Contacts of the helix formed by residues 3 - 21 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1E MET 4.8 0.9 - - - +
2E LEU* 1.3 77.0 - - - +
4E GLU* 1.3 60.6 + - - +
5E LEU 3.6 2.5 + - - -
6E GLU* 3.0 27.3 + - - +
7E LYS* 3.0 26.6 + - - +
43G LYS 3.5 18.4 - - - +
44G ASP* 2.7 35.5 + - - +
46G GLN* 3.9 14.1 - - + +
47G ASN* 3.9 7.4 - - - +
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Residues in contact with GLU 4 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2E LEU 5.3 0.5 - - - +
3E THR* 1.3 75.4 - - - +
5E LEU* 1.3 57.1 + - - +
7E LYS* 2.8 38.4 + - - +
8E ALA* 3.0 28.1 + - - +
14G THR* 3.8 12.6 - - + +
44G ASP* 5.8 0.2 + - - -
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Residues in contact with LEU 5 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3E THR* 3.3 1.0 + - - +
4E GLU* 1.3 76.7 - - - +
6E GLU* 1.3 63.1 + - - +
8E ALA* 3.2 2.5 + - + +
9E LEU* 3.1 29.0 + - + +
14G THR* 4.2 9.1 - - + +
15G ILE* 4.0 30.3 - - + +
18G THR* 4.1 24.3 + - + +
40G LEU* 4.3 6.3 - - + -
44G ASP* 3.8 27.9 + - + +
45G LEU* 3.7 31.6 - - + -
79G PHE* 5.0 1.8 - - + -
83G MET* 3.9 30.7 - - + -
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Residues in contact with GLU 6 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2E LEU* 3.5 7.3 - - + +
3E THR* 3.0 26.8 + - - +
5E LEU* 1.3 76.2 - - - +
7E LYS* 1.3 59.2 + - - +
9E LEU* 3.3 7.2 + - - +
10E ASN* 3.0 32.2 + - - +
44G ASP 3.6 7.0 - - - +
45G LEU* 3.2 14.5 - - + -
47G ASN* 2.4 44.1 + - - +
48G PHE* 2.9 57.2 + - + -
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Residues in contact with LYS 7 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2E LEU* 3.5 31.6 + - + +
3E THR 3.0 22.1 + - - +
4E GLU* 2.8 36.7 + - - +
6E GLU* 1.3 76.2 - - - +
8E ALA* 1.3 56.6 + - - +
10E ASN* 3.4 8.1 + - - +
11E SER* 3.0 29.1 + - - -
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Residues in contact with ALA 8 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E GLU 3.0 15.6 + - - +
5E LEU* 3.2 12.5 + - + +
7E LYS* 1.3 76.0 - - - +
9E LEU* 1.3 61.6 + - - +
11E SER* 3.2 4.0 + - - -
12E ILE* 3.1 26.3 + - - +
11G ASN* 3.5 27.0 - - - +
14G THR* 3.8 27.8 - - + +
15G ILE* 5.0 1.8 - - + -
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Residues in contact with LEU 9 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E LEU* 3.1 16.3 + - + +
6E GLU* 3.3 7.4 + - - +
8E ALA* 1.3 72.7 - - - +
10E ASN* 1.3 65.5 + - - +
12E ILE* 3.1 22.7 + - + +
13E ILE* 3.5 4.8 + - - +
15G ILE* 3.9 29.2 - - + -
45G LEU* 4.5 7.0 - - + -
48G PHE* 4.2 19.3 - - + -
83G MET* 4.1 29.8 - - + +
86G LEU* 4.0 30.7 - - + -
87G THR* 3.5 31.1 - - - +
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Residues in contact with ASN 10 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2E LEU* 3.5 30.9 - - - +
6E GLU 3.0 14.6 + - - +
7E LYS* 3.8 6.7 - - - +
8E ALA 3.4 0.2 - - - -
9E LEU* 1.3 77.3 - - - +
11E SER* 1.3 60.5 + - - +
13E ILE* 3.3 15.0 + - + +
14E ASP* 3.2 18.8 + - - +
48G PHE* 3.6 9.6 - - - -
90G SER* 2.6 32.4 + - - -
94G MET* 5.2 5.8 - - - +
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Residues in contact with SER 11 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E LYS 3.0 16.9 + - - -
8E ALA* 3.5 1.1 - - - -
9E LEU 3.2 0.4 - - - -
10E ASN* 1.3 74.0 - - - +
12E ILE* 1.3 59.3 + - - +
14E ASP* 3.1 10.3 + - - +
15E VAL* 2.8 28.2 + - - +
7G GLN* 2.7 28.0 + - - +
11G ASN* 2.7 33.9 + - - -
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Residues in contact with ILE 12 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E ALA 3.1 14.5 + - - +
9E LEU* 3.1 18.0 + - + +
11E SER* 1.3 75.9 - - - +
13E ILE* 1.3 61.0 + - - +
15E VAL* 3.3 8.4 + - - +
16E TYR 3.1 17.8 + - - -
68E PHE* 4.9 0.4 - - + -
71E PHE* 3.8 24.1 - - + -
72E LEU* 4.5 4.5 - - + -
75E VAL* 4.1 27.1 - - + -
8G LEU* 4.0 11.7 - - + -
11G ASN* 3.8 19.5 - - + +
12G ILE* 5.1 1.8 - - + -
