Contacts of the helix formed by residues 34 - 43 (chain A) in PDB entry 2YS9
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 THR 34 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A ARG* 2.9 24.5 + - + +
33A GLU* 1.3 83.4 - - + +
35A ASP* 1.3 74.7 + - - +
36A ILE 3.3 0.7 - - - -
37A PRO* 3.5 14.2 - - - +
38A GLN* 3.7 10.9 - - - +
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Residues in contact with ASP 35 (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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24A TYR* 3.0 40.9 + - + +
31A LEU* 4.9 0.4 - - - -
32A ARG* 2.8 22.4 + - + +
34A THR* 1.3 90.0 + - - +
36A ILE* 1.3 58.6 + - - +
37A PRO 3.5 0.2 - - - -
38A GLN* 3.9 12.8 - - - +
39A LEU* 2.9 51.0 + - + +
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Residues in contact with ILE 36 (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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31A LEU* 3.4 28.0 - - + -
32A ARG 2.7 14.1 + - - +
33A GLU* 3.6 21.3 - - + +
35A ASP* 1.3 77.9 - - - +
37A PRO* 1.3 69.5 - - + +
39A LEU* 4.0 0.9 - - - +
40A SER* 3.0 31.4 + - - -
47A THR* 3.3 36.3 - - + +
50A VAL* 4.1 9.2 - - + +
51A LEU* 3.3 35.9 - - + -
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Residues in contact with PRO 37 (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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33A GLU 2.8 30.1 - - - +
34A THR* 3.5 9.4 - - - +
36A ILE* 1.3 91.3 - - + +
38A GLN* 1.3 64.0 + - - +
40A SER* 4.0 6.0 - - - -
41A GLN* 2.9 34.6 + - - +
47A THR* 5.0 6.3 - - + +
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Residues in contact with GLN 38 (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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34A THR 3.7 16.8 - - - +
35A ASP* 4.0 12.1 - - - +
36A ILE 3.3 0.4 - - - -
37A PRO* 1.3 84.0 - - - +
39A LEU* 1.3 63.7 + - + +
41A GLN* 3.6 15.6 + - - +
42A ALA* 3.7 14.0 + - - +
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Residues in contact with LEU 39 (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* 3.9 30.3 - - + +
21A LEU* 3.7 11.9 - - + -
24A TYR* 3.5 45.8 - - + -
31A LEU* 4.8 3.1 - - + -
35A ASP* 2.9 35.9 + - + +
36A ILE 4.0 1.6 - - - +
38A GLN* 1.3 76.8 - - + +
40A SER* 1.3 57.0 + - - +
41A GLN 3.1 2.0 - - - -
42A ALA* 2.7 28.4 + - + +
43A SER* 3.0 14.2 + - - -
50A VAL* 4.5 2.7 - - + -
54A PHE* 3.9 15.7 - - + -
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Residues in contact with SER 40 (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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36A ILE 3.0 20.2 + - - -
37A PRO* 4.0 7.4 - - - -
39A LEU* 1.3 76.5 - - - +
41A GLN* 1.3 57.5 + - - +
43A SER* 3.4 1.9 + - - +
44A ARG* 2.9 24.8 + - - -
45A LEU 2.7 43.0 + - - +
46A SER 3.2 14.7 + - - -
47A THR* 4.4 7.0 - - - -
50A VAL* 3.3 18.1 - - - +
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Residues in contact with GLN 41 (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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37A PRO* 2.9 22.7 + - - +
38A GLN* 3.6 24.4 + - - +
39A LEU 3.1 0.8 - - - -
40A SER* 1.3 79.1 - - - +
42A ALA* 1.3 61.7 + - - +
44A ARG* 3.5 20.3 + - - +
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Residues in contact with ALA 42 (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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17A ASP* 4.5 5.5 - - - +
20A PRO* 3.9 23.8 - - + +
38A GLN* 3.7 6.8 + - - +
39A LEU* 2.7 20.7 + - + +
41A GLN* 1.3 71.9 - - - +
43A SER* 1.3 57.0 + - - +
44A ARG* 2.9 21.6 + - - +
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Residues in contact with SER 43 (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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16A PRO* 3.2 20.8 - - - +
17A ASP 2.7 30.7 + - - +
20A PRO* 3.1 17.9 - - - +
21A LEU* 3.2 20.1 - - - +
39A LEU 3.0 9.6 + - - -
40A SER* 4.3 2.0 - - - -
42A ALA* 1.3 73.8 - - - +
44A ARG* 1.3 70.3 + - - +
45A LEU* 3.3 23.0 + - - +
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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