Contacts of the helix formed by residues 31 - 40 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19E PHE* 4.0 21.5 - - + -
27E ILE* 3.9 8.9 - - + +
28E THR* 2.9 29.3 + - + +
30E LYS* 1.3 84.4 - - - +
32E LEU* 1.3 61.7 + - - +
33E GLY 3.4 1.6 - - - -
34E THR* 2.6 46.5 + - - +
35E VAL* 3.1 15.9 + - - +
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Residues in contact with LEU 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27E ILE* 4.8 0.2 - - - +
28E THR 3.9 1.8 + - - -
29E THR 3.3 15.9 + - - +
30E LYS 3.3 2.0 - - - -
31E GLU* 1.3 76.4 - - - +
33E GLY* 1.3 57.4 + - - +
35E VAL* 3.3 7.5 - - - +
36E MET* 3.1 52.3 + - + +
48E LEU* 3.9 14.8 - - + +
51E MET* 4.7 4.7 - - + +
52E ILE* 3.6 39.5 - - + +
63E ILE* 3.7 19.7 - - + -
67E GLU* 5.4 1.3 - - - +
68E PHE* 3.5 37.9 - - + -
71E MET* 5.6 7.9 - - + -
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Residues in contact with GLY 33 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E LYS 4.2 2.6 + - - -
31E GLU 3.4 0.8 - - - -
32E LEU* 1.3 74.9 - - - +
34E THR* 1.3 60.9 + - - +
36E MET* 3.9 11.9 - - - +
37E ARG* 3.2 39.3 + - - +
43E PRO* 5.1 1.2 - - - +
45E GLU* 6.1 3.1 - - - -
48E LEU* 3.1 27.5 - - - +
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Residues in contact with THR 34 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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854A VAL* 4.1 23.5 - - + +
19E PHE* 3.4 16.4 - - - -
30E LYS 5.3 1.3 + - - +
31E GLU* 2.6 46.8 + - - +
33E GLY* 1.3 77.0 - - - +
35E VAL* 1.4 56.9 + - - -
37E ARG* 3.3 9.4 + - - +
38E SER* 2.8 30.1 + - - -
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Residues in contact with VAL 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E PHE* 3.8 24.1 - - + -
15E ALA 5.2 0.9 - - - -
16E PHE* 4.6 11.9 - - + +
19E PHE* 4.1 21.2 - - + -
27E ILE* 3.9 22.2 - - + -
31E GLU 3.1 17.5 + - - +
32E LEU* 3.3 18.8 - - + +
34E THR* 1.4 72.2 + - - +
36E MET* 1.4 62.4 + - - +
38E SER* 3.4 6.0 + - - -
39E LEU* 3.1 23.6 + - - +
68E PHE* 3.5 28.9 - - + -
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Residues in contact with MET 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E LEU* 3.1 45.3 + - + +
33E GLY* 3.9 13.0 - - - +
35E VAL* 1.4 74.9 - - - +
37E ARG* 1.3 62.0 + - - +
39E LEU* 3.4 3.4 + - - +
40E GLY 3.2 17.0 + - - -
41E GLN* 3.3 18.9 + - + +
43E PRO* 3.6 34.3 - - + -
48E LEU* 4.5 7.9 - - - -
51E MET* 3.4 43.1 - - + -
68E PHE* 3.8 22.2 - - + -
79E THR* 5.7 7.4 - - + +
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Residues in contact with ARG 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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850A ARG* 3.5 56.1 + - - +
851A GLY* 3.7 5.9 - - - +
854A VAL* 3.3 24.4 - - + +
855A ARG* 3.4 18.4 + - - +
33E GLY* 3.2 24.2 + - - +
34E THR* 3.3 6.1 + - - +
35E VAL 3.3 0.4 - - - -
36E MET* 1.3 81.7 - - - +
38E SER* 1.3 59.0 + - - +
40E GLY* 3.5 6.8 + - - -
41E GLN 3.2 21.3 - - - +
42E ASN 3.2 14.1 + - - -
43E PRO* 2.7 32.5 + - + -
45E GLU* 2.7 44.4 + - - +
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Residues in contact with SER 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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854A VAL* 3.6 10.0 - - - +
855A ARG* 3.7 15.7 - - - +
858A TYR* 3.4 46.7 - - - +
15E ALA* 4.4 9.2 - - - +
19E PHE* 3.9 19.4 - - - -
34E THR 2.8 20.8 + - - -
35E VAL* 3.5 6.3 - - - -
37E ARG* 1.3 70.5 - - - +
39E LEU* 1.4 64.1 + - - +
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Residues in contact with LEU 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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855A ARG* 5.2 1.1 - - - -
8E GLN* 5.4 5.2 - - - +
11E GLU* 6.3 2.9 - - + -
12E PHE* 3.6 50.6 - - + +
15E ALA* 5.5 1.8 - - - +
35E VAL 3.1 7.5 + - - +
36E MET* 3.6 8.3 - - - +
38E SER* 1.4 78.9 - - - +
40E GLY* 1.3 56.2 + - - +
41E GLN* 3.5 19.3 - - - +
68E PHE* 4.6 6.3 - - + -
72E MET* 3.6 30.3 - - - -
148E LYS* 5.4 1.4 - - - +
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Residues in contact with GLY 40 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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855A ARG* 4.2 17.4 + - - -
36E MET 3.2 1.8 + - - -
37E ARG 3.5 6.2 + - - -
38E SER 3.4 1.8 - - - -
39E LEU* 1.3 82.2 - - - +
41E GLN* 1.3 73.1 - - - +
42E ASN* 4.3 3.8 + - - +
83E GLU* 4.9 1.5 - - - +
148E LYS* 3.2 35.3 - - - -
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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