Contacts of the helix formed by residues 3 - 21 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MET 4.9 0.4 - - - +
2B LEU* 1.3 77.0 - - - +
4B GLU* 1.3 65.9 + - - +
5B LEU 3.4 3.2 + - - -
6B GLU* 3.0 28.8 + - - +
7B LYS* 2.9 24.0 + - - +
43D LYS 3.6 22.4 - - - +
44D ASP* 2.8 30.5 + - - +
46D GLN* 3.9 17.3 - - + +
47D ASN* 4.0 0.9 - - - +
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Residues in contact with GLU 4 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B LEU 4.9 2.1 - - - +
3B THR* 1.3 76.2 - - - +
5B LEU* 1.3 62.7 + - - +
7B LYS* 3.3 32.2 + - - +
8B ALA* 3.0 23.0 + - - +
14D THR* 3.9 12.7 - - + +
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Residues in contact with LEU 5 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B THR* 3.3 1.5 + - - +
4B GLU* 1.3 79.2 - - - +
6B GLU* 1.3 63.1 + - - +
8B ALA* 3.2 3.4 + - + +
9B LEU* 3.0 24.8 + - + +
14D THR* 4.2 7.7 - - + +
15D ILE* 4.1 27.1 - - + -
18D THR* 4.1 20.3 + - + +
40D LEU* 4.3 11.0 - - + -
44D ASP* 3.7 28.3 + - + +
45D LEU* 3.6 32.8 - - + -
79D PHE* 5.1 1.6 - - + -
83D MET* 4.0 27.4 - - - -
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Residues in contact with GLU 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B LEU* 3.5 8.9 - - + +
3B THR* 3.0 29.9 + - - +
5B LEU* 1.3 76.2 - - - +
7B LYS* 1.3 58.0 + - - +
9B LEU* 3.2 5.3 + - - +
10B ASN* 2.9 28.3 + - - +
44D ASP 3.6 6.5 - - - +
45D LEU* 3.2 13.9 - - + -
47D ASN* 2.7 57.0 + - - +
48D PHE* 2.9 48.8 + - + -
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Residues in contact with LYS 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B LEU* 3.7 34.1 + - + +
3B THR 2.9 19.3 + - - +
4B GLU* 3.3 31.6 + - - +
6B GLU* 1.3 75.8 - - - +
8B ALA* 1.3 57.3 + - - +
10B ASN* 3.3 7.1 + - - +
11B SER* 2.9 29.9 + - - -
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Residues in contact with ALA 8 (chain B).
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 3.0 15.2 + - - +
5B LEU* 3.2 8.5 + - - +
7B LYS* 1.3 75.3 - - - +
9B LEU* 1.3 64.6 + - - +
11B SER* 3.2 4.0 + - - -
12B ILE* 3.1 25.9 + - - +
11D ASN* 3.6 32.0 - - - +
14D THR* 3.8 23.1 - - + +
15D ILE* 4.9 4.9 - - + -
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Residues in contact with LEU 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B LEU* 3.0 19.8 + - + +
6B GLU 3.2 6.3 + - - +
8B ALA* 1.3 76.0 - - - +
10B ASN* 1.3 62.1 + - - +
12B ILE* 3.2 22.7 + - + +
13B ILE* 3.5 4.6 + - - +
15D ILE* 3.9 28.3 - - + -
45D LEU* 4.7 6.7 - - + -
48D PHE* 3.9 21.1 - - + -
83D MET* 4.1 26.7 - - + +
86D LEU* 3.8 31.0 - - + -
87D THR* 3.5 31.8 - - - +
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Residues in contact with ASN 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B LEU* 3.5 29.3 - - - +
6B GLU 2.9 13.9 + - - +
7B LYS* 3.3 6.9 + - - +
9B LEU* 1.3 75.3 - - - +
11B SER* 1.3 60.9 + - - +
13B ILE* 3.2 23.1 + - - +
14B ASP* 3.2 12.2 + - - +
48D PHE* 3.5 11.3 - - - -
90D SER* 2.6 31.6 + - - -
94D MET* 5.5 5.8 - - - +
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Residues in contact with SER 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B LYS 2.9 16.6 + - - -
8B ALA 3.4 1.8 - - - -
10B ASN* 1.3 75.8 - - - +
12B ILE* 1.3 59.5 + - - +
14B ASP* 3.1 8.8 + - - +
15B VAL* 2.9 30.1 + - - +
7D GLN* 2.8 27.4 + - - +
11D ASN* 2.9 32.1 + - - -
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Residues in contact with ILE 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B ALA 3.1 15.5 + - - +
9B LEU* 3.2 18.6 + - + +
11B SER* 1.3 77.3 - - - +
13B ILE* 1.3 61.1 + - - +
15B VAL* 3.3 7.3 + - - +
16B TYR 3.2 17.0 + - - -
68B PHE* 4.9 0.7 - - + -
71B PHE* 3.9 24.8 - - + -
72B LEU* 4.6 3.1 - - + -
75B VAL* 4.1 26.7 - - + -
