Contacts of the helix formed by residues 12 - 23 (chain G) 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 GLY 12 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149C HIS* 3.9 11.4 - - - -
153C GLU* 3.7 9.2 - - - -
10G GLY 3.3 8.2 + - - -
11G TPO 1.4 73.0 - - - -
13G ALA* 1.3 65.7 + - - -
14G ARG* 3.2 3.1 - - - -
15G THR* 3.1 15.7 + - - -
16G TRP* 3.2 15.1 + - - -
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Residues in contact with ALA 13 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146C TRP* 3.4 13.2 - - + +
149C HIS* 3.5 21.5 - - + +
150C SER* 3.7 24.9 - - - +
153C GLU* 2.8 33.0 + - - +
155C ASP* 6.2 0.7 - - + -
1F ALA 6.0 0.2 - - - -
12G GLY* 1.3 70.2 - - - -
14G ARG* 1.3 62.6 + - - +
16G TRP* 3.5 2.0 + - - +
17G ARG* 3.2 18.5 + - - +
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Residues in contact with ARG 14 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C GLU* 4.9 1.2 + - - -
1F ALA* 4.1 25.3 + - + +
12G GLY 3.2 1.0 - - - -
13G ALA* 1.3 78.3 - - - +
15G THR* 1.3 58.4 + - - +
17G ARG* 3.4 8.9 + - - +
18G PHE* 3.0 28.7 + - + +
177N SER* 5.1 1.0 + - - -
179N TYR* 3.7 38.6 + - + +
180N GLN* 4.7 5.1 + - - -
271N MET* 3.9 23.3 - - + +
302O CHD 2.9 42.2 + - - +
65S ASP* 3.8 45.8 + - - +
67S SER* 6.0 2.0 - - - -
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Residues in contact with THR 15 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7G ASP* 3.6 19.2 + - + +
10G GLY 4.0 2.8 + - - -
11G TPO 3.6 26.9 - - - +
12G GLY* 3.1 20.5 + - - -
14G ARG* 1.3 79.4 - - - +
16G TRP* 1.3 58.4 + - + +
18G PHE* 3.1 6.0 - - + +
19G LEU* 2.9 36.6 + - + +
179N TYR* 2.8 34.4 + - - +
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Residues in contact with TRP 16 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C VAL* 3.8 32.7 - - + +
145C THR* 3.3 35.4 - - + -
146C TRP* 3.5 24.8 - - + +
149C HIS* 3.7 19.5 + + - -
11G TPO 3.5 47.0 + - + +
12G GLY 3.2 23.4 + - - +
13G ALA* 3.5 2.0 + - - +
14G ARG 3.4 0.2 - - - -
15G THR* 1.3 73.7 - - - +
17G ARG* 1.3 59.8 - - - +
19G LEU* 3.5 21.4 + - + +
20G THR* 2.8 29.6 + - - -
101G CDL 4.3 23.8 - - + -
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Residues in contact with ARG 17 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C TRP* 3.2 47.8 - - + +
158C HIS* 3.4 27.3 + - - -
161C GLN* 4.9 0.4 + - - -
306C PEK 3.1 50.5 + - - +
1F ALA* 3.8 14.0 + - - +
13G ALA 3.2 17.9 + - - +
14G ARG* 3.7 9.1 - - - +
15G THR 3.2 0.4 - - - -
16G TRP* 1.3 75.3 - - - +
18G PHE* 1.3 66.0 + - - +
19G LEU 3.2 0.2 - - - -
20G THR* 3.1 2.0 + - - -
21G PHE* 3.0 43.3 + - + +
302O CHD 3.2 35.7 + - - +
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Residues in contact with PHE 18 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14G ARG 3.0 15.0 + - - +
15G THR* 3.1 12.8 - - + +
17G ARG* 1.3 78.4 - - - +
19G LEU* 1.3 54.3 + - + +
22G GLY* 2.7 32.1 + - - -
179N TYR* 3.7 24.7 - + - -
271N MET* 3.8 27.8 - - + -
274N VAL* 4.0 17.7 - - + -
275N TRP* 3.7 52.3 - + + -
278N MET* 4.1 14.4 - - + -
302O CHD 3.9 31.6 - - + +
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Residues in contact with LEU 19 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C VAL* 3.7 15.9 - - + -
5G LYS* 4.9 7.2 - - + +
11G TPO 4.6 5.4 - - - +
15G THR* 2.9 31.3 + - + +
16G TRP* 3.7 35.2 - - + +
17G ARG 3.2 0.2 - - - -
18G PHE* 1.3 77.8 - - + +
20G THR* 1.3 58.8 + - - +
23G LEU* 3.0 26.4 + - + +
24G ALA* 2.9 26.9 + - - +
101G CDL 4.4 13.0 - - + -
102G PEK 4.2 27.4 - - + -
278N MET* 6.0 4.0 - - + -
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Residues in contact with THR 20 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C ALA 5.2 0.2 - - - +
142C VAL* 3.6 8.6 + - - +
143C SER* 3.5 39.6 - - - +
146C TRP* 3.6 23.5 - - + +
165C ILE* 4.6 3.8 - - + -
169C LEU* 6.2 0.2 - - + -
16G TRP 2.8 21.7 + - - -
17G ARG 3.1 6.0 + - - -
19G LEU* 1.3 76.2 - - - +
21G PHE* 1.3 59.7 + - + +
24G ALA* 3.9 4.9 - - + -
25G LEU* 2.8 54.4 + - + +
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Residues in contact with PHE 21 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146C TRP* 3.5 27.4 - + - -
161C GLN* 4.4 2.5 - - - -
165C ILE* 3.6 21.8 - - + -
306C PEK 3.4 74.8 - - + +
17G ARG* 3.0 36.8 + - + +
20G THR* 1.3 76.9 - - + +
22G GLY* 1.3 58.8 + - - +
23G LEU 3.6 0.2 - - - -
25G LEU* 3.6 25.1 - - + -
26G PRO* 3.1 20.2 - - - +
302O CHD 3.7 33.3 - - + +
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Residues in contact with GLY 22 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306C PEK 3.8 15.4 - - - +
5G LYS* 4.3 2.7 + - - -
18G PHE* 2.7 23.3 + - - -
19G LEU* 5.1 0.2 - - - -
21G PHE* 1.3 74.1 - - - +
23G LEU* 1.3 58.4 + - - +
26G PRO* 3.8 6.5 - - - +
275N TRP* 3.0 36.0 + - - -
302O CHD 3.6 10.7 - - - +
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Residues in contact with LEU 23 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C VAL* 6.1 0.9 - - + -
306C PEK 4.3 4.5 - - + -
5G LYS* 4.2 12.3 - - - +
19G LEU* 3.0 22.8 + - + +
21G PHE 3.6 0.4 - - - -
22G GLY* 1.3 79.5 - - - +
24G ALA* 1.3 63.4 + - - +
26G PRO* 3.4 5.9 - - - +
27G SER* 2.8 32.4 + - - -
101G CDL 3.5 82.3 - - + +
102G PEK 4.1 28.5 - - + -
282N PHE* 5.0 3.6 - - + -
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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