Contacts of the helix formed by residues 19 - 34 (chain G) in PDB entry 2AAZ
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 GLU 19 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17G ASP 3.1 6.8 + - - +
18G HIS* 1.3 73.3 + - - +
20G GLU* 1.3 62.2 + - - +
21G TYR 3.1 0.2 - - - -
22G GLN* 3.0 39.8 + - - +
23G TYR 4.2 0.2 + - - -
55G ARG 4.0 7.1 - - - +
56G PHE* 3.5 28.2 - - + +
57G SER* 2.9 44.9 + - - +
62G THR* 5.6 0.3 - - - +
64G PRO* 5.0 0.2 - - - +
277G PHE* 3.6 19.3 - - + -
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Residues in contact with GLU 20 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G HIS* 2.9 21.6 + - + +
19G GLU* 1.3 77.9 - - - +
21G TYR* 1.3 61.8 + - - +
23G TYR* 3.0 18.3 + - + +
24G LEU* 3.1 15.4 + - + +
56G PHE* 4.9 2.2 - - - -
66G LEU* 3.6 24.0 - - + +
67G THR* 2.8 37.1 + - - -
68G THR* 2.6 43.5 + - - +
274G PRO* 3.8 13.0 - - + +
277G PHE* 3.7 14.6 - - + -
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Residues in contact with TYR 21 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13G ARG* 3.5 64.2 - - + +
14G SER 4.8 0.7 + - - -
15G ASN 3.1 27.8 + - - -
16G PRO 3.7 12.6 - - - +
18G HIS* 3.0 30.1 + - + +
20G GLU* 1.3 76.2 - - - +
22G GLN* 1.3 58.1 + - - +
24G LEU* 4.0 18.6 - - + -
25G ASP* 2.7 41.4 + - - +
272G ARG 5.1 1.8 - - - -
273G GLU* 3.8 15.0 - - - +
274G PRO* 3.4 29.2 - - + +
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Residues in contact with GLN 22 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G HIS 4.5 0.4 + - - +
19G GLU* 3.0 28.2 + - - +
20G GLU 3.0 0.4 - - - -
21G TYR* 1.3 77.9 - - - +
23G TYR* 1.3 61.4 + - - +
25G ASP* 4.1 3.9 - - - +
26G LEU* 3.1 17.5 + - - +
53G SER 4.2 4.8 + - - -
54G PHE* 3.4 37.0 - - + +
55G ARG* 2.9 49.6 + - - +
56G PHE* 3.6 11.1 - - + -
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Residues in contact with TYR 23 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G GLU 4.2 0.4 + - - -
20G GLU* 3.0 12.8 + - + +
22G GLN* 1.3 78.3 - - - +
24G LEU* 1.3 77.9 + - + +
26G LEU* 3.4 3.1 + - - +
27G ILE* 3.2 48.7 + - + +
54G PHE* 3.7 17.5 - + + -
56G PHE* 5.4 2.2 - - + -
66G LEU* 3.7 39.7 - - + -
68G THR* 5.0 0.4 - - - -
69G LYS* 5.0 0.3 + - - -
220G LEU* 2.6 36.1 + - + -
221G GLY* 3.8 6.6 + - - -
224G VAL* 3.9 27.6 - - + -
225G PRO* 3.6 8.9 - - + +
228G ILE* 4.6 4.0 - - + -
266G LEU* 4.4 4.2 - - - +
269G GLN* 3.9 19.0 + - - -
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Residues in contact with LEU 24 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20G GLU* 3.1 12.8 + - + +
21G TYR* 4.0 22.0 - - + +
23G TYR* 1.3 91.5 - - + +
25G ASP* 1.3 63.5 + - - +
27G ILE* 3.3 3.4 + - + -
28G ARG* 3.0 27.0 + - - +
68G THR* 3.9 38.6 - - + +
269G GLN* 4.3 13.5 - - + +
270G LEU* 3.4 35.4 - - + +
272G ARG 4.0 9.2 - - - +
274G PRO* 4.0 17.0 - - + -
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Residues in contact with ASP 25 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13G ARG* 2.7 44.5 + - - -
21G TYR* 2.7 31.8 + - - +
22G GLN* 4.1 4.1 - - - +
24G LEU* 1.3 73.8 - - - +
26G LEU* 1.3 57.4 + - - +
28G ARG* 3.3 13.4 + - - +
29G ARG* 2.9 29.7 + - - +
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Residues in contact with LEU 26 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22G GLN 3.1 18.3 + - - +
23G TYR 3.8 2.2 - - - +
24G LEU 3.3 0.4 - - - -
