Contacts of the helix formed by residues 3 - 21 (chain I) 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 THR 3 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1I MET 5.0 0.7 - - - +
2I LEU* 1.3 76.6 - - - +
4I GLU* 1.3 65.0 + - - +
5I LEU 3.4 2.6 + - - -
6I GLU* 3.0 26.4 + - - +
7I LYS* 3.0 23.1 + - - +
43K LYS 3.4 25.4 - - - +
44K ASP* 2.6 32.0 + - - +
46K GLN* 3.9 18.6 - - + +
47K ASN* 4.3 0.7 - - - +
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Residues in contact with GLU 4 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2I LEU 5.2 1.0 - - - +
3I THR* 1.3 74.9 - - - +
5I LEU* 1.3 58.3 + - - +
7I LYS* 2.9 36.6 + - - +
8I ALA* 3.0 28.2 + - - +
14K THR* 3.8 14.0 - - + +
18K THR* 6.1 0.2 - - - +
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Residues in contact with LEU 5 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3I THR* 3.2 1.6 + - - +
4I GLU* 1.3 78.0 - - - +
6I GLU* 1.3 58.3 + - - +
8I ALA* 3.1 8.8 + - + +
9I LEU* 3.0 28.7 + - + +
14K THR* 4.4 4.2 - - - +
15K ILE* 4.1 28.3 - - + +
18K THR* 4.0 19.3 + - + +
40K LEU* 4.1 12.6 - - + -
44K ASP* 3.5 28.9 + - + +
45K LEU* 3.7 31.0 - - + -
79K PHE* 5.0 1.6 - - + -
83K MET* 4.0 28.9 - - - -
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Residues in contact with GLU 6 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2I LEU* 3.5 8.4 - - + +
3I THR* 3.0 28.2 + - - +
5I LEU* 1.3 78.2 - - - +
7I LYS* 1.3 59.3 + - - +
9I LEU* 3.4 2.6 + - - +
10I ASN* 3.0 33.4 + - - -
44K ASP 3.5 7.6 - - - +
45K LEU* 3.2 16.5 - - + -
47K ASN* 2.6 40.5 + - - +
48K PHE* 2.9 61.7 + - + -
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Residues in contact with LYS 7 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2I LEU* 3.8 31.1 + - + +
3I THR 3.0 21.1 + - - +
4I GLU* 2.9 33.5 + - - +
6I GLU* 1.3 74.8 - - - +
8I ALA* 1.3 57.7 + - - +
10I ASN* 3.4 8.2 + - - +
11I SER* 2.9 29.8 + - - -
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Residues in contact with ALA 8 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4I GLU 3.0 13.7 + - - +
5I LEU* 3.1 10.3 + - - +
7I LYS* 1.3 73.7 - - - +
9I LEU* 1.3 65.1 + - - +
11I SER* 3.2 3.9 + - - -
12I ILE* 3.1 28.0 + - - +
11K ASN* 3.5 26.2 - - - +
14K THR* 3.9 26.5 - - + +
15K ILE* 4.8 7.0 - - + -
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Residues in contact with LEU 9 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5I LEU* 3.0 17.7 + - + +
6I GLU 3.7 5.8 - - - +
7I LYS 3.3 0.2 - - - -
8I ALA* 1.3 76.4 - - - +
10I ASN* 1.3 62.9 + - - +
12I ILE* 3.2 21.5 + - + +
13I ILE* 3.5 5.6 + - - +
15K ILE* 3.7 31.2 - - + -
45K LEU* 4.7 6.5 - - + -
48K PHE* 4.0 20.2 - - + -
83K MET* 4.1 28.7 - - + +
86K LEU* 4.0 29.8 - - + -
87K THR* 3.4 32.9 - - - +
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Residues in contact with ASN 10 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2I LEU* 3.7 27.5 - - - +
6I GLU 3.0 17.9 + - - +
7I LYS* 3.8 6.0 - - - +
8I ALA 3.4 0.4 - - - -
9I LEU* 1.3 75.5 - - - +
11I SER* 1.3 62.1 + - - +
13I ILE* 3.2 11.7 + - - +
14I ASP* 3.1 19.1 + - - +
48K PHE* 3.6 10.8 - - - -
90K SER* 2.6 32.2 + - - -
94K MET* 3.7 21.1 - - + +
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Residues in contact with SER 11 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7I LYS 2.9 18.2 + - - -
8I ALA 3.2 0.4 + - - -
10I ASN* 1.3 77.5 - - - +
12I ILE* 1.3 55.6 + - - +
14I ASP* 3.1 9.4 + - - +
15I VAL* 2.8 28.9 + - - +
7K GLN* 2.9 22.1 + - - +
11K ASN* 2.5 38.2 + - - -
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Residues in contact with ILE 12 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8I ALA 3.1 15.4 + - - +
9I LEU* 3.2 18.3 + - + +
11I SER* 1.3 75.4 - - - +
13I ILE* 1.3 61.1 + - - +
15I VAL* 3.4 8.0 + - - +
16I TYR 3.2 17.2 + - - -
68I PHE* 4.9 0.4 - - + -
71I PHE* 3.5 24.3 - - + -
72I LEU* 4.6 3.1 - - + -
75I VAL* 3.8 29.2 - - + -
8K LEU* 4.1 11.0 - - + -
11K ASN* 3.8 20.4 - - + +