15G ILE* 4.0 27.6 - - + -
87G THR* 4.1 17.3 - - + +
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Residues in contact with ILE 13 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E LEU 3.8 3.6 - - - +
10E ASN* 3.3 16.8 + - - +
11E SER 3.2 0.2 - - - -
12E ILE* 1.3 73.8 - - - +
14E ASP* 1.3 66.2 + - - +
16E TYR* 3.1 6.7 + - + +
17E HIS* 3.0 23.8 + - + +
68E PHE* 3.6 25.6 - - + -
87G THR* 3.6 18.2 - - + +
90G SER* 4.1 10.8 - - - +
91G HIS* 3.6 43.3 - - + +
94G MET* 3.6 29.8 - - + -
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Residues in contact with ASP 14 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E ASN 3.2 8.5 + - - +
11E SER* 3.1 11.6 + - - +
13E ILE* 1.3 79.3 - - - +
15E VAL* 1.3 62.9 + - - +
17E HIS* 3.2 20.0 + - - +
18E LYS* 3.0 28.1 + - - +
7G GLN* 2.9 26.0 + - - +
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Residues in contact with VAL 15 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E SER 2.8 17.7 + - - +
12E ILE* 3.5 9.9 - - - +
13E ILE 3.3 0.2 - - - -
14E ASP* 1.3 71.3 - - - +
16E TYR* 1.3 65.4 + - - +
18E LYS* 3.2 14.2 + - - +
19E TYR* 3.2 22.7 - - + -
37E LEU* 4.8 2.2 - - + -
41E GLU* 3.9 28.0 - - + +
71E PHE* 4.3 15.0 - - + -
7G GLN* 3.4 40.6 - - + +
8G LEU* 4.0 18.6 - - + +
11G ASN* 4.3 4.5 - - - +
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Residues in contact with TYR 16 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E ILE 3.1 3.8 + - - +
13E ILE* 3.1 8.7 + - + +
15E VAL* 1.3 80.3 - - - +
17E HIS* 1.3 59.4 + - + +
19E TYR* 3.1 4.9 + - - +
20E SER* 2.8 46.3 + - - -
26E PHE 4.9 0.2 - - - -
27E HIS* 3.1 27.8 + - - -
28E ALA* 3.5 2.4 - - - -
29E VAL* 3.4 20.4 - - + -
37E LEU* 5.1 3.1 - - + -
66E VAL* 2.8 25.9 + - + -
67E ASN* 3.3 3.6 - - - -
68E PHE* 3.6 34.8 - + + -
71E PHE* 3.5 51.8 - + + -
91G HIS* 5.8 3.1 - + - -
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Residues in contact with HIS 17 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13E ILE* 3.0 16.3 + - + +
14E ASP* 3.4 23.1 - - - +
16E TYR* 1.3 77.4 - - + +
18E LYS* 1.3 65.0 + - + +
20E SER* 3.6 9.6 + - - -
21E LEU* 3.0 67.9 + - + +
26E PHE 5.7 0.8 + - - -
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Residues in contact with LYS 18 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E ASP* 3.0 20.5 + - - +
15E VAL* 3.3 22.0 - - - +
16E TYR 3.2 0.4 - - - -
17E HIS* 1.3 77.9 - - + +
19E TYR* 1.3 73.5 + - + +
21E LEU* 4.3 7.0 + - - +
22E ILE* 3.9 12.5 + - - +
40E THR* 6.0 0.4 - - - +
41E GLU* 2.8 29.0 + - - -
7G GLN* 2.6 37.8 + - - +
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Residues in contact with TYR 19 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E VAL* 3.2 22.7 - - + -
16E TYR 3.1 5.6 + - - +
18E LYS* 1.3 87.2 - - + +
20E SER* 1.3 67.4 + - - +
21E LEU 3.1 2.0 - - - -
22E ILE* 3.2 36.6 + - + +
29E VAL* 4.0 14.1 - - + -
33E ASP* 3.8 26.9 - - + +
36E LYS* 3.8 11.0 - - + -
37E LEU* 3.6 37.9 - - + -
40E THR* 3.1 35.7 + - - +
41E GLU* 3.6 28.0 + - + +
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Residues in contact with SER 20 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E TYR* 2.8 39.8 + - - -
17E HIS* 3.5 15.9 + - - -
19E TYR* 1.3 79.0 - - - +
21E LEU* 1.3 59.8 + - - +
22E ILE 3.3 0.7 - - - -
26E PHE* 2.8 35.2 + - - -
28E ALA 3.5 16.8 - - - -
29E VAL* 3.7 2.4 - - - +
1512E CA 2.2 26.4 - - - -
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Residues in contact with LEU 21 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E HIS* 3.0 60.7 + - + +
18E LYS* 4.4 6.5 - - - +
19E TYR 3.1 0.4 - - - -
20E SER* 1.3 79.3 - - - +
22E ILE* 1.3 65.3 + - - +
23E LYS 3.3 1.9 + - - -
26E PHE* 3.7 50.7 - - + +
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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
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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