Contacts of the helix formed by residues 8 - 20 (chain Y) in PDB entry 3IR0
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 GLY 8 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16W TYR* 3.3 33.7 - - - -
7Y CYS* 1.3 70.9 - - - +
9Y SER* 1.3 65.1 + - - -
11Y LEU* 3.4 9.9 + - - +
12Y VAL* 3.2 24.6 + - - +
26Y TYR* 4.5 7.3 + - - -
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Residues in contact with SER 9 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13W GLU* 3.5 28.0 + - - -
16W TYR* 3.8 23.5 - - - -
17W LEU* 6.2 0.4 - - - -
7Y CYS 3.5 1.4 + - - -
8Y GLY* 1.3 71.3 - - - -
10Y HIS* 1.3 72.9 + - - +
12Y VAL* 3.6 9.8 - - - +
13Y GLU* 3.0 30.8 + - - +
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Residues in contact with HIS 10 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6Y LEU* 4.1 21.6 - - + +
7Y CYS 3.5 14.8 + - - +
8Y GLY 3.3 0.2 - - - -
9Y SER* 1.3 84.4 + - - +
11Y LEU* 1.3 62.1 + - - +
13Y GLU* 3.5 8.3 + - - +
14Y ALA* 3.1 22.7 + - - +
31Y CU 2.1 32.4 - - - -
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Residues in contact with LEU 11 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2X ILE* 4.1 24.7 - - + +
3X VAL* 4.6 3.6 - - + +
6X CYS* 4.0 13.9 - - + -
7X CYS* 4.4 11.0 - - + -
16X LEU* 4.0 21.7 - - + +
6Y LEU* 3.3 36.8 - - + +
7Y CYS* 3.6 12.5 + - - +
8Y GLY 3.4 12.5 + - - +
9Y SER 3.2 0.2 - - - -
10Y HIS* 1.3 79.3 - - - +
12Y VAL* 1.4 55.7 + - - +
14Y ALA* 3.2 18.5 + - + +
15Y LEU* 3.4 8.9 + - + +
26Y TYR* 3.9 26.7 - - + +
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Residues in contact with VAL 12 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12W VAL* 3.5 23.5 - - + +
13W GLU* 5.6 0.7 - - - +
16W TYR* 4.0 21.5 - - + -
24W PHE* 4.0 9.4 - - + -
8Y GLY 3.2 16.5 + - - +
9Y SER* 3.6 13.7 - - - +
11Y LEU* 1.4 71.7 - - - +
13Y GLU* 1.3 62.5 + - + +
14Y ALA 3.1 0.9 - - - -
15Y LEU* 3.5 8.3 - - + +
16Y TYR 2.9 24.9 + - - -
24Y PHE* 4.1 7.5 - - + -
26Y TYR* 3.5 50.0 - - + -
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Residues in contact with GLU 13 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9W SER* 4.1 21.8 + - - +
10W HIS* 5.6 2.1 + - - -
12W VAL* 4.2 7.4 - - + +
13W GLU* 2.9 46.0 - - + +
9Y SER 3.0 20.0 + - - +
10Y HIS* 3.6 9.4 - - - +
12Y VAL* 1.3 76.2 - - + +
14Y ALA* 1.3 61.0 + - - +
16Y TYR* 3.6 4.9 + - - +
17Y LEU* 3.3 29.0 + - + +
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Residues in contact with ALA 14 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13X LEU* 6.1 0.9 - - + -
16X LEU* 4.0 19.1 - - + -
6Y LEU* 4.2 17.9 - - + -
10Y HIS 3.1 13.6 + - - +
11Y LEU 3.2 13.0 - - - +
12Y VAL 3.1 0.4 - - - -
13Y GLU* 1.3 77.9 - - - +
15Y LEU* 1.3 55.9 + - - +
17Y LEU* 3.5 7.3 - - - +
18Y VAL* 2.8 36.5 + - + +
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Residues in contact with LEU 15 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2X ILE* 4.1 22.4 - - + -
16X LEU* 3.8 24.0 - - + +
19X TYR* 3.7 24.9 - - + -
11Y LEU 3.4 13.5 + - - +
12Y VAL* 3.3 16.9 + - + +
14Y ALA* 1.3 75.0 - - - +
16Y TYR* 1.3 70.7 + - - +
18Y VAL* 3.1 5.0 + - - -
19Y CYS* 2.9 32.5 + - - +
24Y PHE* 3.8 43.5 - - + -
25Y PHE 4.6 5.2 - - - +
26Y TYR* 4.8 1.8 - - + -
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Residues in contact with TYR 16 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8W GLY* 3.4 16.1 - - - -
9W SER* 3.3 39.0 + - - -
12W VAL* 3.8 21.5 - - + -
26W TYR* 3.6 37.2 - + - -
12Y VAL 2.9 16.2 + - - +
13Y GLU 4.0 6.1 - - - +
14Y ALA 3.4 0.2 - - - -
15Y LEU* 1.3 74.6 - - - +
17Y LEU* 1.3 80.4 + - + +
19Y CYS 2.9 3.1 + - - -
20Y GLY* 2.7 42.2 + - - +
24Y PHE* 3.7 10.4 - - - -
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Residues in contact with LEU 17 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13Y GLU* 3.3 19.8 + - + +
14Y ALA* 3.5 7.4 - - - +
16Y TYR* 1.3 94.5 - - + +
18Y VAL* 1.3 63.3 - - + +
19Y CYS 3.6 0.3 + - - -
20Y GLY 4.6 1.7 + - - -
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Residues in contact with VAL 18 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13X LEU* 3.7 41.3 - - + +
16X LEU* 4.2 9.0 - - + -
17X GLU* 3.6 43.8 - - + +
20X CYS* 4.0 7.2 - - - -
14Y ALA 2.8 25.4 + - - +
15Y LEU* 3.6 7.0 - - - +
16Y TYR 3.1 0.4 - - - -
17Y LEU* 1.3 80.6 - - + +
19Y CYS* 1.3 55.8 + - - +
22Y ARG* 5.3 1.7 + - - -
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Residues in contact with CYS 19 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20X CYS* 2.0 53.8 - - + -
15Y LEU* 2.9 24.3 + - - +
16Y TYR 2.9 2.0 + - - +
17Y LEU 5.1 0.2 - - - -
18Y VAL* 1.3 79.1 - - - +
20Y GLY* 1.3 70.2 + - - +
21Y GLU* 3.0 4.9 + - - +
22Y ARG* 3.2 23.4 + - - +
23Y GLY 3.2 20.6 - - - +
24Y PHE* 3.6 12.6 - - + -
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Residues in contact with GLY 20 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26W TYR* 3.8 8.0 - - - -
28W PRO* 3.8 7.7 - - - +
16Y TYR* 2.7 37.5 + - - +
17Y LEU 4.6 1.8 + - - -
19Y CYS* 1.3 68.3 - - - +
21Y GLU* 1.3 58.6 + - - -
23Y GLY* 3.0 23.9 + - - -
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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