12K ILE* 5.4 1.6 - - + -
15K ILE* 3.9 27.4 - - + -
87K THR* 4.3 15.5 - - + +
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Residues in contact with ILE 13 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9I LEU 3.8 5.2 - - - +
10I ASN* 3.2 27.5 + - - +
12I ILE* 1.3 74.3 - - - +
14I ASP* 1.3 65.2 + - - +
16I TYR* 3.3 4.7 + - - +
17I HIS* 3.1 46.0 + - + +
68I PHE* 3.8 15.9 - - + -
87K THR* 3.6 24.7 - - + +
90K SER* 4.0 3.1 - - - +
91K HIS* 3.5 44.0 - - + +
94K MET* 4.1 17.7 - - - -
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Residues in contact with ASP 14 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10I ASN 3.1 11.3 + - - +
11I SER* 3.1 10.7 + - - +
13I ILE* 1.3 77.8 - - - +
15I VAL* 1.3 61.0 + - - +
17I HIS* 3.3 11.2 + - - +
18I LYS* 3.0 30.2 + - - +
7K GLN* 3.0 25.5 + - - +
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Residues in contact with VAL 15 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11I SER 2.8 21.8 + - - +
12I ILE* 3.5 10.5 - - - +
13I ILE 3.3 0.2 - - - -
14I ASP* 1.3 71.7 - - - +
16I TYR* 1.3 64.7 + - - +
18I LYS* 3.2 13.3 + - - +
19I TYR* 3.1 28.2 - - + -
37I LEU* 5.1 1.1 - - + -
41I GLU* 3.9 28.3 - - + +
71I PHE* 4.2 16.4 - - + -
7K GLN* 3.6 31.2 - - + +
8K LEU* 4.1 22.0 - - + +
11K ASN* 4.2 4.9 - - - +
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Residues in contact with TYR 16 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12I ILE 3.2 3.8 + - - -
13I ILE 3.5 7.6 - - - +
15I VAL* 1.3 78.1 - - - +
17I HIS* 1.3 76.3 + + - +
19I TYR* 3.0 7.5 + - - +
20I SER* 2.9 37.0 + - - -
26I PHE 4.7 0.7 - - - -
27I HIS* 3.1 28.4 + - - -
28I ALA* 3.6 2.4 + - - -
29I VAL* 3.3 23.8 - - + -
37I LEU* 5.3 1.8 - - + -
66I VAL* 2.8 25.1 + - + -
67I ASN* 3.2 13.5 - - - -
68I PHE* 3.5 39.3 - + + -
71I PHE* 3.6 38.1 - + + -
91K HIS* 5.7 0.4 - - - -
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Residues in contact with HIS 17 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13I ILE* 3.1 39.7 + - + +
14I ASP* 3.3 11.2 + - - +
16I TYR* 1.3 85.6 - + - +
18I LYS* 1.3 66.0 + - - +
20I SER* 3.5 15.9 - - - -
21I LEU* 3.0 42.6 + - + +
26I PHE 4.6 5.2 - - - -
27I HIS* 5.7 1.6 + - - -
91K HIS* 4.3 6.6 + + - -
94K MET* 5.7 4.3 - - + -
95K HIS* 3.9 31.8 + + - -
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Residues in contact with LYS 18 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14I ASP* 3.0 21.8 + - - +
15I VAL* 3.4 19.1 - - - +
16I TYR 3.2 0.2 - - - -
17I HIS* 1.3 76.4 - - - +
19I TYR* 1.3 71.1 + - + +
21I LEU* 4.2 6.9 + - - +
22I ILE* 3.8 13.5 + - - +
40I THR* 5.9 0.6 - - - +
41I GLU* 2.7 31.6 + - - -
7K GLN* 2.6 35.5 + - - +
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Residues in contact with TYR 19 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15I VAL* 3.1 25.1 - - + -
16I TYR 3.0 5.7 + - - +
18I LYS* 1.3 92.0 + - + +
20I SER* 1.3 63.8 + - - +
21I LEU 3.1 1.8 - - - -
22I ILE* 3.2 39.7 + - + +
23I LYS 4.8 0.2 + - - -
28I ALA 4.6 0.2 - - - +
29I VAL* 4.0 14.3 - - + +
33I ASP* 4.0 18.2 - - + +
36I LYS* 4.0 10.1 - - + -
37I LEU* 3.6 48.0 - - + -
40I THR* 3.4 25.9 - - - +
41I GLU* 3.0 35.9 + - + +
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Residues in contact with SER 20 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16I TYR* 2.9 34.4 + - - -
17I HIS* 3.5 21.8 + - - -
19I TYR* 1.3 76.4 - - - +
21I LEU* 1.3 60.9 + - - +
22I ILE 3.3 0.7 - - - -
25I ASN 3.4 6.2 - - - +
26I PHE* 2.8 32.0 + - - -
28I ALA 3.4 17.5 - - - -
29I VAL* 3.7 2.4 - - - +
1522I CA 2.4 22.7 - - - -
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Residues in contact with LEU 21 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17I HIS* 3.0 33.4 + - + +
18I LYS* 4.6 5.8 - - - +
19I TYR 3.1 0.4 - - - -
20I SER* 1.3 82.2 + - - +
22I ILE* 1.3 63.9 + - - +
23I LYS 3.4 0.7 - - - -
26I PHE* 3.9 48.4 - - + +
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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