Contacts of the helix formed by residues 30 - 41 (chain A) in PDB entry 2AG1
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 ILE 30 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A LEU 3.8 17.0 - - - +
27A GLY 3.4 16.4 - - - +
29A HIS* 1.3 81.0 - - - +
31A ASP* 1.3 63.7 + - - +
32A THR 3.2 3.6 - - - +
33A ILE* 3.3 16.6 + - + +
34A PHE* 3.5 31.4 + - + -
71A LEU* 3.4 33.7 - - + +
72A VAL 3.7 15.0 - - - +
73A THR* 4.0 6.7 - - - +
99A THR 4.5 0.7 - - - -
100A GLY* 3.6 33.4 - - - +
161A LEU* 6.3 0.4 - - + -
166A LEU* 4.2 13.5 - - + -
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Residues in contact with ASP 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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26A HIS* 2.9 19.3 - - + +
27A GLY 3.3 3.0 + - - -
28A ALA 3.2 16.2 + - - +
29A HIS 3.6 0.6 - - - -
30A ILE* 1.3 76.0 - - - +
32A THR* 1.3 61.4 + - + +
33A ILE 3.2 0.2 - - - -
34A PHE* 3.3 4.2 + - - +
35A GLN* 2.9 46.3 + - - +
484B PHE* 3.8 15.2 - - + -
485B GLN* 2.9 36.4 + - - -
489B VAL* 3.3 18.4 - - - +
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Residues in contact with THR 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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5A THR* 3.8 18.7 + - + +
7A GLY* 3.4 25.4 - - - -
8A GLU 4.3 0.5 + - - -
28A ALA 5.0 0.2 + - - -
29A HIS 5.0 0.7 + - - -
30A ILE 4.7 0.2 - - - -
31A ASP* 1.3 78.8 - - + +
33A ILE* 1.3 58.2 + - - +
35A GLN* 3.9 7.6 - - + +
36A ALA* 3.1 27.9 + - - +
166A LEU* 3.5 35.2 - - - +
167A MSE 4.1 23.1 - - + -
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Residues in contact with ILE 33 (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 GLY* 4.0 23.1 - - - +
10A VAL* 4.1 22.0 - - + -
11A VAL* 3.7 15.1 - - + +
22A LEU* 4.2 11.4 - - + -
30A ILE* 3.3 12.3 + - + +
31A ASP 3.2 0.6 - - - -
32A THR* 1.3 77.4 + - - +
34A PHE* 1.3 58.8 + - - +
36A ALA 3.4 0.7 + - - -
37A CYS* 2.9 31.8 + - - -
71A LEU* 3.6 42.4 - - + -
98A LEU* 4.9 2.7 - - + -
161A LEU* 4.3 10.1 - - + -
166A LEU* 4.2 21.8 - - + -
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Residues in contact with PHE 34 (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 GLY 5.0 0.2 - - - -
25A LEU* 4.2 5.4 - - - -
26A HIS* 3.6 46.7 - - + +
30A ILE* 3.5 37.9 - - + -
31A ASP* 3.3 17.0 + - - +
33A ILE* 1.3 74.8 - - - +
35A GLN* 1.3 65.9 + - - +
37A CYS* 3.2 2.6 + - - +
38A LEU* 2.9 24.9 + - - +
44A ILE* 3.5 42.1 - - + +
46A ASP* 5.1 4.3 - - + -
71A LEU* 3.8 11.0 - - + -
485B GLN* 4.6 3.1 - - - +
495B THR* 4.0 25.6 + - + +
496B GLY* 4.3 13.2 - - - -
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Residues in contact with GLN 35 (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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31A ASP* 2.9 52.1 + - - +
32A THR* 3.9 7.0 - - - +
34A PHE* 1.3 72.5 - - - +
36A ALA* 1.3 62.9 + - - +
38A LEU* 3.3 4.6 + - - +
39A ASP* 3.0 21.8 + - - +
485B GLN* 4.1 3.6 - - - +
489B VAL* 3.6 26.6 - - + +
493B ARG* 2.7 77.8 + - - +
495B THR* 5.2 2.1 + - - -
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Residues in contact with ALA 36 (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 GLY 3.8 6.5 - - - +
8A GLU* 3.3 28.9 - - + +
11A VAL* 3.3 31.4 - - + -
32A THR 3.1 18.4 + - - +
35A GLN* 1.3 76.1 - - - +
37A CYS* 1.3 56.9 + - - +
39A ASP* 3.1 5.2 + - - +
40A HIS* 2.9 33.1 + - - -
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Residues in contact with CYS 37 (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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11A VAL* 3.7 20.2 - - - -
22A LEU* 4.2 14.8 - - - -
33A ILE* 2.9 24.6 + - - +
34A PHE 3.2 3.6 + - - +
36A ALA* 1.3 72.7 - - - +
38A LEU* 1.3 57.1 + - - +
40A HIS* 4.4 0.4 - - - +
41A ASP* 3.0 10.2 + - - -
42A VAL* 2.8 64.3 + - - +
44A ILE* 3.9 25.8 - - + -
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Residues in contact with LEU 38 (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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34A PHE 2.9 13.4 + - - +
35A GLN* 3.4 9.6 - - - +
37A CYS* 1.3 78.7 - - - +
39A ASP* 1.3 61.0 + - - +
40A HIS 3.4 0.2 + - - -
41A ASP* 3.5 14.3 + - - +
492B ASN 4.8 9.0 - - - +
493B ARG* 3.3 35.4 - - - +
494B VAL 5.7 0.4 - - - +
495B THR* 3.2 35.6 - - + +
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Residues in contact with ASP 39 (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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8A GLU* 4.7 7.0 - - - +
35A GLN 3.0 14.9 + - - +
36A ALA* 3.1 10.2 + - - +
38A LEU* 1.3 78.3 - - - +
40A HIS* 1.3 70.4 + - + +
41A ASP* 3.7 1.9 + - - -
493B ARG* 2.9 34.1 + - - -
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Residues in contact with HIS 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A GLU* 3.3 34.6 + - - -
11A VAL* 4.1 7.7 - - + +
12A ARG* 4.3 20.2 + - + +
15A ILE* 4.0 30.8 - - + +
36A ALA 2.9 21.9 + - - +
37A CYS 3.3 0.4 + - - +
38A LEU 3.3 0.2 - - - -
39A ASP* 1.3 83.6 - - + +
41A ASP* 1.3 71.1 + - - +
42A VAL* 3.2 10.1 + - + +
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Residues in contact with ASP 41 (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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37A CYS 3.0 5.4 + - - -
38A LEU* 3.5 10.1 + - - +
39A ASP 3.4 4.2 - - - -
40A HIS* 1.3 81.5 - - - +
42A VAL* 1.3 59.3 + - - +
43A PRO* 3.2 12.4 - - - +
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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