Contacts of the helix formed by residues 20 - 34 (chain A) in PDB entry 1YRT
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 20 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A TYR* 3.7 4.7 - - - +
18A GLY 3.6 6.9 - - - +
19A ILE* 1.3 87.5 - - + +
21A ALA* 1.3 59.8 + - - +
22A ALA* 4.7 1.8 - - + +
23A VAL* 3.2 18.0 + - + +
24A LEU* 2.9 25.3 + - - +
48A THR* 3.3 29.6 - - + +
51A ILE* 3.7 29.4 - - + -
52A ALA* 3.8 21.8 - - + +
189A ILE* 4.9 4.3 - - + -
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Residues in contact with ALA 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A GLY* 3.5 29.6 - - - +
9A TYR* 3.4 31.0 + - + -
19A ILE 3.3 2.2 + - - -
20A PRO* 1.3 70.1 - - - +
22A ALA* 1.3 58.3 + - - +
24A LEU* 3.3 4.0 + - - +
25A ASP* 2.8 33.5 + - - +
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Residues in contact with ALA 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A PRO* 3.2 2.7 + - + +
21A ALA* 1.3 78.3 - - - +
23A VAL* 1.3 63.0 + - + +
25A ASP* 3.2 20.3 + - - +
26A GLY* 3.3 9.7 + - - -
286A ARG 5.4 0.7 - - - +
290A VAL* 3.4 41.8 - - + +
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Residues in contact with VAL 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ILE* 3.8 14.8 - - + -
20A PRO* 3.2 26.2 + - + +
22A ALA* 1.3 75.5 - - - +
24A LEU* 1.3 65.5 + - - +
26A GLY* 3.0 12.7 + - - +
27A ILE* 3.1 20.2 + - + +
51A ILE* 4.3 5.4 - - + +
52A ALA* 5.5 1.8 - - - -
189A ILE* 4.0 19.3 - - + -
286A ARG* 5.6 1.8 - - - +
287A ALA* 4.5 11.7 - - + +
290A VAL* 4.2 10.5 - - + -
292A ALA* 4.0 27.4 - - + -
295A VAL* 4.5 11.2 - - + -
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Residues in contact with LEU 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A TYR* 3.8 19.1 - - + +
14A ASP* 3.6 41.5 - - + +
17A SER* 4.7 0.2 - - - +
19A ILE* 3.7 22.0 - - + -
20A PRO 2.9 13.6 + - - +
21A ALA* 3.5 8.7 - - - +
23A VAL* 1.3 76.8 - - - +
25A ASP* 1.3 64.2 + - - +
27A ILE* 3.2 9.9 + - + -
28A LYS* 3.0 41.7 + - + +
314A PHE* 3.8 27.4 - - + -
316A VAL* 4.4 5.8 - - + -
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Residues in contact with ASP 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A ALA* 3.4 32.9 + - - +
8A GLY* 3.9 14.8 - - - -
9A TYR 4.7 1.6 + - - -
21A ALA 2.8 17.4 + - - +
22A ALA* 3.3 16.2 - - - +
23A VAL 3.1 0.2 - - - -
24A LEU* 1.3 79.3 - - - +
26A GLY* 1.3 61.3 + - - +
28A LYS* 3.4 14.5 + - - +
29A ALA* 3.1 20.6 + - - +
286A ARG* 4.9 2.0 + - - +
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Residues in contact with GLY 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ALA 3.3 5.7 + - - -
23A VAL 3.0 7.7 + - - -
25A ASP* 1.3 79.6 - - - +
27A ILE* 1.3 51.5 + - - +
29A ALA* 3.1 3.1 + - - +
30A VAL* 2.7 40.5 + - - +
283A LEU* 4.7 0.9 - - - -
286A ARG* 3.7 38.1 - - - -
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Residues in contact with ILE 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ILE* 3.9 31.0 - - + -
23A VAL* 3.1 24.2 + - + +
24A LEU* 3.2 10.5 + - + +
26A GLY* 1.3 76.5 - - - +
