Contacts of the helix formed by residues 30 - 39 (chain A) in PDB entry 2DT5
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 SER 30 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A THR* 1.3 78.7 + - - +
31A SER* 1.3 64.8 + - - +
32A GLU* 3.4 14.2 + - - +
33A GLN* 3.0 25.0 + - - +
34A LEU* 3.0 22.2 + - - +
60A VAL 5.9 0.4 - - - -
61A GLY* 4.2 4.0 - - - -
62A TYR* 4.6 0.7 - - - -
401A SO4 3.0 21.1 - - - -
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Residues in contact with SER 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A SER* 1.3 73.7 - - - +
32A GLU* 1.3 60.0 + - - +
34A LEU* 3.8 1.4 - - - +
35A GLY 2.9 23.6 + - - -
42A ALA* 3.4 19.5 - - - +
45A VAL* 4.2 12.1 - - - +
46A ARG* 2.8 43.0 + - - -
62A TYR* 4.2 12.3 - - - -
401A SO4 2.5 30.2 + - - -
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Residues in contact with GLU 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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30A SER* 3.0 11.6 + - - +
31A SER* 1.3 80.9 + - - +
33A GLN* 1.3 65.2 + - - +
35A GLY 3.4 0.5 + - - -
36A GLY* 2.9 21.7 + - - -
42A ALA* 3.7 15.2 - - + +
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Residues in contact with GLN 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LEU* 4.0 17.8 - - - +
26A VAL* 3.8 16.5 - - - +
28A ARG 4.1 0.9 - - - +
29A THR* 2.6 38.7 + - - +
30A SER* 3.0 17.7 + - - +
32A GLU* 1.3 77.0 - - - +
34A LEU* 1.3 61.2 + - - +
36A GLY* 3.3 2.8 + - - -
37A LEU* 3.0 42.9 + - + +
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Residues in contact with LEU 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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14A TYR* 5.0 12.1 - - + +
17A ILE* 3.9 16.7 - - + +
18A LEU* 4.1 10.5 - - + -
21A LEU* 3.9 26.5 - - + -
29A THR* 3.7 18.8 - - + +
30A SER 3.0 18.4 + - - +
31A SER 3.8 3.4 - - - +
33A GLN* 1.3 74.8 - - - +
35A GLY* 1.3 61.1 + - - +
37A LEU* 3.1 5.6 + - - +
38A ALA* 2.8 31.6 + - - +
45A VAL* 3.8 28.3 - - + -
49A LEU* 4.4 7.9 - - + -
62A TYR* 4.3 15.0 - - + -
67A LEU* 4.4 8.7 - - + -
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Residues in contact with GLY 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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31A SER 2.9 20.6 + - - -
32A GLU 3.9 0.9 - - - -
34A LEU* 1.3 73.3 - - - +
36A GLY* 1.3 52.4 + - - +
38A ALA* 4.5 1.6 - - - -
39A GLN* 2.5 32.9 + - - -
40A VAL 2.9 29.6 + - - -
42A ALA 4.6 2.5 - - - -
45A VAL* 3.7 13.2 - - - +
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Residues in contact with GLY 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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32A GLU 2.9 16.0 + - - -
33A GLN* 3.6 4.5 - - - -
34A LEU 3.1 0.2 - - - -
35A GLY* 1.3 76.7 - - - +
37A LEU* 1.3 61.8 + - - +
39A GLN* 3.5 15.5 + - - +
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Residues in contact with LEU 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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17A ILE* 3.7 34.1 - - + +
21A LEU* 4.2 14.1 - - + -
33A GLN* 3.0 47.7 + - + +
34A LEU 3.7 4.5 - - - +
36A GLY* 1.3 76.6 - - - +
38A ALA* 1.3 59.2 + - - +
39A GLN* 3.6 1.9 + - - +
1B MET* 4.1 9.4 - - + +
2B LYS* 3.7 17.7 + - - +
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Residues in contact with ALA 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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13A THR* 4.3 0.7 - - + -
14A TYR* 3.9 23.8 - - + -
17A ILE* 3.5 17.7 - - + -
34A LEU 2.8 16.1 + - - +
35A GLY* 4.1 3.1 - - - +
37A LEU* 1.3 76.1 - - - +
39A GLN* 1.3 70.7 + - - +
40A VAL* 4.5 4.3 - - + +
2B LYS* 4.0 5.4 - - - +
3B VAL* 2.8 38.0 + - + +
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Residues in contact with GLN 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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35A GLY 2.5 15.3 + - - -
36A GLY* 3.8 13.5 - - - +
37A LEU 3.3 2.8 - - - +
38A ALA* 1.3 77.2 - - - +
40A VAL* 1.3 64.4 + - - +
208A GLU* 5.2 7.5 + - - -
2B LYS* 3.8 21.9 - - + +
3B VAL* 5.0 5.0 + - - +
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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