Contacts of the helix formed by residues 6 - 19 (chain I) in PDB entry 2DSP
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 CYS 6 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4I THR* 4.9 3.8 - - - -
5I LEU* 1.3 75.0 - - - +
7I GLY* 1.3 69.3 + - - +
8I ALA 3.4 0.3 + - - -
9I GLU* 3.3 12.4 + - - +
10I LEU* 3.2 12.3 + - - -
48I CYS* 2.1 58.6 - - - -
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Residues in contact with GLY 7 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6I CYS* 1.3 74.0 - - - +
8I ALA* 1.3 58.1 + - - -
10I LEU* 3.0 8.5 + - - +
11I VAL* 3.0 32.4 + - - +
44I VAL* 6.2 1.8 - - - +
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Residues in contact with ALA 8 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6I CYS 3.4 0.4 + - - -
7I GLY* 1.3 67.8 - - - -
9I GLU* 1.3 61.1 + - - +
11I VAL* 3.9 7.3 - - - +
12I ASP* 2.9 43.8 + - - +
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Residues in contact with GLU 9 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B TYR* 4.5 4.3 - - + +
70B HIS* 4.2 18.7 + - - -
73B MET* 3.8 36.6 - - + +
74B HIS* 5.0 5.4 + - - -
5I LEU* 4.2 20.7 - - + +
6I CYS 3.3 9.7 + - - +
7I GLY 3.3 0.8 - - - -
8I ALA* 1.3 77.9 - - + +
10I LEU* 1.3 58.2 + - - +
12I ASP* 3.4 2.8 + - - +
13I ALA* 2.9 31.2 + - - +
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Residues in contact with LEU 10 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5I LEU* 3.6 33.5 - - + +
6I CYS* 3.2 10.0 + - - -
7I GLY 3.0 11.3 + - - +
9I GLU* 1.3 78.0 - - - +
11I VAL* 1.3 58.7 + - + +
13I ALA* 3.2 4.5 + - - +
14I LEU* 2.8 36.8 + - + +
25I PHE* 5.2 4.3 - - + -
43I ILE* 3.9 16.8 - - + +
44I VAL* 3.8 38.8 - - + -
47I CYS* 3.8 22.7 - - + -
57I LEU* 3.9 20.2 - - + -
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Residues in contact with VAL 11 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ILE* 6.2 0.4 - - + -
7I GLY 3.0 18.4 + - - +
8I ALA* 3.9 6.7 - - - +
10I LEU* 1.3 76.1 - - + +
12I ASP* 1.3 63.5 - - - +
14I LEU* 2.9 10.5 + - + +
15I GLN* 2.9 55.5 + - + +
23I PHE* 4.2 8.1 - - + -
25I PHE* 3.8 32.5 - - + -
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Residues in contact with ASP 12 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B VAL* 3.8 14.1 - - + +
49B TYR* 2.6 38.3 + - - +
73B MET* 4.5 0.2 - - + -
8I ALA* 2.9 34.3 + - - +
9I GLU 3.8 3.1 - - - +
11I VAL* 1.3 78.5 - - - +
13I ALA* 1.3 62.5 + - - +
15I GLN* 4.1 12.7 - - - +
16I PHE* 3.2 24.9 + - - +
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Residues in contact with ALA 13 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B VAL* 4.5 7.6 - - + +
69B LEU* 5.6 1.1 - - + -
73B MET* 4.1 10.7 - - - -
5I LEU* 3.7 24.2 - - + -
9I GLU 2.9 17.7 + - - +
10I LEU 3.5 4.3 - - - +
12I ASP* 1.3 75.2 - - - +
14I LEU* 1.3 58.2 + - - +
16I PHE* 3.4 4.3 + - - +
17I VAL* 3.0 37.4 + - + +
57I LEU* 4.0 13.5 - - + -
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Residues in contact with LEU 14 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10I LEU* 2.8 37.4 + - + +
11I VAL* 2.9 9.0 + - - +
13I ALA* 1.3 77.6 - - - +
15I GLN* 1.3 55.5 + - - +
17I VAL* 4.9 1.3 - - - -
18I CYS* 2.9 38.5 + - - +
23I PHE* 3.6 50.9 - - + -
25I PHE* 5.1 1.3 - - + -
43I ILE* 4.0 16.6 - - + -
57I LEU* 3.9 41.3 - - + +
60I TYR* 4.2 10.8 - - + -
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Residues in contact with GLN 15 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ILE* 4.3 13.1 + - - +
5B HIS* 4.8 9.3 - - - +
6B CYS* 4.8 3.9 - - - +
31B GLY* 5.6 10.1 - - - -
32B CYS* 4.0 26.8 + - - -
52B ARG* 5.7 1.7 + - - -
11I VAL* 2.9 37.7 + - - +
12I ASP* 4.2 10.7 - - - +
14I LEU* 1.3 71.4 - - - +
16I PHE* 1.3 56.8 + - - +
18I CYS* 4.9 1.3 - - - -
19I GLY* 2.8 34.4 + - - +
22I GLY* 6.0 0.4 - - - -
23I PHE* 3.7 26.1 - - + -
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Residues in contact with PHE 16 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B GLY 3.6 22.4 - - - -
48B VAL* 3.6 37.5 - - + +
52B ARG* 5.4 21.6 + - + +
59B CYS* 3.6 32.5 - - + -
72B LEU* 4.2 24.7 - - + -
12I ASP 3.2 19.2 + - - +
13I ALA* 3.7 2.9 - - - +
14I LEU 3.2 0.8 - - - -
15I GLN* 1.3 77.0 - - - +
17I VAL* 1.3 74.9 + - + +
19I GLY* 4.0 4.7 + - - -
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Residues in contact with VAL 17 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ARG* 4.0 18.8 + - - +
69B LEU* 5.8 0.2 - - + -
72B LEU* 5.4 1.1 - - + -
13I ALA* 3.0 18.6 + - - +
14I LEU* 4.2 1.6 - - - +
16I PHE* 1.3 89.6 - - + +
18I CYS* 1.3 60.9 + - - +
19I GLY 3.8 0.3 + - - -
21I ARG* 4.1 8.8 + - - -
54I LEU* 3.7 25.1 - - + -
57I LEU* 4.0 15.7 - - + -
58I GLU* 3.8 39.9 - - + +
61I CYS* 4.4 2.2 - - - -
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Residues in contact with CYS 18 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14I LEU* 2.9 23.7 + - - +
15I GLN* 4.6 0.9 - - - +
17I VAL* 1.3 78.1 - - - +
19I GLY* 1.3 64.4 + - - +
21I ARG* 3.3 28.4 + - - +
22I GLY* 3.3 21.5 - - - +
23I PHE* 3.8 11.2 - - - -
57I LEU 4.2 7.0 - - - -
61I CYS* 2.1 58.3 - - + -
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Residues in contact with GLY 19 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ARG* 6.2 0.2 - - - -
52B ARG* 5.8 6.3 - - - -
15I GLN* 2.8 22.9 + - - +
16I PHE 4.0 4.4 + - - -
17I VAL 3.5 2.4 - - - -
18I CYS* 1.3 77.1 - - - +
20I ASP* 1.3 66.5 + - - -
21I ARG 2.9 2.4 + - - -
22I GLY* 3.0 14.7 + - - -
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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
------------------------------------------------------------
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