Contacts of the helix formed by residues 8 - 20 (chain W) 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 W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3V VAL* 6.2 2.2 - - - +
7V CYS* 5.1 0.6 - - - -
7W CYS* 1.3 73.5 - - - +
9W SER* 1.3 58.8 + - - -
10W HIS* 5.9 0.2 - - - -
11W LEU* 2.9 25.6 + - - +
12W VAL 3.8 1.6 + - - -
26W TYR* 4.5 6.3 + - - -
16Y TYR* 3.4 26.3 - - - -
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Residues in contact with SER 9 (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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8W GLY* 1.3 69.5 - - - -
10W HIS* 1.3 66.5 + - - +
11W LEU 3.1 0.2 - - - -
12W VAL* 3.1 8.1 + - - +
13W GLU* 3.0 32.7 + - - +
13Y GLU* 4.1 22.8 + - - -
16Y TYR* 3.3 39.1 + - - -
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Residues in contact with HIS 10 (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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5W HIS 5.4 1.6 - - - +
6W LEU* 3.3 27.8 - - + +
7W CYS* 3.3 19.3 - - + +
8W GLY* 3.2 1.8 - - - -
9W SER* 1.3 84.2 + - - +
11W LEU* 1.3 59.1 + - - +
13W GLU* 4.0 12.2 - - - +
14W ALA 3.5 11.6 + - - -
31W CU 2.6 29.9 - - - -
13Y GLU* 5.6 1.5 + - - -
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Residues in contact with LEU 11 (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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2V ILE* 4.4 7.2 - - + +
3V VAL* 3.8 35.4 - - + +
6V CYS* 3.9 11.7 - - - -
16V LEU* 3.5 34.5 - - + -
6W LEU* 3.9 26.0 - - + +
7W CYS 3.5 3.6 + - - -
8W GLY 2.9 14.3 + - - +
10W HIS* 1.3 74.6 - - - +
12W VAL* 1.3 65.8 + - - +
13W GLU 3.1 2.1 + - - -
14W ALA* 3.1 4.6 + - - +
15W LEU* 3.0 30.4 + - + +
26W TYR* 3.8 21.1 - - + -
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Residues in contact with VAL 12 (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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8W GLY 3.8 0.2 + - - -
9W SER* 3.1 12.2 + - - +
11W LEU* 1.3 77.7 - - - +
13W GLU* 1.3 58.0 + - - +
15W LEU* 3.5 7.1 + - + -
16W TYR* 3.1 26.7 + - - +
24W PHE* 3.7 5.5 - - + -
26W TYR* 3.7 27.8 - - + -
12Y VAL* 3.5 39.5 - - + +
13Y GLU* 4.2 7.0 - - + +
16Y TYR* 3.8 17.7 - - + -
24Y PHE* 3.5 28.7 - - + -
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Residues in contact with GLU 13 (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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9W SER 3.0 14.5 + - - +
10W HIS* 4.0 12.8 - - - +
11W LEU 3.1 0.2 - - - -
12W VAL* 1.3 75.9 - - - +
14W ALA* 1.3 58.8 + - - +
16W TYR* 3.4 5.8 + - - +
17W LEU* 3.0 38.8 + - - +
9Y SER* 3.5 26.7 + - - -
12Y VAL* 5.9 0.9 - - - -
13Y GLU* 2.9 46.0 - - + +
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Residues in contact with ALA 14 (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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13V LEU* 4.9 7.9 - - + -
16V LEU* 3.3 25.8 - - + -
6W LEU* 3.9 16.8 - - + -
10W HIS 3.5 12.2 + - - +
11W LEU 3.1 7.1 + - - +
13W GLU* 1.3 77.0 - - - +
15W LEU* 1.3 59.1 + - - +
17W LEU* 3.4 6.2 + - - +
18W VAL* 2.9 35.2 + - - +
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Residues in contact with LEU 15 (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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2V ILE* 6.0 3.1 - - + -
16V LEU* 3.8 40.8 - - + +
19V TYR* 3.9 18.8 - - + -
11W LEU* 3.0 28.4 + - + +
12W VAL* 3.8 8.5 - - - +
13W GLU 3.3 0.4 - - - -
14W ALA* 1.3 73.2 - - - +
16W TYR* 1.3 61.6 + - - +
18W VAL* 4.6 1.3 - - - -
19W CYS* 2.8 40.3 + - - +
24W PHE* 3.6 37.9 - - + -
25W PHE 4.5 4.9 - - - +
26W TYR* 4.1 19.3 - - + -
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Residues in contact with TYR 16 (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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12W VAL 3.1 17.9 + - - +
13W GLU* 3.7 6.7 - - - +
15W LEU* 1.3 76.3 - - - +
17W LEU* 1.3 74.1 + - + +
20W GLY* 2.5 50.0 + - - +
21W GLU* 5.5 1.8 + - - +
24W PHE* 3.5 12.2 - + + -
8Y GLY* 3.3 31.7 - - - -
9Y SER* 3.9 22.4 - - - -
12Y VAL* 4.0 22.9 - - + -
26Y TYR* 3.9 27.8 + + - -
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Residues in contact with LEU 17 (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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13W GLU* 3.0 25.5 + - - +
14W ALA* 3.7 6.5 - - - +
15W LEU 3.3 0.2 - - - -
16W TYR* 1.3 97.3 - - + +
18W VAL* 1.3 62.7 + - + +
19W CYS 4.8 0.2 - - - -
20W GLY* 4.3 2.3 + - - -
9Y SER* 6.2 0.4 - - - -
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Residues in contact with VAL 18 (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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13V LEU* 4.3 37.5 - - + +
16V LEU* 4.5 4.3 - - + -
17V GLU* 3.5 43.5 - - + +
20V CYS* 4.0 7.9 - - - -
14W ALA 2.9 21.9 + - - +
15W LEU* 4.0 3.1 - - - +
17W LEU* 1.3 80.6 - - + +
19W CYS* 1.3 60.4 + - - +
22W ARG* 5.6 1.6 + - - -
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Residues in contact with CYS 19 (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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16V LEU 4.4 6.1 - - - -
19V TYR 4.5 0.2 - - - -
20V CYS* 2.0 52.9 - - + -
15W LEU* 2.8 25.8 + - - +
17W LEU 4.8 0.2 - - - -
18W VAL* 1.3 78.9 - - - +
20W GLY* 1.3 65.7 + - - +
21W GLU 3.3 0.3 + - - -
22W ARG* 3.2 23.4 + - - +
23W GLY 3.3 18.4 - - - +
24W PHE* 3.8 12.3 - - + -
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Residues in contact with GLY 20 (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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16W TYR* 2.5 46.4 + - - +
17W LEU 4.3 1.7 + - - -
18W VAL 3.7 0.4 - - - -
19W CYS* 1.3 71.9 - - - +
21W GLU* 1.3 57.8 + - - -
23W GLY* 3.1 16.1 + - - -
24W PHE* 4.8 0.7 - - - -
26Y TYR* 3.6 15.2 - - - -
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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