Contacts of the helix formed by residues 38 - 48 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217A LYS* 3.7 35.2 - - + +
220A GLY* 3.9 24.2 - - - +
221A GLY* 5.2 0.2 - - - -
9C ALA* 3.8 24.7 - - + -
14C GLN* 5.1 4.3 - - - +
36C ALA* 4.3 6.7 - - + -
37C PRO* 1.3 79.5 - - + +
39C THR* 1.3 55.7 + - - +
40C PRO* 3.4 0.4 - - - -
41C GLY* 2.8 28.8 + - - -
42C VAL* 3.1 18.5 + - + -
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Residues in contact with THR 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C ALA* 4.4 5.6 - - + -
9C ALA* 3.6 7.5 - - - +
32C LEU* 3.7 28.2 - - + +
33C TYR 4.0 0.9 - - - -
34C ASP* 3.1 28.3 - - + +
36C ALA 2.8 20.8 + - - -
37C PRO 3.1 0.4 - - - -
38C VAL* 1.3 78.1 - - - +
40C PRO* 1.3 67.6 - - - +
41C GLY 3.2 0.5 + - - -
42C VAL* 3.2 18.0 + - + +
43C ALA 3.3 8.7 + - - -
57C GLY* 3.7 3.6 - - - -
58C PHE 3.4 25.1 - - - +
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Residues in contact with PRO 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A ALA* 3.8 13.5 - - + +
37C PRO 3.4 13.9 - - - +
38C VAL 3.6 0.7 - - - -
39C THR* 1.3 91.8 - - - +
41C GLY* 1.3 54.1 + - - +
43C ALA* 3.4 5.7 - - - +
44C VAL* 3.1 31.2 + - + +
57C GLY* 3.6 28.4 + - - +
58C PHE* 4.2 2.0 - - - +
59C SER* 4.0 18.2 - - - +
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Residues in contact with GLY 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A VAL* 3.7 6.4 - - - +
216A ALA* 3.4 21.7 + - - -
217A LYS* 3.4 21.0 - - - -
38C VAL 2.8 16.7 + - - -
40C PRO* 1.3 69.6 - - - +
42C VAL* 1.3 57.6 + - - -
43C ALA 3.2 0.9 - - - -
44C VAL* 3.7 1.8 - - - -
45C ASP* 2.9 31.0 + - - +
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Residues in contact with VAL 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A LYS* 4.1 13.2 - - - +
225A LEU* 4.0 22.7 - - + -
8C ALA 4.3 4.9 - - - +
9C ALA* 4.8 4.0 - - - -
14C GLN* 4.0 31.0 - - + +
32C LEU* 3.8 19.3 - - + -
38C VAL* 3.1 27.9 + - + +
39C THR* 3.2 15.7 + - + +
41C GLY* 1.3 76.2 - - - +
43C ALA* 1.3 57.2 + - - +
45C ASP* 3.3 6.9 - - - +
46C LEU* 3.0 28.8 + - + +
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Residues in contact with ALA 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C LEU* 4.0 9.5 - - + +
39C THR 3.3 2.6 + - - -
40C PRO 3.4 7.2 - - - +
42C VAL* 1.3 77.9 - - - +
44C VAL* 1.3 54.1 + - + +
46C LEU 3.2 1.2 + - - -
47C SER* 2.7 36.1 + - - -
55C ILE* 3.5 14.8 - - + +
56C LYS* 3.5 15.0 - - - +
57C GLY* 3.1 36.8 - - - +
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Residues in contact with VAL 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A GLU* 3.9 30.7 - - + +
213A VAL* 3.9 16.2 - - + -
216A ALA* 3.5 20.4 - - + -
40C PRO* 3.1 17.7 + - + +
41C GLY* 3.4 5.8 + - - +
43C ALA* 1.3 71.0 - - + +
45C ASP* 1.3 67.3 + - - +
47C SER* 2.7 27.0 + - - +
48C HIS* 3.3 13.6 - - - +
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Residues in contact with ASP 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A VAL* 3.8 19.5 - - + +
217A LYS* 4.2 7.7 + - - -
223A ALA* 3.9 4.1 - - - -
224A THR* 3.2 19.7 + - - -
225A LEU* 3.2 30.2 + - - +
226A SER* 2.6 62.6 + - - -
14C GLN* 5.4 0.3 - - - +
41C GLY 2.9 19.1 + - - +
42C VAL* 3.3 6.5 - - - +
44C VAL* 1.3 74.0 - - - +
46C LEU* 1.3 63.7 + - - +
48C HIS* 3.2 10.8 + - - +
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Residues in contact with LEU 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A LEU* 3.7 35.4 - - + -
17C ALA* 3.7 32.5 - - + +
18C LEU* 3.8 16.6 - - + -
21C LYS* 2.9 28.7 - - + -
32C LEU* 4.2 4.5 - - + -
42C VAL 3.0 20.0 + - - +
43C ALA 3.2 4.0 + - - +
45C ASP* 1.3 76.6 - - - +
47C SER* 1.3 57.6 + - - +
49C ILE* 3.1 36.3 + - + +
55C ILE* 3.5 27.8 - - + -
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Residues in contact with SER 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A THR* 3.4 18.2 - - - +
205A ARG* 5.8 0.5 + - - -
212A GLU* 5.2 0.5 + - - -
21C LYS* 4.1 3.8 + - - +
43C ALA 2.7 20.0 + - - -
44C VAL* 2.7 23.8 + - - +
46C LEU* 1.3 74.0 - - - +
48C HIS* 1.3 66.5 + - - +
49C ILE 3.2 6.2 + - - +
55C ILE* 3.7 21.3 - - - -
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Residues in contact with HIS 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A LEU* 5.1 0.4 - - + -
152A ILE* 3.5 17.7 - - - +
153A ARG* 3.3 35.8 + - + +
156A THR* 2.9 21.0 + - + -
157A PHE* 3.8 15.5 - + - -
205A ARG* 5.1 0.7 - - - -
209A ALA* 3.4 35.7 - - + -
212A GLU* 2.8 25.5 + - - -
213A VAL* 3.8 16.6 - - + +
226A SER* 4.4 10.2 + - - -
44C VAL* 3.3 15.2 + - - +
45C ASP 3.2 9.1 + - - +
46C LEU 3.1 1.8 - - - -
47C SER* 1.3 82.9 - - - +
49C ILE* 1.3 59.1 + - - +
50C PRO* 3.6 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