6 + - - +
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Residues in contact with ARG 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D MET* 4.1 41.5 - - + +
6D SER 2.9 19.6 + - - +
7D GLN* 3.2 10.7 + - - +
9D GLU* 1.3 73.0 - - - +
11D ASN* 1.3 64.1 + - - +
13D GLU* 3.4 3.6 + - - +
14D THR* 2.9 32.5 + - - -
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Residues in contact with ASN 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ALA* 3.6 25.2 - - + +
11B SER* 2.9 50.9 + - - -
12B ILE* 3.6 16.5 - - + +
15B VAL* 4.2 0.4 - - - +
7D GLN* 3.0 23.1 + - - +
8D LEU* 3.1 9.3 + - - +
10D ARG* 1.3 79.9 - - - +
12D ILE* 1.3 62.7 + - - +
14D THR* 3.3 5.4 + - - -
15D ILE* 3.1 27.3 + - - +
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Residues in contact with ILE 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B ILE* 5.3 0.9 - - + -
75B VAL* 4.4 12.6 - - + +
78B MET* 3.7 46.0 - - + -
79B GLY* 3.9 16.6 - - - +
82B ALA* 3.9 16.2 - - + -
8D LEU* 3.0 31.1 + - + +
9D GLU* 3.8 7.2 - - - +
11D ASN* 1.3 74.3 - - + +
13D GLU* 1.3 65.5 + - - +
15D ILE* 3.0 15.4 + - + +
16D ILE* 2.9 40.9 + - + +
76D PHE* 5.9 0.2 - - + -
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Residues in contact with GLU 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B SER* 5.1 6.3 - - - -
5D MET* 4.5 15.0 - - + -
9D GLU 2.9 18.2 + - - +
10D ARG* 3.7 7.9 - - - +
11D ASN 3.4 0.2 - - - -
12D ILE* 1.3 78.5 - - - +
14D THR* 1.3 62.6 + - - +
16D ILE* 3.3 19.6 + - - +
17D ASN* 2.9 42.7 + - + +
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Residues in contact with THR 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B GLU* 3.9 21.3 - - + +
5B LEU* 4.2 10.1 - - - -
8B ALA* 3.8 21.8 - - + +
10D ARG* 2.9 14.5 + - - +
11D ASN* 3.4 10.0 - - - -
12D ILE 3.2 0.2 - - - -
13D GLU* 1.3 75.4 - - - +
15D ILE* 1.3 62.1 + - - +
17D ASN* 4.0 4.2 - - - +
18D THR* 2.8 35.9 + - - +
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Residues in contact with ILE 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B LEU* 4.1 22.7 - - + -
8B ALA* 4.9 1.8 - - + -
9B LEU* 3.9 21.5 - - + -
12B ILE* 4.0 16.8 - - + -
75B VAL* 5.8 2.5 - - + -
11D ASN 3.1 15.5 + - - +
12D ILE* 3.0 16.9 + - + +
14D THR* 1.3 76.5 - - - +
16D ILE* 1.3 62.2 + - - +
18D THR* 3.7 2.1 - - - -
19D PHE* 3.0 22.2 + - - +
76D PHE* 4.0 23.6 - - + -
79D PHE* 4.2 6.8 - - + -
80D ILE* 4.8 9.2 - - + -
83D MET* 3.8 29.8 - - + -
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Residues in contact with ILE 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B GLY 4.2 0.7 - - - +
82B ALA* 3.6 21.1 - - + +
83B HIS* 3.4 39.5 - - + +
86B SER* 3.7 24.2 - - - +
12D ILE* 2.9 25.6 + - + +
13D GLU* 3.8 19.5 - - - +
15D ILE* 1.3 75.7 - - - +
17D ASN* 1.3 58.1 + - - +
19D PHE* 3.3 4.3 + - - +
20D HIS* 2.9 31.2 + - + +
76D PHE* 3.7 27.8 - - + -
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Residues in contact with ASN 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D GLU* 2.9 31.0 + - + +
14D THR* 4.0 4.9 - - - +
16D ILE* 1.3 77.7 - - - +
18D THR* 1.3 60.9 + - - +
20D HIS* 3.4 13.7 + - - +
