Contacts of the helix formed by residues 12 - 23 (chain T) 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 T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149P HIS* 3.8 11.2 - - - -
153P GLU* 3.6 9.4 - - - -
10T GLY 3.2 7.6 + - - -
11T TPO 1.4 73.9 - - - -
13T ALA* 1.3 65.7 + - - -
14T ARG 3.2 3.1 - - - -
15T THR* 3.1 15.9 + - - -
16T TRP* 3.2 16.0 + - - -
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Residues in contact with ALA 13 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146P TRP* 3.3 14.7 - - + +
149P HIS* 3.6 20.3 - - + +
150P SER* 3.8 24.2 - - - +
153P GLU* 2.8 32.4 + - - +
155P ASP* 6.3 0.2 - - + -
1S ALA 6.0 0.2 - - - -
12T GLY* 1.3 72.9 - - - -
14T ARG* 1.3 61.1 + - - +
16T TRP* 3.5 1.6 + - - +
17T ARG* 3.2 18.0 + - - +
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Residues in contact with ARG 14 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A SER* 4.9 1.6 + - - -
179A TYR* 3.6 41.7 + - + +
180A GLN* 4.8 4.2 + - - -
271A MET* 4.0 22.7 - - + +
304B CHD 3.1 40.1 + - - +
65F ASP* 3.7 47.2 + - - +
67F SER* 5.9 2.4 - - - -
153P GLU* 4.9 1.2 + - - -
1S ALA* 4.2 23.3 + - + +
12T GLY 3.2 0.8 - - - -
13T ALA* 1.3 78.9 - - - +
15T THR* 1.3 57.3 + - - +
17T ARG* 3.3 10.3 + - - +
18T PHE* 2.9 29.4 + - + +
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Residues in contact with THR 15 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A TYR* 2.8 33.5 + - - +
7T ASP* 3.5 23.5 + - + +
10T GLY 4.0 7.6 + - - -
11T TPO 4.0 18.2 - - - +
12T GLY 3.1 16.0 + - - -
14T ARG* 1.3 78.7 - - - +
16T TRP* 1.3 59.9 + - + +
18T PHE* 3.2 5.4 - - + +
19T LEU* 3.0 41.5 + - + +
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Residues in contact with TRP 16 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142P VAL* 3.8 24.9 - - + +
145P THR* 3.5 31.6 - - + -
146P TRP* 3.6 24.9 - - + +
149P HIS* 3.7 19.8 + + - -
11T TPO 3.5 46.8 + - + +
12T GLY 3.2 28.1 + - - +
13T ALA 3.5 1.1 + - - +
14T ARG 3.4 0.2 - - - -
15T THR* 1.3 74.1 - - + +
17T ARG* 1.3 54.7 + - - +
19T LEU* 3.4 30.0 + - + +
20T THR* 2.7 34.8 + - - -
102T CDL 4.4 17.9 - - + -
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Residues in contact with ARG 17 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304B CHD 3.6 21.0 + - - -
146P TRP* 3.3 48.1 - - + +
158P HIS* 3.5 23.2 + - - -
161P GLN* 4.5 0.2 + - - -
306P PEK 3.1 67.1 + - - +
1S ALA* 3.4 20.3 + - - +
13T ALA 3.2 17.3 + - - +
14T ARG* 3.5 9.8 - - - +
16T TRP* 1.3 74.2 - - - +
18T PHE* 1.3 67.6 + - - +
20T THR* 3.1 3.0 + - - -
21T PHE* 3.0 38.2 + - + -
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Residues in contact with PHE 18 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A TYR* 3.9 28.3 - + - -
271A MET* 4.0 24.0 - - + -
274A VAL* 4.1 5.2 - - + -
275A TRP* 3.6 44.0 - + + -
278A MET* 4.0 23.8 - - + -
304B CHD 3.6 44.0 - - + -
14T ARG 2.9 14.2 + - - +
15T THR* 3.2 11.4 - - + +
17T ARG* 1.3 77.2 - - - +
19T LEU* 1.3 52.9 + - + +
22T GLY* 2.7 32.4 + - - -
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Residues in contact with LEU 19 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278A MET* 5.9 4.5 - - + -
142P VAL* 3.6 15.5 - - + -
5T LYS* 4.9 6.5 - - + +
11T TPO 4.8 4.3 - - - +
15T THR* 3.0 27.9 + - + +
16T TRP* 3.7 37.9 - - + +
17T ARG 3.2 0.2 - - - -
18T PHE* 1.3 76.4 - - + +
20T THR* 1.3 59.0 + - - +
22T GLY 5.1 0.2 - - - -
23T LEU* 3.0 35.2 + - + +
24T ALA* 2.9 26.7 + - - +
101T PEK 4.2 22.2 - - + -
102T CDL 4.2 13.9 - - + -
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Residues in contact with THR 20 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139P ALA 5.4 0.2 - - - +
142P VAL* 3.8 4.1 + - - +
143P SER* 3.7 35.3 - - - +
146P TRP* 3.6 27.5 - - + -
165P ILE* 4.6 3.4 - - + -
16T TRP 2.7 20.0 + - - -
17T ARG 3.1 7.6 + - - -
19T LEU* 1.3 77.9 - - - +
21T PHE* 1.3 60.3 + - + +
24T ALA* 3.9 9.9 - - + -
25T LEU* 2.8 55.9 + - + +
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Residues in contact with PHE 21 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304B CHD 3.8 35.9 - - + +
146P TRP* 3.7 34.3 - + - -
161P GLN* 4.5 1.6 - - - -
165P ILE* 4.1 11.7 - - + -
306P PEK 3.6 74.4 - - + +
17T ARG* 3.0 33.2 + - + +
20T THR* 1.3 78.9 - - + +
22T GLY* 1.3 59.8 + - - +
25T LEU* 3.6 27.8 - - + -
26T PRO* 3.2 20.3 - - - +
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Residues in contact with GLY 22 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A TRP* 3.1 29.0 + - - -
304B CHD 3.6 16.5 - - - +
306P PEK 3.8 15.6 - - - +
5T LYS* 4.4 2.2 + - - -
18T PHE* 2.7 21.6 + - - -
19T LEU* 5.1 0.2 - - - -
21T PHE* 1.3 75.0 - - - +
23T LEU* 1.3 58.5 + - - +
26T PRO* 3.8 7.1 - - - +
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Residues in contact with LEU 23 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282A PHE* 4.7 4.3 - - + -
142P VAL* 5.9 0.9 - - + -
306P PEK 4.3 6.3 - - + -
5T LYS* 4.3 14.1 - - - +
19T LEU* 3.0 32.1 + - + +
21T PHE 3.6 0.4 - - - -
22T GLY* 1.3 79.5 - - - +
24T ALA* 1.3 68.7 + - + +
26T PRO* 3.4 5.0 - - - +
27T SER* 3.0 28.1 + - - -
101T PEK 4.4 14.1 - - + -
102T CDL 3.8 81.7 - - + +
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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
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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