8D LEU* 4.2 9.4 - - + -
11D ASN* 3.8 21.5 - - + +
12D ILE* 5.3 1.6 - - + -
15D ILE* 4.0 26.7 - - + -
87D THR* 4.1 16.6 - - + +
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Residues in contact with ILE 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B LEU 3.5 6.2 + - - +
10B ASN* 3.2 29.7 + - - +
12B ILE* 1.3 76.8 - - - +
14B ASP* 1.3 55.3 + - - +
16B TYR* 3.3 6.2 + - + +
17B HIS* 3.0 29.2 + - + +
68B PHE* 3.6 26.0 - - + -
87D THR* 3.5 14.4 - - + +
90D SER* 4.0 3.1 - - - +
91D HIS* 3.5 47.1 - - + +
94D MET* 4.2 27.8 - - + -
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Residues in contact with ASP 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ASN 3.2 8.1 + - - +
11B SER* 3.1 11.8 + - - +
13B ILE* 1.3 77.3 - - - +
15B VAL* 1.3 64.8 + - - +
17B HIS* 3.3 16.3 + - - +
18B LYS* 3.0 29.1 + - - +
7D GLN* 2.9 25.4 + - - +
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Residues in contact with VAL 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B SER 2.9 17.8 + - - +
12B ILE* 3.3 9.6 + - - +
14B ASP* 1.3 76.0 - - - +
16B TYR* 1.3 64.4 + - - +
18B LYS* 3.1 27.2 + - - +
19B TYR* 3.3 13.9 - - + -
37B LEU* 4.8 3.1 - - + -
41B GLU* 3.8 28.9 - - + +
71B PHE* 4.4 14.1 - - + -
7D GLN* 3.6 30.1 - - + +
8D LEU* 3.9 24.5 - - + +
11D ASN* 4.2 4.9 - - - +
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Residues in contact with TYR 16 (chain B).
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 3.2 3.4 + - - -
13B ILE* 3.3 8.0 + - + +
15B VAL* 1.3 79.5 - - - +
17B HIS* 1.3 61.2 + - + +
19B TYR* 3.1 5.5 + - - +
20B SER* 2.9 45.8 + - - -
26B PHE 4.9 0.4 - - - -
27B HIS* 3.3 27.3 + - - -
28B ALA* 3.6 2.4 - - - -
29B VAL* 3.5 19.0 + - + -
37B LEU* 5.1 3.6 - - + -
66B VAL* 2.9 25.1 + - + -
67B ASN* 3.4 12.5 - - - -
68B PHE* 3.5 42.2 - + + -
71B PHE* 3.6 39.6 - + + -
91D HIS* 5.8 3.4 - + - -
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Residues in contact with HIS 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ILE* 3.0 16.3 + - + +
14B ASP* 3.5 20.4 - - - +
16B TYR* 1.3 78.8 - - + +
18B LYS* 1.3 62.0 + - - +
20B SER* 3.6 10.6 + - - -
21B LEU* 3.2 69.6 + - + +
26B PHE* 5.1 3.6 + - + -
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Residues in contact with LYS 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ASP* 3.0 21.8 + - - +
15B VAL* 3.1 24.2 + - - +
17B HIS* 1.3 76.8 - - - +
19B TYR* 1.3 72.9 + - + +
21B LEU* 4.2 7.5 + - - +
22B ILE* 3.9 13.7 + - - +
41B GLU* 2.6 31.4 + - - -
7D GLN* 2.7 34.8 + - - +
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Residues in contact with TYR 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B VAL* 3.3 15.0 - - + -
16B TYR 3.1 5.6 + - - +
18B LYS* 1.3 92.8 + - + +
20B SER* 1.3 64.2 + - - +
21B LEU 3.2 2.0 - - - -
22B ILE* 3.4 35.6 + - + +
29B VAL* 3.9 14.1 - - + -
33B ASP* 3.7 30.0 - - + +
36B LYS* 3.8 11.2 - - + -
37B LEU* 3.6 39.0 - - + -
40B THR* 3.2 34.1 + - - +
41B GLU* 3.7 26.9 + - + +
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Residues in contact with SER 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B TYR* 2.9 41.8 + - - -
17B HIS* 3.6 15.4 + - - -
19B TYR* 1.3 76.5 - - - +
21B LEU* 1.3 60.4 + - - +
25B ASN 3.4 4.2 - - - +
26B PHE* 2.8 31.1 + - - -
28B ALA 3.5 16.8 - - - -
29B VAL* 3.7 2.4 - - - +
2502B CA 2.2 26.4 - - - -
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Residues in contact with LEU 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B HIS* 3.2 60.2 + - + +
18B LYS* 4.3 7.0 - - - +
19B TYR 3.2 0.8 - - - -
20B SER* 1.3 78.3 - - - +
22B ILE* 1.3 65.7 + - - +
23B LYS 3.4 0.8 + - - -
26B PHE* 3.5 52.8 - - + -
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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