Contacts of the helix formed by residues 28 - 38 (chain C) in PDB entry 3WA9
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 28 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C SER* 3.5 6.3 - - - +
27C PHE* 1.4 91.2 - - + +
29C VAL* 1.3 64.6 + - - +
30C GLY 3.3 2.2 - - - +
31C ARG* 3.5 28.4 + - + +
32C ILE* 3.1 27.0 + - + +
37D TYR* 4.4 9.2 - - + -
40D TYR* 3.5 49.6 - - + +
29I A 6.4 0.4 - - - -
268J G 4.5 4.7 - - - +
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Residues in contact with VAL 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C ARG* 3.9 33.9 - - + +
20C SER* 3.1 29.0 + - - +
23C ALA* 4.5 0.2 - - + -
25C LEU* 4.1 13.0 - - + -
27C PHE 4.2 0.9 - - - +
28C PRO* 1.3 71.0 - - - +
30C GLY* 1.3 57.4 + - - +
32C ILE* 3.3 2.5 + - - -
33C HIS* 2.9 27.7 + - - +
51C ALA* 3.6 15.5 - - + +
52C VAL* 3.9 28.3 - - + -
55C ALA* 4.0 23.3 - - + -
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Residues in contact with GLY 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C ARG* 3.7 18.8 + - - +
20C SER* 4.8 0.6 + - - -
28C PRO 3.3 0.6 - - - -
29C VAL* 1.3 78.9 - - - +
31C ARG* 1.3 61.8 + - - +
33C HIS* 3.1 4.7 + - - +
34C ARG* 3.0 22.2 + - - +
29I A 3.8 23.6 + - - -
30I A 3.9 12.4 + - - -
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Residues in contact with ARG 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C PRO* 3.5 24.3 + - + +
29C VAL 3.4 0.6 - - - -
30C GLY* 1.3 74.0 - - - +
32C ILE* 1.3 60.5 + - + +
34C ARG* 3.2 10.4 + - - +
35C HIS* 2.9 50.0 + - + +
33D ARG* 3.8 7.9 - - - +
35D GLU* 3.4 32.2 + - - +
36D SER 2.5 33.1 + - - +
37D TYR* 4.9 8.2 - - - -
40D TYR* 3.6 20.5 + - - -
29I A 3.8 23.4 + - - +
268J G 3.0 34.2 + - - -
269J T 3.2 6.6 + - - -
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Residues in contact with ILE 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C PHE* 4.5 10.1 - - + -
28C PRO* 3.1 20.8 + - + +
29C VAL 3.8 3.6 - - - +
31C ARG* 1.3 73.8 - - + +
33C HIS* 1.3 60.8 + - - +
35C HIS* 3.2 8.1 + - - +
36C LEU* 2.9 29.7 + - + +
51C ALA* 3.8 20.6 - - - +
54C SER* 3.9 16.4 - - - -
55C ALA* 3.6 31.6 - - + -
58C LEU* 3.7 20.6 - - + -
37D TYR* 4.1 22.2 - - + +
70D PHE* 4.0 12.8 - - + -
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Residues in contact with HIS 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C ARG* 3.2 29.5 + - - +
29C VAL 2.9 10.0 + - - +
30C GLY 3.1 9.2 + - - +
32C ILE* 1.3 76.2 - - - +
34C ARG* 1.3 56.7 + - - +
36C LEU* 3.3 3.2 + - - +
37C LYS* 3.0 47.9 + - + +
46C VAL* 3.1 51.5 + - + +
47C GLY 3.9 6.5 + - - -
48C ALA* 5.1 3.6 - - - -
51C ALA* 3.5 23.5 - - + +
259J A 4.5 8.1 - - - -
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Residues in contact with ARG 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C GLY 3.0 13.1 + - - +
31C ARG* 3.5 10.6 - - - +
32C ILE 3.2 0.2 - - - -
33C HIS* 1.3 77.3 - - - +
35C HIS* 1.3 80.4 + - - +
37C LYS* 3.2 23.7 + - - +
38C SER* 2.8 34.5 + - - +
35D GLU* 2.6 39.7 + - - -
28I A 3.6 22.6 + - - -
29I A 2.2 43.3 + - - +
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Residues in contact with HIS 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C ARG* 2.9 33.7 + - + +
32C ILE* 3.2 5.9 + - - +
34C ARG* 1.3 106.4 + - - +
36C LEU* 1.3 59.5 + - - +
38C SER* 3.6 6.6 + - - -
39C ARG* 3.4 24.1 + - - +
35D GLU* 3.3 10.1 + - + -
37D TYR* 3.6 25.6 + + - -
67D ASN* 5.4 4.8 + - - -
70D PHE* 3.4 29.4 - - + -
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Residues in contact with LEU 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C ILE* 2.9 19.5 + - + +
33C HIS 3.7 4.9 - - - +
34C ARG 3.2 0.2 - - - -
35C HIS* 1.3 76.9 - - - +
37C LYS* 1.3 64.1 + - - +
38C SER 3.2 0.4 + - - -
39C ARG* 3.5 9.2 + - + +
40C THR* 3.2 17.7 - - - +
46C VAL* 3.7 34.0 - - + +
50C ALA* 4.3 13.0 - - + -
51C ALA* 4.3 9.6 - - + +
54C SER* 4.2 19.7 - - - +
70D PHE* 3.5 26.0 - - + -
73D ILE* 6.5 0.2 - - + -
74D ALA* 4.0 22.9 - - + -
89D ILE* 5.3 11.6 - - + +
94D ILE* 4.6 6.7 - - + -
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Residues in contact with LYS 37 (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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33C HIS* 3.0 42.7 + - + +
34C ARG* 3.2 27.2 + - - +
36C LEU* 1.3 76.2 - - - +
38C SER* 1.3 55.5 + - - +
40C THR* 2.4 33.3 + - + +
45C ARG* 6.0 0.7 - - - -
46C VAL* 4.0 15.0 - - + +
42G SER* 2.8 18.6 + - - +
259J A 4.5 14.8 - - - +
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Residues in contact with SER 38 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C ARG* 2.8 23.8 + - - +
35C HIS* 3.6 8.5 + - - -
36C LEU 3.2 0.2 - - - -
37C LYS* 1.3 78.6 - - - +
39C ARG* 1.3 56.0 + - - +
40C THR* 2.8 7.2 - - - -
41G THR* 4.0 5.5 + - - +
42G SER* 4.6 3.1 - - - -
82H HIS* 3.0 24.8 - - - -
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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