Contacts of the helix formed by residues 14 - 24 (chain W) in PDB entry 1YIT
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 HIS 14 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10660 U 3.4 34.4 + - - -
10670 A 4.3 6.0 - - - -
849 G 3.5 25.9 + - - -
859 A 2.9 33.3 + - - -
12W ASN 3.7 3.6 + - - -
13W MET* 1.3 75.2 - - - +
15W THR* 1.3 61.0 + - - +
16W ASP* 3.3 19.2 + - - +
17W ILE* 3.1 20.9 + - + +
18W GLN* 2.9 23.7 + - - +
51W PHE* 5.1 0.8 - + - -
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Residues in contact with THR 15 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9430 A 4.9 0.9 - - - +
10670 A 2.7 34.5 + - - -
13W MET 3.3 4.0 + - - -
14W HIS* 1.3 72.3 + - - +
16W ASP* 1.3 58.9 + - - +
18W GLN* 3.1 7.8 + - + +
19W ASP* 2.9 51.3 + - - +
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Residues in contact with ASP 16 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9430 A 4.1 6.5 - - - +
9440 G 3.5 27.2 - - - +
14W HIS* 3.3 19.7 - - - +
15W THR* 1.3 75.8 - - - +
17W ILE* 1.3 79.6 + - - +
19W ASP* 4.0 8.1 + - - +
20W THR* 2.8 24.8 + - - -
47W LYS* 3.2 24.2 + - - -
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Residues in contact with ILE 17 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
849 G 4.1 16.8 - - - +
13W MET* 3.1 20.2 - - + +
14W HIS* 3.1 29.1 + - + +
15W THR 3.0 0.6 - - - -
16W ASP* 1.3 93.2 + - - +
18W GLN* 1.3 64.8 + - - +
20W THR* 3.1 17.3 + - - -
21W LEU* 3.1 11.5 + - + +
47W LYS* 3.7 36.6 - - + +
48W VAL* 4.3 8.9 - - + +
51W PHE* 3.6 32.5 - - + -
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Residues in contact with GLN 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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10680 C 5.5 0.9 + - - -
10W GLU* 3.3 51.3 + - + +
13W MET* 3.0 28.0 - - + +
14W HIS 2.9 11.6 + - - +
15W THR* 3.6 11.0 - - + +
17W ILE* 1.3 77.1 - - - +
19W ASP* 1.3 65.0 + - - +
21W LEU* 3.2 7.6 + - + +
22W GLU* 3.0 40.1 + - + +
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Residues in contact with ASP 19 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9430 A 2.5 52.1 + - + +
9440 G 4.7 0.2 - - - +
15W THR* 2.9 35.8 + - - +
16W ASP 4.1 3.6 - - - +
18W GLN* 1.3 78.2 + - - +
20W THR* 1.3 57.4 + - - +
22W GLU* 3.1 19.7 + - - +
23W MET* 2.8 40.9 + - + +
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Residues in contact with THR 20 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9440 G 2.7 32.8 + - - +
16W ASP 2.8 19.6 + - - -
17W ILE* 3.1 10.2 + - - -
19W ASP* 1.3 76.5 - - - +
21W LEU* 1.3 66.2 + - - +
23W MET* 2.8 19.5 + - - +
24W LEU* 2.9 14.7 + - + +
44W MET* 3.7 34.3 - - + +
47W LYS* 3.7 6.5 - - + +
48W VAL* 3.9 16.8 - - + -
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Residues in contact with LEU 21 (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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4W LEU* 4.7 7.4 - - + -
6W GLN* 3.6 20.6 - - + +
13W MET* 3.5 24.9 - - + -
17W ILE 3.1 11.2 + - - +
18W GLN* 3.2 10.3 + - + +
20W THR* 1.3 78.9 - - - +
22W GLU* 1.3 59.9 + - - +
24W LEU* 3.2 11.3 + - + -
26W ILE* 2.8 63.8 + - + +
48W VAL* 3.1 38.4 - - + -
51W PHE* 4.9 6.7 - - + +
52W VAL* 4.6 2.9 - - + -
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Residues in contact with GLU 22 (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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9430 A 5.4 7.1 - - + -
10250 C 4.3 8.6 + - - +
18W GLN* 3.0 39.1 + - + +
19W ASP* 3.3 22.5 - - - +
20W THR 3.0 0.4 - - - -
21W LEU* 1.3 75.1 - - - +
23W MET* 1.3 65.8 + - - +
24W LEU 3.0 1.6 - - - -
25W ASN* 3.0 14.0 + - - +
26W ILE 3.6 8.3 - - - +
27W HIS* 3.3 40.9 + - + +
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Residues in contact with MET 23 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9430 A 3.5 42.4 - - + +
9440 G 3.1 62.4 - - + +
10240 G 2.7 49.0 + - + +
10250 C 3.1 30.9 - - - +
19W ASP* 2.8 22.8 + - + +
20W THR* 2.8 6.5 + - - +
22W GLU* 1.3 76.5 - - + +
24W LEU* 1.3 58.1 + - + +
25W ASN* 3.0 1.6 + - - -
44W MET* 5.1 4.5 - - - +
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Residues in contact with LEU 24 (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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10240 G 4.7 1.1 - - - +
4W LEU* 3.6 27.1 - - + -
20W THR* 2.9 22.0 + - + +
21W LEU* 3.3 5.4 - - - +
22W GLU 3.0 0.4 - - - -
23W MET* 1.3 78.5 - - - +
25W ASN* 1.3 66.0 + - - +
26W ILE* 3.0 23.3 - - + +
33W THR* 3.4 16.6 - - + +
35W VAL* 4.7 6.3 - - + -
41W TYR* 3.6 35.2 - - + -
44W MET* 3.7 35.7 - - + -
45W VAL* 4.5 9.2 - - + +
48W VAL* 4.9 3.8 - - + -
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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
------------------------------------------------------------
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