21D GLN* 2.9 38.1 + - - +
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Residues in contact with THR 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B LEU* 4.1 23.7 + - + +
14D THR* 2.8 28.3 + - - +
15D ILE 3.7 3.8 - - - -
17D ASN* 1.3 75.9 + - - +
19D PHE* 1.3 65.9 + - - +
21D GLN* 3.3 13.2 + - - +
22D TYR* 3.2 27.1 - - + -
40D LEU* 4.2 11.4 - - + -
44D ASP* 3.5 34.9 + - + +
79D PHE* 6.0 1.3 - - + -
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Residues in contact with PHE 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B HIS* 4.6 3.4 - + - -
15D ILE 3.0 14.0 + - - +
16D ILE 3.5 8.3 - - - +
18D THR* 1.3 78.1 - - - +
20D HIS* 1.3 63.1 + - + +
22D TYR 3.3 0.5 + - - -
23D SER* 2.9 35.7 + - - -
30D ASP* 3.3 42.4 - - - -
31D THR* 4.0 4.0 - - - -
32D LEU* 3.6 27.9 - - + +
40D LEU* 4.3 8.7 - - - +
74D LEU 3.5 14.6 - - - -
76D PHE* 3.4 41.7 - + + -
79D PHE* 3.6 39.9 - + + -
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Residues in contact with HIS 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D ILE* 2.9 20.4 + - + +
17D ASN* 3.7 15.5 - - - +
18D THR 3.3 0.2 - - - -
19D PHE* 1.3 77.0 - - + +
21D GLN* 1.3 72.9 + - - +
22D TYR 3.1 0.7 + - - -
23D SER* 3.4 10.9 + - - -
24D VAL* 3.2 49.0 + - + +
29D PRO* 4.8 4.3 + - + -
30D ASP* 5.7 3.0 + - - +
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Residues in contact with GLN 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D ASN* 2.9 25.6 + - - +
18D THR* 3.4 15.2 + - - +
19D PHE 3.3 0.4 - - - -
20D HIS* 1.3 83.2 - - - +
22D TYR* 1.3 90.8 + - + +
24D VAL* 3.7 8.8 - - - +
25D LYS* 3.7 20.5 - - - +
44D ASP* 5.0 2.0 + - - -
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Residues in contact with TYR 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D THR* 3.2 24.0 - - + -
19D PHE 3.3 1.4 + - - +
21D GLN* 1.3 101.9 + - + +
23D SER* 1.3 64.4 + - - +
24D VAL 3.1 2.2 - - - -
25D LYS* 3.1 26.6 + - + +
32D LEU* 3.7 18.6 - - + -
36D GLU* 3.1 26.0 - - + +
39D GLU* 3.5 46.0 - - + -
40D LEU* 3.7 22.2 - - + -
43D LYS* 3.9 22.9 - - - +
44D ASP* 2.9 32.8 + - - -
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Residues in contact with SER 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D PHE* 2.9 29.2 + - - -
20D HIS* 3.3 13.4 + - - -
22D TYR* 1.3 76.4 - - - +
24D VAL* 1.3 62.2 + - - +
25D LYS 3.3 1.4 + - - -
26D LEU 3.4 1.7 - - - +
28D HIS 3.2 5.4 - - - +
29D PRO* 2.8 22.2 + - - +
30D ASP* 4.0 3.3 + - - -
31D THR 3.2 30.7 - - - -
32D LEU* 3.5 8.4 - - - +
36D GLU* 3.8 1.1 - - - -
4502D CA 2.4 25.8 - - - -
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Residues in contact with VAL 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D HIS* 3.2 40.8 + - + +
21D GLN* 3.7 10.5 - - - +
22D TYR 3.1 1.4 - - - -
23D SER* 1.3 79.7 + - - +
25D LYS* 1.3 66.5 + - + +
26D LEU* 3.2 2.6 + - - -
27D GLY 5.7 0.3 - - - +
29D PRO* 3.8 27.4 - - + +
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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) + - + + + + + -
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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