Contacts of the helix formed by residues 30 - 38 (chain W) in PDB entry 1I84
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 GLN 30 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18W PHE* 3.1 39.7 + - + +
19W ASP* 5.0 0.9 - - - +
20W ARG* 5.2 9.7 + - - +
25W LYS 4.4 2.1 - - - +
26W ILE* 3.4 19.8 - - + -
27W LEU* 2.9 29.5 + - + +
29W SER* 1.3 86.2 + - - +
31W CYS* 1.3 67.8 + - - +
32W GLY 2.8 2.0 + - - -
33W ASP* 2.9 23.1 + - - +
34W VAL* 3.0 16.9 + - + +
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Residues in contact with CYS 31 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26W ILE* 3.5 13.0 - - - +
27W LEU 3.6 0.4 + - - -
28W TYR 3.7 16.4 - - - +
29W SER 2.9 0.8 + - - -
30W GLN* 1.3 75.5 - - - +
32W GLY* 1.3 56.6 + - - +
34W VAL* 3.2 5.4 + - - +
35W MET* 2.7 54.1 + - - +
47W VAL* 4.5 9.6 - - + -
51W LEU* 4.4 14.6 - - + -
64W LEU* 4.3 18.8 - - + -
69W PHE* 4.1 19.1 - - - -
72W MET* 4.6 8.1 - - - -
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Residues in contact with GLY 32 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29W SER 3.3 8.0 + - - -
30W GLN 2.8 4.4 + - - -
31W CYS* 1.3 75.7 - - - +
33W ASP* 1.3 55.6 + - - -
35W MET* 3.1 8.6 + - - +
36W ARG* 2.9 48.0 + - - -
42W PRO* 5.0 0.6 - - - +
47W VAL* 4.0 20.7 - - - +
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Residues in contact with ASP 33 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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804V ARG 5.3 0.2 - - - +
808V ALA* 4.2 17.2 - - + +
812V PHE* 6.0 1.5 - - + +
18W PHE* 4.2 15.9 - - + -
29W SER 4.9 0.6 + - - -
30W GLN* 2.9 17.7 + - - +
32W GLY* 1.3 71.0 - - - -
34W VAL* 1.3 53.0 + - - +
36W ARG* 3.1 19.8 + - - +
37W ALA* 2.6 37.1 + - - +
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Residues in contact with VAL 34 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14W ALA 5.0 0.4 - - - -
15W PHE* 4.2 20.4 - - + +
18W PHE* 3.5 48.5 - - + -
26W ILE* 4.1 14.4 - - + -
30W GLN* 3.0 18.0 + - + +
31W CYS* 3.6 6.5 - - - +
33W ASP* 1.3 73.0 - - - +
35W MET* 1.3 65.4 + - - +
37W ALA* 3.6 0.9 + - - +
38W LEU* 3.1 29.2 + - + +
69W PHE* 3.7 24.9 - - + -
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Residues in contact with MET 35 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31W CYS* 2.7 47.3 + - - +
32W GLY* 3.4 6.5 - - - +
34W VAL* 1.3 74.2 - - - +
36W ARG* 1.3 59.4 + - - +
38W LEU* 3.1 11.8 + - - +
40W GLN* 2.8 30.0 + - + +
42W PRO* 3.9 14.1 - - + -
47W VAL* 4.5 5.8 - - - -
69W PHE* 4.2 6.3 - - + -
72W MET* 4.0 2.2 - - - +
73W MET* 3.4 44.2 - - + +
76W ILE* 3.2 49.1 - - + -
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Residues in contact with ARG 36 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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801V ALA* 5.0 1.6 + - - +
804V ARG* 4.0 35.5 - - - +
805V GLY* 3.3 22.4 - - - +
808V ALA* 4.0 8.7 - - + -
809V ARG* 3.0 20.0 - - - -
32W GLY* 2.9 32.8 + - - -
33W ASP* 3.3 22.4 + - - +
35W MET* 1.3 72.0 - - - +
37W ALA* 1.3 56.4 + - - +
38W LEU 2.9 1.3 - - - -
39W GLY 2.4 26.2 + - - -
40W GLN 2.9 24.3 + - - +
41W ASN* 4.8 1.0 - - - -
42W PRO* 2.7 33.2 + - + +
43W THR* 4.2 5.7 + - - +
44W ASN* 4.1 19.6 + - - -
47W VAL* 4.4 5.0 - - - +
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Residues in contact with ALA 37 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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808V ALA 5.9 0.2 - - - -
809V ARG* 4.2 18.4 - - - +
812V PHE* 3.8 37.1 - - + -
18W PHE* 4.0 17.7 - - + -
33W ASP 2.6 20.8 + - - +
34W VAL 3.8 5.4 - - - +
36W ARG* 1.3 72.7 - - - +
38W LEU* 1.3 62.7 + - + +
39W GLY* 2.9 4.7 + - - -
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Residues in contact with LEU 38 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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812V PHE* 6.4 0.2 - - + -
11W PHE* 3.6 38.4 - - + +
14W ALA* 3.2 33.2 - - + -
34W VAL* 3.1 22.7 + - + +
35W MET 3.1 10.2 + - - +
36W ARG 2.9 1.6 + - - -
37W ALA* 1.3 80.8 - - + +
39W GLY* 1.3 60.5 + - - +
40W GLN* 3.4 6.7 + - - -
69W PHE* 4.7 5.4 - - + -
73W MET* 3.4 39.7 - - + +
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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