Contacts of the helix formed by residues 21 - 32 (chain A) in PDB entry 1X3B
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 PHE 21 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A VAL* 4.6 4.3 - - + -
15A LEU* 3.1 34.2 - - + +
18A ASP* 3.1 47.5 + - + -
19A ASN 2.9 0.6 - - - -
20A ARG* 1.3 96.0 - - + +
22A SER* 1.3 59.4 + - - +
23A MET 3.8 0.2 - - - -
24A LEU* 4.0 11.8 - - + +
25A VAL* 3.1 17.3 + - - +
47A ALA* 4.0 17.5 - - + -
48A PRO 2.9 29.4 - - - -
49A THR* 4.3 3.6 - - + -
53A PHE* 6.1 0.4 - - - -
133A VAL* 3.6 41.7 - - + -
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Residues in contact with SER 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A LEU 4.7 0.2 - - - -
16A LYS 5.6 2.9 - - - -
18A ASP 4.2 2.5 - - - -
19A ASN* 2.8 42.1 + - - -
20A ARG 3.4 1.2 + - - -
21A PHE* 1.3 69.8 - - - +
23A MET* 1.3 66.5 + - - +
24A LEU 2.7 13.8 + - - -
25A VAL* 2.7 25.1 + - - +
26A ALA* 3.3 5.6 + - - +
50A ASN* 4.5 4.9 + - - -
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Residues in contact with MET 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ARG 5.3 0.8 + - - +
22A SER* 1.3 84.5 + - - +
24A LEU* 1.3 62.7 + - - +
26A ALA* 3.6 12.0 - - + +
27A ALA* 3.4 15.1 + - - +
50A ASN* 5.8 3.4 - - - +
53A PHE* 3.8 43.1 - - + -
54A ARG* 6.2 2.2 - - + +
61A ARG* 5.1 10.5 - - - +
65A LEU* 4.4 32.0 - - + +
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Residues in contact with LEU 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A LEU* 4.7 4.7 - - + -
21A PHE* 4.0 17.2 - - + +
22A SER 2.7 2.0 + - - +
23A MET* 1.3 76.8 - - - +
25A VAL* 1.3 56.6 + - - +
27A ALA* 2.6 41.3 + - + +
28A ILE* 3.0 27.5 + - + +
45A VAL* 5.9 3.1 - - + -
46A PHE 4.3 4.5 - - - +
47A ALA* 3.0 44.9 - - + -
48A PRO* 3.7 9.2 - - + -
53A PHE* 3.7 26.5 - - + -
75A LEU* 4.4 12.1 - - + -
78A HIS* 6.4 1.6 - - + -
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Residues in contact with VAL 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A MET* 3.9 7.4 - - + -
15A LEU* 3.6 10.8 - - + -
16A LYS* 3.3 59.9 - - + +
21A PHE 3.1 20.4 - - - +
22A SER* 2.7 13.3 + - - +
24A LEU* 1.3 70.9 - - - +
26A ALA* 1.3 56.4 + - - +
28A ILE* 2.5 34.1 + - + +
29A GLN* 2.7 18.2 + - + -
34A THR* 5.0 2.0 - - - +
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Residues in contact with ALA 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A SER 3.3 4.6 + - - +
23A MET* 3.6 17.3 - - + +
24A LEU 3.2 0.2 - - - -
25A VAL* 1.3 79.6 - - - +
27A ALA* 1.3 56.8 + - - +
29A GLN* 3.7 7.9 - - - +
30A SER* 2.8 33.9 + - - -
65A LEU* 6.4 0.9 - - + -
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Residues in contact with ALA 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A MET 3.4 7.4 + - - +
24A LEU* 2.6 29.2 + - + +
26A ALA* 1.3 76.2 - - - +
28A ILE* 1.3 50.6 + - - +
30A SER* 3.7 1.6 - - - -
31A ALA* 2.8 35.0 + - - +
53A PHE* 5.5 4.9 - - + -
65A LEU* 5.6 7.8 - - + +
71A LEU* 3.7 34.1 - - + +
75A LEU* 3.2 8.6 - - + +
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Residues in contact with ILE 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A MET* 3.4 30.7 - - + -
15A LEU* 4.1 10.1 - - + -
24A LEU* 3.0 25.3 + - + +
25A VAL* 2.5 30.1 + - - +
27A ALA* 1.3 68.7 - - - +
29A GLN* 1.3 54.1 + - - +
31A ALA* 2.9 2.3 + - - -
32A GLY 2.6 33.3 + - - -
33A LEU* 3.2 18.5 + - + -
34A THR* 3.2 33.7 - - - +
37A LEU* 4.1 3.8 - - + -
45A VAL* 5.5 5.6 - - + -
75A LEU* 3.3 19.7 - - + -
79A ILE* 5.7 2.9 - - + -
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Residues in contact with GLN 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A LYS* 5.7 3.1 - - - +
25A VAL* 2.7 19.7 + - + +
26A ALA* 3.7 11.7 - - - +
28A ILE* 1.3 72.5 - - - +
30A SER* 1.3 64.3 + - - +
32A GLY* 3.1 13.5 + - - -
34A THR* 3.5 26.7 + - + +
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Residues in contact with SER 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ALA 2.8 22.2 + - - -
27A ALA 3.7 4.0 - - - -
29A GLN* 1.3 77.1 + - - +
31A ALA* 1.3 63.0 + - - +
32A GLY* 3.2 1.2 + - - -
68A ALA* 4.7 15.0 - - - +
71A LEU* 4.3 13.8 - - - +
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Residues in contact with ALA 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ALA 2.8 22.5 + - - +
28A ILE 2.9 3.8 + - - +
30A SER* 1.3 74.0 - - - +
32A GLY* 1.3 62.5 + - - +
33A LEU* 4.0 7.0 - - + +
68A ALA* 5.2 6.5 - - - -
71A LEU* 4.7 2.6 - - + +
72A ALA* 3.5 37.1 - - + +
75A LEU* 3.4 19.3 - - + -
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Residues in contact with GLY 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ILE 2.6 11.1 + - - -
29A GLN* 3.1 11.9 + - - -
30A SER 3.1 3.5 - - - -
31A ALA* 1.3 77.8 - - - +
33A LEU* 1.3 61.2 + - - +
34A THR* 3.6 1.6 - - - -
35A GLU* 4.9 6.9 + - - +
36A THR* 4.7 6.6 + - - -
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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