Contacts of the helix formed by residues 31 - 40 (chain Q) in PDB entry 2DFS
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 GLU 31 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19Q PHE* 4.0 21.4 - - + -
27Q ILE* 3.9 9.2 - - + +
28Q THR* 2.9 28.2 + - + +
30Q LYS* 1.3 83.6 - - - +
32Q LEU* 1.3 62.0 + - - +
33Q GLY 3.4 1.6 - - - -
34Q THR* 2.6 45.8 + - - +
35Q VAL* 3.1 16.3 + - - +
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Residues in contact with LEU 32 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28Q THR 3.9 2.0 + - - -
29Q THR 3.3 16.1 + - - +
30Q LYS 3.3 1.4 - - - -
31Q GLU* 1.3 77.0 - - - +
33Q GLY* 1.3 58.5 + - - +
35Q VAL* 3.3 7.2 - - - +
36Q MET* 3.1 53.9 + - + +
48Q LEU* 3.9 15.0 - - + +
51Q MET* 4.7 4.0 - - + +
52Q ILE* 3.6 38.8 - - + +
63Q ILE* 3.7 20.2 - - + -
67Q GLU* 5.4 1.8 - - - +
68Q PHE* 3.5 38.1 - - + -
71Q MET* 5.6 7.9 - - + -
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Residues in contact with GLY 33 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30Q LYS 4.2 2.8 + - - -
31Q GLU 3.4 0.6 - - - -
32Q LEU* 1.3 75.5 - - - +
34Q THR* 1.3 60.6 + - - +
36Q MET* 3.9 11.7 - - - +
37Q ARG* 3.2 39.5 + - - +
43Q PRO* 5.2 1.2 - - - +
45Q GLU* 6.0 3.4 - - - -
48Q LEU* 3.1 27.6 - - - +
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Residues in contact with THR 34 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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854M VAL* 4.2 22.8 - - + +
19Q PHE* 3.4 18.1 - - - -
30Q LYS 5.7 1.3 - - - +
31Q GLU* 2.6 45.0 + - - +
33Q GLY* 1.3 77.2 - - - +
35Q VAL* 1.4 56.6 + - - +
37Q ARG* 3.4 9.6 + - - +
38Q SER* 2.8 30.5 + - - -
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Residues in contact with VAL 35 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12Q PHE* 3.8 23.1 - - + -
15Q ALA 5.2 0.9 - - - -
16Q PHE* 4.6 11.4 - - + +
19Q PHE* 4.1 20.3 - - + -
27Q ILE* 3.9 23.1 - - + -
31Q GLU 3.1 16.9 + - - +
32Q LEU* 3.3 18.8 - - - +
34Q THR* 1.4 73.0 + - - +
36Q MET* 1.4 63.0 + - - +
38Q SER* 3.4 6.6 + - - -
39Q LEU* 3.1 23.4 + - - +
68Q PHE* 3.5 28.5 - - + -
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Residues in contact with MET 36 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32Q LEU* 3.1 46.1 + - + +
33Q GLY* 3.9 11.9 - - - +
35Q VAL* 1.4 75.7 - - - +
37Q ARG* 1.3 62.0 + - - +
39Q LEU* 3.4 3.0 + - - +
40Q GLY 3.2 17.2 + - - -
41Q GLN* 3.3 18.9 + - + +
43Q PRO* 3.6 33.4 - - + -
48Q LEU* 4.5 9.0 - - - -
51Q MET* 3.4 42.6 - - + -
68Q PHE* 3.8 22.7 - - + -
79Q THR* 5.7 7.0 - - + +
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Residues in contact with ARG 37 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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847M ALA* 5.0 0.2 - - - +
850M ARG* 3.5 51.3 + - - +
851M GLY* 3.7 9.8 - - - +
854M VAL* 3.3 23.1 - - + +
855M ARG* 3.4 18.5 - - - +
33Q GLY* 3.2 23.5 + - - +
34Q THR* 3.4 6.5 + - - +
35Q VAL 3.3 0.4 - - - -
36Q MET* 1.3 80.2 - - - +
38Q SER* 1.3 58.5 + - - +
40Q GLY* 3.5 7.1 + - - -
41Q GLN 3.2 21.5 - - - +
42Q ASN 3.2 14.2 + - - -
43Q PRO* 2.7 32.3 + - + -
44Q THR* 4.2 0.6 - - - +
45Q GLU* 2.7 41.8 + - - +
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Residues in contact with SER 38 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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854M VAL* 3.6 9.3 - - - +
855M ARG* 3.8 16.0 - - - +
858M TYR* 3.4 45.2 - - - +
15Q ALA* 4.4 10.3 - - - +
19Q PHE* 3.9 19.9 - - - -
34Q THR 2.8 20.6 + - - -
35Q VAL* 3.5 6.7 - - - -
36Q MET 3.4 0.2 - - - -
37Q ARG* 1.3 71.4 - - - +
39Q LEU* 1.4 63.0 - - - +
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Residues in contact with LEU 39 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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855M ARG* 5.2 0.9 - - - -
8Q GLN* 5.3 6.1 - - - +
11Q GLU* 6.4 0.7 - - + -
12Q PHE* 3.6 49.9 - - + +
15Q ALA* 5.5 1.8 - - - +
35Q VAL 3.1 9.6 + - - +
36Q MET 3.4 8.5 + - - +
38Q SER* 1.4 77.9 - - - +
40Q GLY* 1.3 57.3 + - - +
41Q GLN* 3.5 20.2 - - - +
68Q PHE* 4.6 6.3 - - + -
72Q MET* 3.6 30.5 - - - -
148Q LYS* 5.4 1.6 - - - +
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Residues in contact with GLY 40 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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855M ARG* 4.3 14.0 + - - -
36Q MET 3.2 1.8 + - - -
37Q ARG 3.5 6.3 + - - -
38Q SER 3.4 1.8 - - - -
39Q LEU* 1.3 81.2 - - - +
41Q GLN* 1.3 72.7 + - - +
42Q ASN* 4.3 7.4 + - - +
83Q GLU* 5.0 1.2 - - - +
148Q LYS* 3.2 36.3 + - - -
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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