Contacts of the helix formed by residues 31 - 40 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19C PHE* 3.6 22.9 - - + +
21C LYS* 5.7 7.3 + - - -
27C ILE* 4.0 9.7 - - + +
28C THR* 2.9 30.9 + - + +
30C LYS* 1.3 80.2 - - + +
32C LEU* 1.3 62.7 + - - +
33C GLY 3.4 2.0 - - - -
34C THR* 2.6 38.9 + - - +
35C VAL* 3.1 17.7 + - - +
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Residues in contact with LEU 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C THR 3.9 1.8 + - - -
29C THR 3.3 16.8 + - - +
30C LYS 3.3 0.8 - - - -
31C GLU* 1.3 76.1 - - - +
33C GLY* 1.3 61.4 + - - +
35C VAL* 3.2 8.1 - - - +
36C MET* 3.1 47.4 + - + +
48C LEU* 3.9 18.6 - - + +
51C MET* 4.7 3.8 - - + +
52C ILE* 3.7 37.9 - - + +
63C ILE* 3.6 20.6 - - + -
67C GLU* 5.4 1.8 - - - +
68C PHE* 3.5 36.8 - - + -
71C MET* 5.6 7.0 - - + -
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Residues in contact with GLY 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C LYS 4.4 2.4 + - - -
31C GLU 3.4 0.8 - - - -
32C LEU* 1.3 74.2 - - - +
34C THR* 1.3 56.8 + - - +
36C MET* 3.5 11.5 + - - +
37C ARG* 3.0 52.7 + - - +
43C PRO* 4.5 0.2 - - - +
45C GLU* 5.0 0.2 - - - -
48C LEU* 3.1 26.6 - - - +
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Residues in contact with THR 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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806A ALA* 4.4 14.5 - - + +
19C PHE* 3.7 13.5 - - - -
30C LYS 4.7 1.1 + - - -
31C GLU* 2.6 46.2 + - - +
33C GLY* 1.3 72.5 - - - +
35C VAL* 1.4 54.9 + - - -
37C ARG* 3.4 16.3 + - - +
38C SER* 2.8 29.8 + - - -
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Residues in contact with VAL 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C PHE* 3.8 24.2 - - + -
15C ALA* 4.9 1.8 - - + +
16C PHE* 4.5 12.1 - - + +
19C PHE* 4.0 20.3 - - + -
27C ILE* 3.9 22.9 - - + -
31C GLU 3.1 17.6 + - - +
32C LEU* 3.2 19.3 - - - +
34C THR* 1.4 71.7 - - - +
36C MET* 1.4 62.8 + - - +
38C SER* 3.4 6.8 + - - -
39C LEU* 3.1 23.4 + - - +
68C PHE* 3.5 26.7 - - + -
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Residues in contact with MET 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C LEU* 3.1 42.5 + - + +
33C GLY* 3.6 11.9 - - - +
35C VAL* 1.4 74.2 - - - +
37C ARG* 1.3 61.9 + - - +
39C LEU* 3.4 4.7 + - - +
40C GLY 3.2 17.8 + - - -
41C GLN* 3.2 20.7 + - + +
43C PRO* 3.8 31.4 - - + -
48C LEU* 4.7 6.7 - - - -
51C MET* 3.5 42.6 - - + +
68C PHE* 3.7 23.1 - - + -
79C THR* 5.7 8.1 - - + +
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Residues in contact with ARG 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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799A ARG 5.2 0.4 + - - -
802A ARG* 3.6 33.2 - - - +
803A GLY* 3.9 13.2 - - - +
806A ALA* 3.9 10.1 - - + -
807A ARG* 2.8 34.2 + - - +
33C GLY* 3.0 33.3 + - - +
34C THR* 3.7 14.4 - - - +
35C VAL 3.4 0.2 - - - -
36C MET* 1.3 76.6 - - - +
38C SER* 1.3 58.0 + - - +
40C GLY 3.4 2.1 + - - -
41C GLN 3.3 16.6 - - - +
42C ASN* 4.5 1.2 - - - -
43C PRO* 2.7 45.2 + - + +
44C THR 3.7 6.1 + - - -
45C GLU* 2.7 45.9 + - - -
48C LEU* 5.1 0.8 - - - +
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Residues in contact with SER 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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806A ALA* 4.4 5.0 - - - +
807A ARG* 3.7 21.3 - - - +
810A ALA* 3.9 20.3 - - - +
15C ALA* 4.3 17.2 - - - +
18C LEU* 5.7 0.2 - - - +
19C PHE* 4.0 17.5 - - - -
34C THR 2.8 20.9 + - - -
35C VAL* 3.5 11.2 - - - -
37C ARG* 1.3 70.1 - - - +
39C LEU* 1.4 65.0 + - - +
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Residues in contact with LEU 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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807A ARG* 5.1 0.7 - - - -
8C GLN* 5.6 4.7 - - - +
12C PHE* 3.6 50.2 - - + +
15C ALA* 5.5 1.8 - - - +
35C VAL 3.1 10.2 + - - +
36C MET* 3.4 8.5 + - - +
38C SER* 1.4 75.5 - - - +
40C GLY* 1.4 58.1 + - - +
41C GLN* 3.5 20.2 - - - +
68C PHE* 4.6 5.8 - - + -
72C MET* 3.6 31.0 - - - -
148C LYS* 6.0 0.3 - - - +
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Residues in contact with GLY 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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807A ARG* 2.9 29.4 + - - -
36C MET 3.2 3.4 + - - -
37C ARG 3.4 3.0 + - - -
39C LEU* 1.4 80.0 - - - +
41C GLN* 1.3 70.7 + - - +
42C ASN* 3.5 7.6 + - - -
83C GLU* 4.1 1.6 - - - +
148C LYS* 3.6 28.3 - - - -
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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