Contacts of the helix formed by residues 19 - 32 (chain B) in PDB entry 1MOX
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 19 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16B GLN* 4.0 1.8 - - - +
18B GLY* 1.3 75.2 - - - -
20B PHE* 1.3 56.6 + - - +
21B GLU* 3.3 12.9 + - - +
22B ASP* 2.5 54.0 + - - +
23B HIS* 2.8 10.5 + - - -
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Residues in contact with PHE 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 GLN* 2.9 36.1 - - - +
19B THR* 1.3 70.8 - - - +
21B GLU* 1.3 61.3 + - - +
23B HIS* 3.6 6.7 - - - +
24B PHE* 3.0 26.0 + - - +
45B TYR* 4.1 19.8 - + + +
47B GLN* 3.3 53.8 - - + -
50B TYR* 5.0 5.5 - - + +
5D PHE* 5.4 9.6 - + - -
22D ARG* 5.2 2.5 - - - -
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Residues in contact with GLU 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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19B THR* 2.7 15.4 + - - +
20B PHE* 1.3 79.2 - - - +
22B ASP* 1.3 68.2 + - - +
24B PHE* 3.7 4.9 + - - +
25B LEU* 3.5 32.2 + - + +
50B TYR* 3.2 29.9 + - - +
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Residues in contact with ASP 22 (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 LEU* 3.4 12.3 - - + +
18B GLY* 4.3 3.8 - - - -
19B THR* 2.5 37.1 + - - +
21B GLU* 1.3 77.0 - - - +
23B HIS* 1.3 66.0 + - - +
25B LEU* 2.8 26.9 + - - +
26B SER* 3.1 13.7 + - - -
36D SER* 5.2 9.9 - - - -
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Residues in contact with HIS 23 (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 ASN* 5.6 4.3 - - + -
15B THR 3.7 18.6 - - - -
16B GLN* 3.6 11.8 - - + -
17B LEU* 3.0 44.4 + - + +
19B THR 2.8 12.9 + - - +
20B PHE* 3.6 13.0 - - - +
22B ASP* 1.3 72.4 - - - +
24B PHE* 1.3 66.2 + - - +
26B SER* 3.4 4.3 + - - +
27B LEU* 3.1 25.9 + - + +
42B GLU 5.5 1.2 + - - -
44B THR* 2.6 51.2 + - - -
45B TYR* 3.8 11.2 - + + -
46B VAL* 5.3 2.0 - - + -
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Residues in contact with PHE 24 (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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20B PHE 3.0 17.8 + - - +
21B GLU* 3.7 6.7 - - - +
23B HIS* 1.3 78.9 - - - +
25B LEU* 1.3 63.0 + - + +
27B LEU* 2.9 11.2 + - + +
28B GLN* 2.6 56.4 + - + +
46B VAL* 4.1 17.9 - - + -
50B TYR* 3.5 42.0 - + + -
51B ASP* 3.0 31.6 - - + -
52B LEU* 3.6 21.1 - - + -
54B PHE* 4.0 12.8 - + - -
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Residues in contact with LEU 25 (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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21B GLU* 3.5 27.8 + - + +
22B ASP* 2.8 21.0 + - - +
24B PHE* 1.3 79.6 - - + +
26B SER* 1.3 52.2 + - - +
28B GLN* 3.0 27.6 + - - +
29B ARG* 2.6 55.0 + - - +
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Residues in contact with SER 26 (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 LEU* 3.6 31.4 - - - +
22B ASP 3.1 7.5 + - - -
23B HIS 3.6 7.9 - - - -
25B LEU* 1.3 76.5 - - - +
27B LEU* 1.3 56.1 + - - +
29B ARG* 3.0 27.1 + - - +
30B MET* 2.7 49.3 + - - +
39D VAL* 5.6 1.2 - - - +
47D ASP* 5.5 1.2 + - - -
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Residues in contact with LEU 27 (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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10B THR* 6.3 0.7 - - + -
23B HIS* 3.1 14.3 + - + +
24B PHE* 2.9 14.3 + - + +
26B SER* 1.3 80.8 - - - +
28B GLN* 1.3 61.5 + - - +
30B MET* 4.8 1.6 - - - -
31B PHE* 3.2 51.5 + - + +
42B GLU 3.1 27.6 - - - +
43B ILE* 4.0 16.2 - - + -
44B THR 4.9 3.1 - - - +
46B VAL* 3.8 29.6 - - + -
52B LEU* 4.1 17.5 - - + -
54B PHE* 4.2 9.8 - - + -
55B LEU* 5.7 0.2 - - + -
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Residues in contact with GLN 28 (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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24B PHE* 2.6 39.4 + - + +
25B LEU* 3.5 28.2 + - - +
27B LEU* 1.3 73.2 - - - +
29B ARG* 1.3 58.3 + - - +
32B ASN* 3.1 32.2 + - - +
51B ASP 5.1 0.5 - - - +
54B PHE* 3.6 33.4 - - + -
1G NAG 4.8 19.6 - - - +
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Residues in contact with ARG 29 (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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25B LEU* 2.6 38.0 + - - +
26B SER* 3.2 32.8 + - - +
28B GLN* 1.3 75.1 - - - +
30B MET* 1.3 78.7 + - + +
31B PHE 3.4 0.9 + - - -
32B ASN* 4.0 8.2 + - - +
47D ASP* 4.9 10.1 + - - -
49D LEU* 5.4 17.7 + - + +
1G NAG 4.8 11.7 - - - +
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Residues in contact with MET 30 (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 CYS* 3.9 17.2 - - - +
8B GLN* 5.3 4.6 + - - -
9B GLY 5.3 4.5 + - - +
10B THR* 4.4 10.8 - - + -
26B SER* 2.7 31.6 + - - +
27B LEU* 4.0 3.1 - - - +
29B ARG* 1.3 88.5 - - + +
31B PHE* 1.3 78.4 + - + +
409B HIS* 6.3 2.7 - - + +
706B PT 2.0 29.4 - - - -
39D VAL* 5.7 6.1 - - + -
47D ASP* 5.6 9.6 - - + -
49D LEU* 3.9 34.5 - - + -
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Residues in contact with PHE 31 (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 CYS* 3.8 13.0 - - - -
9B GLY* 3.8 25.8 - - - -
10B THR* 4.3 10.3 - - + -
27B LEU* 3.2 49.8 + - + +
30B MET* 1.3 92.7 - - + +
32B ASN* 1.3 66.8 + - - +
33B ASN 3.4 2.0 - - - -
34B CYS* 2.8 21.9 + - + +
37B VAL* 4.0 13.7 - - + -
40B ASN 3.9 13.0 - - - -
41B LEU* 3.6 34.8 - - + -
42B GLU 4.3 4.9 - - - -
54B PHE* 4.2 22.1 - + + +
55B LEU* 4.6 6.1 - - + -
58B ILE* 4.4 5.8 - - + +
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Residues in contact with ASN 32 (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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28B GLN* 3.1 23.3 + - - +
29B ARG 4.0 7.5 + - - +
30B MET 3.8 0.8 - - - -
31B PHE* 1.3 74.9 - - - +
33B ASN* 1.3 67.8 + - - +
34B CYS 3.8 0.2 + - - -
54B PHE* 3.9 32.9 - - - +
57B THR* 4.1 5.4 + - - +
1G NAG 1.4 69.4 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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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