Contacts of the helix formed by residues 14 - 27 (chain S) in PDB entry 2DYS
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 THR 14 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65P SER 4.7 0.2 - - - +
66P THR 4.1 2.9 - - - +
67P PHE 3.4 18.4 - - - +
69P GLY* 3.2 33.9 - - - +
12S GLN 3.3 0.4 + - - -
13S ALA* 1.3 75.3 - - - +
15S GLY* 1.3 76.3 + - - +
17S GLU* 3.3 7.3 + - - +
18S ARG* 2.9 18.1 + - - +
9W GLN* 3.4 25.0 - - - +
13W GLN* 2.8 19.6 + - - +
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Residues in contact with GLY 15 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68P GLN 3.4 17.3 - - - -
14S THR* 1.3 89.2 + - - +
16S LEU* 1.3 62.0 + - - -
18S ARG* 3.0 10.7 + - - +
19S GLU* 3.2 17.9 + - - +
13W GLN* 4.4 6.1 + - - +
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Residues in contact with LEU 16 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3P HIS* 5.7 1.8 - - - +
4P GLN* 3.5 30.5 - - + +
6P HIS 4.1 7.2 - - - +
7P ALA* 4.4 6.3 - - - +
8P TYR 4.9 1.3 - - - +
68P GLN 4.4 0.4 + - - -
69P GLY 3.4 10.2 + - - +
70P HIS* 5.0 13.2 + - - +
72P THR* 3.6 20.2 - - + -
15S GLY* 1.3 68.5 - - - -
17S GLU* 1.3 66.5 + - - +
19S GLU* 3.2 11.0 + - + +
20S VAL* 2.9 31.8 + - + +
31S TYR* 3.4 45.5 - - + +
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Residues in contact with GLU 17 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65P SER 4.5 2.3 - - - +
69P GLY* 2.8 26.6 + - - +
71P HIS* 3.5 18.8 - - - +
72P THR* 3.9 14.1 - - - +
73P PRO* 5.2 5.6 - - + +
231P HIS* 2.8 34.8 + - - +
307P PGV 4.3 9.3 + - - -
9S ASP* 4.0 15.6 - - - +
13S ALA* 4.1 19.4 - - + +
14S THR 3.5 4.8 + - - +
15S GLY 3.1 0.2 - - - -
16S LEU* 1.3 75.8 - - - +
18S ARG* 1.3 58.9 + - - +
20S VAL* 3.5 3.2 + - - +
21S MET* 3.1 28.4 + - + +
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Residues in contact with ARG 18 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9S ASP 3.4 10.9 + - - -
10S GLU* 3.0 46.8 + - - +
11S GLU 4.7 2.0 - - - -
13S ALA* 3.0 27.4 + - - +
14S THR* 2.9 19.1 + - - +
15S GLY 3.3 9.9 - - - +
17S GLU* 1.3 75.2 - - - +
19S GLU* 1.3 55.9 + - + +
21S MET* 3.0 19.8 + - + +
22S LEU* 2.7 63.9 + - + +
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Residues in contact with GLU 19 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3P HIS* 5.1 4.5 + - - -
15S GLY 3.2 11.3 + - - +
16S LEU* 3.2 18.2 + - + +
18S ARG* 1.3 77.6 - - + +
20S VAL* 1.3 54.8 + - - +
22S LEU* 3.2 9.6 + - + +
23S ALA* 2.8 38.9 + - + +
31S TYR* 2.9 38.5 + - + -
96S LEU* 5.6 0.7 - - - +
97S ALA* 5.8 3.6 - - - +
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Residues in contact with VAL 20 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7P ALA* 4.8 1.1 - - + -
72P THR* 4.0 16.6 - - + -
73P PRO* 4.2 21.8 - - + -
16S LEU* 2.9 23.5 + - + +
17S GLU 3.8 4.5 - - - +
19S GLU* 1.3 73.4 - - - +
21S MET* 1.3 57.8 + - - +
23S ALA* 3.8 5.4 - - - +
24S ALA* 2.8 36.7 + - + +
30S PRO* 5.8 0.2 - - - -
31S TYR* 3.9 24.7 - - + -
33S ILE* 3.4 32.8 - - + -
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Residues in contact with MET 21 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9S ASP* 3.9 30.3 - - - +
10S GLU* 4.5 4.7 - - - -
13S ALA* 3.7 25.1 - - + -
17S GLU* 3.1 15.1 + - + +
18S ARG* 3.0 35.4 + - + +
20S VAL* 1.3 79.8 - - - +
22S LEU* 1.3 66.8 + - + +
24S ALA* 3.5 6.0 + - - +
25S ARG* 3.1 37.4 + - - +
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Residues in contact with LEU 22 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10S GLU* 4.8 0.2 - - - +
18S ARG* 2.7 60.9 + - + +
19S GLU* 3.8 7.9 - - + +
21S MET* 1.3 73.2 - - + +
23S ALA* 1.3 66.9 + - - +
25S ARG* 2.9 57.4 + - - +
26S LYS* 3.2 21.2 + - - +
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Residues in contact with ALA 23 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19S GLU* 2.8 22.2 + - + +
20S VAL* 3.8 4.3 - - - +
22S LEU* 1.3 71.8 - - - +
24S ALA* 1.3 64.8 + - - +
26S LYS* 3.0 18.9 + - - +
28S GLN* 2.9 28.6 + - + +
30S PRO* 3.5 38.1 - - + -
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Residues in contact with ALA 24 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20S VAL* 2.8 24.6 + - + +
21S MET* 3.6 8.1 - - - +
23S ALA* 1.3 75.7 - - - +
25S ARG* 1.3 60.7 + - - +
27S GLY* 3.2 12.8 + - - -
28S GLN 3.8 10.0 + - - -
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Residues in contact with ARG 25 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10S GLU* 3.2 34.4 + - - +
21S MET* 3.1 33.9 + - - +
22S LEU* 2.9 47.5 + - - +
24S ALA* 1.3 77.9 - - - +
26S LYS* 1.3 61.1 + - + +
27S GLY* 3.4 0.9 + - - -
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Residues in contact with LYS 26 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22S LEU* 3.2 19.7 + - - +
23S ALA* 3.0 10.4 + - - +
25S ARG* 1.3 80.1 - - + +
27S GLY* 1.3 59.9 + - - +
28S GLN* 3.3 37.0 + - - +
98S HIS* 5.1 12.9 - - - -
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Residues in contact with GLY 27 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23S ALA 3.1 2.0 + - - -
24S ALA 3.2 9.5 + - - -
25S ARG 3.1 6.0 + - - -
26S LYS* 1.3 79.3 - - - +
28S GLN* 1.3 61.8 + - - +
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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