Contacts of the helix formed by residues 31 - 40 (chain O) 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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19O PHE* 3.6 22.7 - - + +
21O LYS* 5.4 9.1 + - - -
27O ILE* 4.0 10.8 - - + +
28O THR* 2.9 29.0 + - + +
30O LYS* 1.3 80.0 - - + +
32O LEU* 1.3 62.2 + - - +
33O GLY 3.4 2.0 - - - -
34O THR* 2.7 31.8 + - - +
35O VAL* 3.1 25.1 + - - +
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Residues in contact with LEU 32 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28O THR 3.9 1.6 + - - -
29O THR 3.3 16.6 + - - +
30O LYS 3.3 0.6 - - - -
31O GLU* 1.3 76.7 - - - +
33O GLY* 1.3 62.5 + - - +
35O VAL* 3.2 9.5 - - - +
36O MET* 3.1 46.6 + - + +
48O LEU* 3.9 19.1 - - + +
51O MET* 4.7 3.6 - - + +
52O ILE* 3.7 36.6 - - + +
63O ILE* 3.6 21.3 - - + -
67O GLU* 5.4 1.8 - - - +
68O PHE* 3.5 36.8 - - + -
71O MET* 5.6 7.4 - - + -
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Residues in contact with GLY 33 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30O LYS 4.4 2.4 + - - -
31O GLU 3.4 0.8 - - - -
32O LEU* 1.3 75.4 - - - +
34O THR* 1.3 56.3 + - - +
36O MET* 3.5 11.6 + - - +
37O ARG* 3.0 54.4 + - - +
43O PRO* 4.5 0.2 - - - +
48O LEU* 3.1 26.6 - - - +
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Residues in contact with THR 34 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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806M ALA* 4.4 15.8 - - + +
19O PHE* 3.7 13.7 - - - -
30O LYS 4.7 0.7 + - - -
31O GLU* 2.7 46.3 + - - +
33O GLY* 1.3 72.7 - - - +
35O VAL* 1.4 54.1 + - - -
37O ARG* 3.4 15.2 + - - +
38O SER* 2.8 30.0 + - - -
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Residues in contact with VAL 35 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12O PHE* 3.8 23.4 - - + -
15O ALA 4.9 1.3 - - - +
16O PHE* 4.5 11.2 - - + +
19O PHE* 3.9 19.8 - - + -
27O ILE* 3.9 23.1 - - + -
31O GLU 3.1 17.6 + - - +
32O LEU* 3.2 19.1 - - - +
34O THR* 1.4 72.3 - - - +
36O MET* 1.4 63.2 + - - +
38O SER* 3.4 6.7 + - - -
39O LEU* 3.1 22.9 + - - +
68O PHE* 3.5 27.8 - - + -
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Residues in contact with MET 36 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32O LEU* 3.1 43.2 + - + +
33O GLY* 3.6 11.4 - - - +
34O THR 3.5 0.2 - - - -
35O VAL* 1.4 74.0 - - - +
37O ARG* 1.3 63.5 + - - +
39O LEU* 3.4 4.7 + - - +
40O GLY 3.2 17.0 + - - -
41O GLN* 3.2 20.8 + - + +
43O PRO* 3.8 30.7 - - + -
48O LEU* 4.7 7.2 - - - -
51O MET* 3.5 41.5 - - + +
68O PHE* 3.7 23.1 - - + -
79O THR* 5.7 9.4 - - + +
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Residues in contact with ARG 37 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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799M ARG 5.1 0.6 + - - -
802M ARG* 3.5 33.6 - - - +
803M GLY* 3.9 9.4 - - - +
806M ALA* 3.9 14.8 - - + -
807M ARG* 2.8 32.2 + - - +
33O GLY* 3.0 31.6 + - - +
34O THR* 3.7 14.0 - - - +
35O VAL 3.4 0.2 - - - -
36O MET* 1.3 77.0 - - - +
38O SER* 1.3 59.5 + - - +
40O GLY 3.4 2.4 + - - -
41O GLN 3.3 16.4 - - - +
42O ASN* 4.5 1.9 - - - -
43O PRO* 2.7 43.3 + - + +
44O THR 3.7 6.7 + - - -
45O GLU* 2.7 46.3 + - - +
48O LEU* 5.1 0.6 - - - +
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Residues in contact with SER 38 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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806M ALA* 4.5 3.0 - - - +
807M ARG* 3.8 21.7 - - - +
810M ALA* 3.8 22.5 - - - +
15O ALA* 4.3 17.1 - - - +
18O LEU* 5.6 0.2 - - - +
19O PHE* 4.0 17.4 - - - -
34O THR 2.8 20.5 + - - -
35O VAL* 3.4 11.9 + - - -
37O ARG* 1.3 70.5 - - - +
39O LEU* 1.4 63.1 + - - +
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Residues in contact with LEU 39 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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807M ARG* 5.2 0.7 - - - -
8O GLN* 5.5 4.5 - - - +
12O PHE* 3.6 49.1 - - + +
15O ALA* 5.7 1.8 - - - -
35O VAL 3.1 10.8 + - - +
36O MET* 3.6 7.6 - - - +
38O SER* 1.4 76.0 - - - +
40O GLY* 1.3 57.1 + - - +
41O GLN* 3.5 20.4 - - - +
68O PHE* 4.6 6.7 - - + -
72O MET* 3.6 30.3 - - - -
148O LYS* 5.4 0.9 - - - +
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Residues in contact with GLY 40 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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807M ARG* 3.0 28.2 + - - -
36O MET 3.2 3.0 + - - -
37O ARG 3.4 3.0 + - - -
39O LEU* 1.3 80.1 - - - +
41O GLN* 1.3 70.0 + - - +
42O ASN* 3.5 9.2 + - - -
83O GLU* 4.2 1.2 - - - +
148O LYS* 3.6 29.3 - - - -
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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