Contacts of the helix formed by residues 38 - 48 (chain G) in PDB entry 2PWZ
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 VAL 38 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217E LYS* 3.5 47.5 - - + +
220E GLY* 4.0 16.8 - - - +
9G ALA* 3.7 27.1 - - + +
14G GLN* 5.2 3.4 - - - +
36G ALA* 4.1 9.4 - - + -
37G PRO* 1.3 79.4 - - + +
39G THR* 1.3 59.6 + - - +
40G PRO* 3.5 0.7 - - - -
41G GLY* 3.0 21.1 + - - -
42G VAL* 3.1 17.5 + - + -
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Residues in contact with THR 39 (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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8G ALA* 4.6 3.6 - - + -
9G ALA* 3.6 7.5 - - + +
32G LEU* 3.7 25.6 - - + +
33G TYR 4.0 1.3 - - - -
34G ASP* 3.0 30.4 - - + +
36G ALA 2.6 21.4 + - - -
37G PRO 3.1 0.2 - - - -
38G VAL* 1.3 73.3 - - - +
40G PRO* 1.4 72.7 - - - +
42G VAL* 3.1 21.7 + - + +
43G ALA* 3.2 12.0 + - - +
57G GLY* 4.0 0.6 - - - -
58G PHE 3.4 23.3 - - - +
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Residues in contact with PRO 40 (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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216E ALA* 4.0 9.4 - - + +
37G PRO 3.4 15.3 - - - +
38G VAL 3.7 0.4 - - - -
39G THR* 1.4 91.4 - - - +
41G GLY* 1.3 55.6 + - - +
43G ALA* 3.4 6.1 + - - +
44G VAL* 3.1 29.4 + - + +
57G GLY* 3.7 29.7 + - - +
58G PHE* 4.1 2.2 - - - +
59G SER* 4.0 17.7 - - - +
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Residues in contact with GLY 41 (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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213E VAL* 4.2 2.8 - - - +
216E ALA* 3.1 38.5 + - - -
217E LYS* 3.7 13.8 - - - +
38G VAL 3.0 7.9 + - - -
40G PRO* 1.3 73.9 - - - +
42G VAL* 1.3 58.8 + - - +
43G ALA 3.2 1.3 - - - -
44G VAL* 3.6 1.6 - - - +
45G ASP* 2.9 30.1 + - - +
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Residues in contact with VAL 42 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217E LYS* 4.0 13.2 - - - +
225E LEU* 4.0 23.1 - - + -
8G ALA 4.4 5.6 - - - +
9G ALA* 4.8 4.5 - - + -
14G GLN* 3.9 33.2 - - + +
17G ALA* 5.2 1.1 - - + -
32G LEU* 3.8 18.6 - - + -
38G VAL* 3.1 27.8 + - + +
39G THR* 3.1 15.4 + - + +
41G GLY* 1.3 74.8 - - - +
43G ALA* 1.3 61.1 + - - +
45G ASP* 3.3 8.2 - - - +
46G LEU* 3.1 24.4 + - + +
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Residues in contact with ALA 43 (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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32G LEU* 4.0 13.9 - - + +
39G THR 3.2 4.8 + - - +
40G PRO 3.4 7.2 - - - +
42G VAL* 1.3 75.5 - - - +
44G VAL* 1.3 54.2 + - + +
46G LEU* 3.2 1.2 + - - -
47G SER* 2.8 33.1 + - - -
55G ILE* 3.3 17.1 - - + +
56G LYS* 3.4 14.1 - - - +
57G GLY* 3.3 35.4 - - - +
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Residues in contact with VAL 44 (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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212E GLU* 3.9 35.2 - - + +
213E VAL* 3.8 20.2 - - + -
216E ALA* 3.8 16.4 - - + -
40G PRO* 3.1 14.6 + - + +
41G GLY 3.7 6.3 - - - +
42G VAL 3.3 0.4 - - - -
43G ALA* 1.3 73.9 - - + +
45G ASP* 1.3 67.5 - - - +
47G SER* 2.7 25.1 + - - +
48G HIS* 3.4 8.5 - - - +
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Residues in contact with ASP 45 (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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213E VAL* 4.1 17.4 - - + +
217E LYS* 3.1 13.8 + - - +
223E ALA* 3.9 5.7 - - - -
224E THR* 2.9 26.6 + - - -
225E LEU* 3.1 17.7 + - - +
226E SER* 2.6 62.3 + - - -
41G GLY 2.9 16.3 + - - +
42G VAL* 3.3 13.4 - - - +
44G VAL* 1.3 74.4 - - - +
46G LEU* 1.3 62.5 + - - +
48G HIS* 3.2 7.4 + - - +
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Residues in contact with LEU 46 (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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225E LEU* 3.6 35.7 - - + -
17G ALA* 3.6 30.7 - - + +
18G LEU* 3.7 20.2 - - + -
21G LYS* 3.3 19.3 - - + -
32G LEU* 4.1 4.3 - - + -
42G VAL 3.1 14.0 + - - +
43G ALA 3.2 6.7 + - - +
45G ASP* 1.3 73.8 - - - +
47G SER* 1.3 56.2 + - - +
48G HIS 3.0 5.6 - - - -
49G ILE* 2.9 44.5 + - + +
55G ILE* 3.6 26.7 - - + -
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Residues in contact with SER 47 (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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156E THR* 3.2 22.9 - - - +
157E PHE* 5.3 0.2 - - - -
205E ARG* 6.0 0.2 + - - -
212E GLU* 5.1 1.2 + - - -
21G LYS* 4.1 6.0 + - - +
43G ALA 2.8 17.9 + - - -
44G VAL* 2.7 25.5 + - - +
46G LEU* 1.3 70.6 - - - +
48G HIS* 1.3 66.0 + - - +
49G ILE 3.2 5.5 + - - +
55G ILE* 3.6 22.3 - - - +
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Residues in contact with HIS 48 (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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149E LEU* 5.1 0.4 - - + -
152E ILE* 3.5 18.4 - - - +
153E ARG* 3.1 38.8 + - + +
156E THR* 2.9 18.5 + - - -
157E PHE* 3.6 17.8 - + - -
205E ARG* 5.3 0.2 - - - -
209E ALA* 3.5 33.2 - - + -
212E GLU* 3.0 23.2 + - - -
213E VAL* 3.6 16.2 - - + +
226E SER* 4.2 10.4 + - - +
44G VAL* 3.4 15.0 + - - +
45G ASP 3.2 10.0 + - - +
46G LEU 3.0 1.4 + - - -
47G SER* 1.3 82.6 - - - +
49G ILE* 1.3 61.9 + - - +
50G PRO* 3.8 1.0 - - - +
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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