Contacts of the helix formed by residues 22 - 29 (chain A) in PDB entry 2AJA
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 PRO 22 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A LEU 3.8 2.7 - - - +
21A ILE* 1.3 88.1 - - + +
23A TRP* 1.3 67.8 + - - +
24A ILE* 3.1 25.8 - - + -
25A LEU* 2.8 20.1 + - + +
26A TRP* 3.1 9.9 + - - +
71A TYR* 3.5 42.6 - - + +
208B GLY* 6.0 1.1 - - - +
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Residues in contact with TRP 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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6A ILE* 4.7 0.9 - - + -
7A HIS* 3.3 33.7 - - - -
9A ILE* 3.5 38.8 - - + +
12A TYR* 3.4 51.6 - + + -
21A ILE 3.1 6.8 + - - -
22A PRO* 1.3 70.5 - - - +
24A ILE* 1.3 69.7 + - + +
26A TRP* 3.2 20.2 + + - +
27A GLU* 2.7 63.5 + - + +
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Residues in contact with ILE 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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22A PRO* 3.3 25.6 - - + -
23A TRP* 1.3 80.2 - - + +
25A LEU* 1.3 89.3 + - + +
27A GLU* 3.3 5.9 + - - +
28A ASN* 2.7 41.0 + - - +
138A ASN* 5.7 0.9 - - - +
208B GLY* 3.4 39.0 - - - +
209B ARG* 4.6 20.6 - - + +
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Residues in contact with LEU 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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21A ILE* 4.3 7.4 - - + -
22A PRO* 2.8 24.6 + - + +
24A ILE* 1.3 91.6 - - + +
26A TRP* 1.3 58.0 + - - +
27A GLU 2.9 4.9 + - - -
28A ASN* 4.3 2.7 - - + +
29A LEU* 2.6 57.3 + - + +
30A PHE* 3.3 6.7 + - + -
67A LEU* 5.1 4.9 - - + -
71A TYR* 3.3 36.1 - - + +
101A ILE* 4.2 20.9 - - + +
138A ASN* 5.0 1.1 - - - +
209B ARG* 3.9 20.2 - - - +
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Residues in contact with TRP 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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4A LEU 4.8 0.4 - - - -
5A THR 4.7 0.4 - - - -
6A ILE* 3.1 30.2 + - + -
12A TYR* 3.3 47.3 - + + +
18A LEU* 3.5 32.5 - - + -
21A ILE* 4.3 7.7 - - + +
22A PRO 3.1 5.5 + - - +
23A TRP* 3.2 21.5 + + - +
25A LEU* 1.3 76.7 - - - +
27A GLU* 1.3 61.4 + - + +
30A PHE* 3.5 37.4 - + + +
31A GLN 3.3 5.2 + - - -
32A HIS* 2.8 49.4 + - - +
33A PHE* 3.7 7.0 - - - -
34A ILE* 3.6 36.1 - - + -
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Residues in contact with GLU 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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7A HIS 5.2 0.3 - - - +
23A TRP* 2.7 62.7 + - + +
24A ILE* 3.8 8.5 - - - +
25A LEU 2.9 0.8 - - - -
26A TRP* 1.3 84.3 - - + +
28A ASN* 1.3 65.8 + - - +
29A LEU 3.5 0.4 - - - -
31A GLN* 3.9 14.6 - - - +
32A HIS* 3.2 40.1 + - + +
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Residues in contact with ASN 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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24A ILE* 2.7 29.1 + - - +
25A LEU* 3.0 4.5 + - + +
27A GLU* 1.3 87.3 - - - +
29A LEU* 1.3 66.3 + - + +
31A GLN* 4.9 2.9 - - - +
60A MSE 5.2 1.6 - - - +
209B ARG* 4.5 23.1 - - - +
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Residues in contact with LEU 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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25A LEU* 2.6 39.4 + - + +
27A GLU 3.5 0.2 - - - -
28A ASN* 1.3 78.9 - - + +
30A PHE* 1.3 71.4 + - + +
31A GLN* 3.3 11.1 + - - +
60A MSE 3.3 46.4 - - + +
63A VAL* 5.0 5.2 - - + -
64A ARG* 3.7 15.9 + - + -
67A LEU* 3.9 25.8 - - + -
101A ILE* 4.6 17.0 - - + -
134A LEU* 6.3 2.0 - - + -
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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