25G ASP* 1.3 75.8 - - - +
27G ILE* 1.3 58.6 + - - +
29G ARG* 3.2 10.3 + - - +
30G ILE* 2.8 55.3 + - + +
48G LEU* 4.6 8.1 - - + -
51G PRO* 3.9 31.6 - - + -
52G PRO* 5.9 0.4 - - + -
54G PHE* 3.4 30.5 - - + -
220G LEU* 3.8 15.3 - - + -
253G MET* 3.9 17.3 - - - -
256G ALA* 4.7 0.4 - - + -
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Residues in contact with ILE 27 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23G TYR* 3.2 53.7 + - + +
24G LEU* 3.6 8.5 - - + +
25G ASP 3.3 0.2 - - - -
26G LEU* 1.3 76.9 - - - +
28G ARG* 1.3 64.0 + - - +
30G ILE* 3.3 7.7 + - - +
31G ILE* 3.0 43.4 + - + +
220G LEU* 3.7 23.1 - - + -
258G VAL* 4.5 3.6 - - + -
266G LEU* 3.9 34.1 - - + -
269G GLN* 5.6 0.4 - - - +
270G LEU* 4.2 14.1 - - + -
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Residues in contact with ARG 28 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13G ARG* 3.8 11.8 - - - +
24G LEU* 3.0 20.7 + - - +
25G ASP* 3.4 30.6 + - - +
27G ILE* 1.3 78.3 - - - +
29G ARG* 1.3 57.4 + - - +
31G ILE* 3.4 3.5 + - - +
32G ASN* 2.9 50.4 + - - +
270G LEU* 3.6 51.5 + - + +
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Residues in contact with ARG 29 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25G ASP 2.9 17.4 + - - +
26G LEU* 3.5 12.2 - - - +
28G ARG* 1.3 75.4 - - - +
30G ILE* 1.3 59.7 + - - +
32G ASN* 3.1 4.6 + - - -
33G VAL* 2.8 52.8 + - + +
48G LEU* 3.6 23.2 - - + +
51G PRO* 4.1 12.5 - - - +
52G PRO* 3.7 27.7 - - - +
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Residues in contact with ILE 30 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26G LEU* 2.8 38.0 + - + +
27G ILE 3.7 3.4 - - - +
29G ARG* 1.3 72.4 - - - +
31G ILE* 1.3 60.8 + - - +
34G GLY* 2.8 30.1 + - - +
46G VAL* 3.0 48.5 - - + +
47G ALA* 4.1 4.5 - - - -
48G LEU* 3.9 22.0 - - + -
220G LEU* 3.6 32.8 - - + -
256G ALA* 3.8 14.1 - - + +
258G VAL* 3.8 13.5 - - + -
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Residues in contact with ILE 31 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27G ILE* 3.0 35.5 + - + +
28G ARG* 3.7 4.0 - - - +
30G ILE* 1.3 77.4 - - - +
32G ASN* 1.3 72.2 + - - +
34G GLY 4.5 1.0 + - - +
46G VAL* 4.6 10.6 - - + +
258G VAL* 4.6 15.5 - - + -
263G VAL* 4.3 42.2 - - + +
266G LEU* 4.8 2.9 - - + -
267G LYS* 4.7 12.6 - - + -
270G LEU* 4.4 14.6 - - + -
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Residues in contact with ASN 32 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28G ARG* 2.9 38.3 + - - +
29G ARG* 3.7 4.8 - - - +
31G ILE* 1.3 88.9 - - - +
33G VAL* 1.3 70.3 + - + +
34G GLY 3.7 0.7 - - - +
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Residues in contact with VAL 33 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29G ARG* 2.8 46.9 + - + +
32G ASN* 1.3 82.7 - - + +
34G GLY* 1.3 64.9 + - - +
35G GLU* 3.8 0.5 + - - +
48G LEU* 4.0 13.6 - - + +
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Residues in contact with GLY 34 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29G ARG 3.6 2.4 + - - -
30G ILE 2.8 29.3 + - - -
31G ILE 5.3 0.3 - - - +
32G ASN 3.7 1.3 - - - +
33G VAL* 1.3 77.5 - - - +
35G GLU* 1.3 61.2 + - - -
36G VAL* 3.9 3.8 + - - +
46G VAL* 3.3 13.9 - - - +
47G ALA 3.6 10.5 - - - -
48G LEU* 3.8 10.1 - - - -
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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