28A LYS* 1.3 59.1 + - - +
30A VAL 3.3 0.5 + - - -
31A ALA* 2.8 27.4 + - - +
38A LEU* 3.6 10.3 - - + +
40A PHE* 3.8 41.5 - - + -
189A ILE* 5.0 5.2 - - + -
283A LEU* 3.5 26.0 - - + +
295A VAL* 6.1 2.0 - - + -
316A VAL* 4.0 17.5 - - + -
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Residues in contact with LYS 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A ALA* 6.0 3.1 - - + +
9A TYR 5.7 0.4 - - - +
10A ALA* 3.7 18.0 - - - +
11A ASN* 5.0 0.4 + - - -
14A ASP* 2.6 40.3 + - - -
24A LEU* 3.0 32.7 + - + +
25A ASP* 3.8 14.6 - - - +
27A ILE* 1.3 78.1 - - - +
29A ALA* 1.3 62.6 + - - +
31A ALA* 3.3 3.3 + - - +
32A LYS* 3.2 32.4 + - - +
316A VAL* 4.1 17.0 - - + -
320A GLY* 3.6 25.8 + - - +
322A SER* 3.8 11.8 + - - -
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Residues in contact with ALA 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ASP 3.1 12.7 + - - +
26A GLY 3.1 7.2 + - - +
28A LYS* 1.3 76.6 - - - +
30A VAL* 1.3 55.9 + - - +
32A LYS* 3.3 11.6 + - - +
33A GLU* 3.0 38.1 + - - +
286A ARG* 3.4 38.1 - - - +
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Residues in contact with VAL 30 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A GLY 2.7 23.1 + - - +
29A ALA* 1.3 69.8 - - - +
31A ALA* 1.3 68.6 + - - +
33A GLU* 4.1 12.8 - - - +
34A LYS* 2.9 39.4 + - + +
38A LEU* 4.6 3.1 - - + -
279A VAL* 4.6 8.1 - - + -
282A ALA* 3.8 36.8 - - + +
283A LEU* 3.7 24.0 - - + -
286A ARG* 3.7 21.5 - - + -
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Residues in contact with ALA 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ILE 2.8 18.1 + - - +
28A LYS 3.5 6.7 - - - +
30A VAL* 1.3 76.3 - - - +
32A LYS* 1.3 57.1 + - + +
35A ASN* 3.1 8.0 + - - -
36A ALA* 3.1 40.0 + - - +
38A LEU* 3.8 13.4 - - + +
316A VAL* 3.8 13.5 - - + -
317A SER 3.5 22.9 - - - +
318A ALA 3.7 3.9 - - - +
320A GLY 5.1 0.2 - - - +
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Residues in contact with LYS 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A LYS* 3.2 21.8 + - - +
29A ALA* 3.8 9.8 - - - +
30A VAL 3.1 0.4 - - - -
31A ALA* 1.3 77.6 - - - +
33A GLU* 1.3 65.0 + - + +
35A ASN* 3.3 13.0 + - - +
318A ALA 3.2 18.0 - - - +
319A THR* 3.4 28.0 + - - +
320A GLY* 3.8 9.3 - - - +
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Residues in contact with GLU 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ALA* 3.0 24.3 + - - +
30A VAL* 3.9 15.2 - - - +
32A LYS* 1.3 78.6 - - + +
34A LYS* 1.3 65.6 + - + +
35A ASN* 3.6 1.2 + - - +
282A ALA* 5.9 0.7 - - - +
285A ARG* 5.6 2.3 + - - -
286A ARG* 3.1 29.1 + - - -
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Residues in contact with LYS 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A VAL* 2.9 35.9 + - + +
33A GLU* 1.3 81.4 - - + +
35A ASN* 1.3 66.2 + - - +
36A ALA* 3.5 4.5 - - + -
200A ASN* 3.1 27.9 + - - +
275A PHE* 3.7 26.0 - - + -
278A GLU* 2.8 46.9 + - - +
279A VAL* 3.9 13.7 - - + -
282A ALA* 4.2 14.6 - - + -
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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