Contacts of the helix formed by residues 8 - 18 (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 GLN 8 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9C ILE* 1.3 92.7 + - + +
10C ALA* 3.1 6.8 + - + +
11C GLU* 3.2 10.2 + - - +
12C PHE* 3.2 22.5 + - - +
39C LEU* 5.6 3.8 - - - +
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Residues in contact with ILE 9 (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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8C GLN* 1.3 98.4 - - + +
10C ALA* 1.3 59.2 + - + +
12C PHE* 4.3 9.4 - - + -
13C LYS* 2.7 32.5 + - - +
65C PHE* 4.0 11.5 - - + -
69C LEU* 4.0 26.2 - - + -
72C MET* 6.0 4.3 - - + -
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Residues in contact with ALA 10 (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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8C GLN* 3.1 4.1 + - + +
9C ILE* 1.3 83.1 - - + +
11C GLU* 1.4 60.8 + - - +
13C LYS* 3.9 4.9 - - - +
14C GLU* 3.2 21.7 + - - +
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Residues in contact with GLU 11 (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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814A ARG* 2.7 39.6 + - - -
8C GLN 3.2 11.4 + - - +
10C ALA* 1.4 74.3 - - - +
12C PHE* 1.3 60.7 + - - +
14C GLU* 3.1 5.6 + - - +
15C ALA* 2.9 29.5 + - + +
94D LYS* 4.2 18.6 + - - +
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Residues in contact with PHE 12 (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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8C GLN 3.2 16.1 + - - +
9C ILE* 4.0 8.7 - - + +
11C GLU* 1.3 77.2 - - - +
13C LYS* 1.3 55.3 + - - +
15C ALA* 3.3 10.7 + - + -
16C PHE* 2.8 32.2 + + - +
35C VAL* 3.8 30.3 - - + -
39C LEU* 3.6 50.2 - - + +
65C PHE* 3.5 35.0 - + - -
68C PHE* 3.3 40.6 - + - -
69C LEU* 5.5 5.8 - - + -
72C MET* 5.6 4.7 - - + -
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Residues in contact with LYS 13 (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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9C ILE 2.7 23.2 + - - +
10C ALA* 3.9 5.8 - - - +
12C PHE* 1.3 71.3 - - - +
14C GLU* 1.3 56.7 + - - +
16C PHE* 3.3 9.0 + - + +
17C SER* 2.9 45.5 + - - +
65C PHE* 3.5 41.4 - - + -
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Residues in contact with GLU 14 (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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814A ARG* 2.7 47.8 + - - +
10C ALA 3.2 12.2 + - - +
11C GLU* 3.1 11.1 + - - +
13C LYS* 1.3 74.4 - - - +
15C ALA* 1.3 61.9 + - - +
17C SER* 3.0 20.5 + - - -
18C LEU* 3.0 17.0 + - - +
89D PHE* 3.1 28.8 - - + -
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Residues in contact with ALA 15 (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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814A ARG* 5.4 5.8 - - - +
11C GLU* 2.9 15.8 + - + +
12C PHE* 3.4 23.1 - - + +
14C GLU* 1.3 75.0 - - - +
16C PHE* 1.3 60.6 + - - +
18C LEU* 3.3 10.4 + - - +
19C PHE* 3.3 29.5 + - - -
35C VAL* 5.1 2.0 - - + -
38C SER* 4.3 22.0 - - - +
39C LEU* 5.7 0.9 - - - -
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Residues in contact with PHE 16 (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* 2.8 30.6 + + + +
13C LYS* 3.4 16.4 - - + +
15C ALA* 1.3 71.3 - - - +
17C SER* 1.3 57.9 + - - +
18C LEU 3.2 0.2 - - - -
19C PHE* 2.9 7.2 + - - +
20C ASP* 2.8 32.1 + - + -
25C GLY* 3.4 23.8 - - - -
27C ILE* 3.6 33.2 - - + -
35C VAL* 4.5 9.3 - - + +
63C ILE* 3.4 19.1 - - + -
64C ASP 3.7 3.6 - - - -
65C PHE* 3.4 55.0 - + + -
68C PHE* 4.5 9.0 - + + -
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Residues in contact with SER 17 (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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13C LYS* 2.9 32.5 + - - +
14C GLU* 3.0 14.5 + - - -
16C PHE* 1.3 76.4 - - - +
18C LEU* 1.3 55.2 + - - +
19C PHE 3.4 0.4 - - - -
20C ASP* 3.1 24.5 + - - +
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Residues in contact with LEU 18 (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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809A TYR* 6.2 0.7 - - + -
810A ALA* 4.6 14.4 - - + -
813A LEU* 4.4 32.8 - - + +
814A ARG* 3.8 37.7 - - + +
817A ARG* 5.3 11.9 - - + -
14C GLU* 3.0 13.2 + - - +
15C ALA* 3.5 11.7 - - - +
17C SER* 1.3 74.9 - - - +
19C PHE* 1.3 76.5 + - + +
20C ASP 3.6 4.3 - - - -
21C LYS* 3.1 19.0 + - - +
38C SER* 5.7 0.2 - - - +
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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