Contacts of the helix formed by residues 23 - 39 (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 LEU 23 (chain T).
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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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Residues in contact with ALA 24 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139P ALA* 3.7 31.5 - - + +
142P VAL* 4.1 15.9 - - + -
19T LEU 2.9 13.9 + - - +
20T THR* 3.4 16.2 - - + +
23T LEU* 1.3 73.6 - - - +
25T LEU* 1.3 63.7 + - + +
27T SER* 3.1 6.6 + - - -
28T VAL* 3.1 24.1 + - - +
102T CDL 4.3 10.3 - - - +
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Residues in contact with LEU 25 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139P ALA* 4.8 3.6 - - + -
165P ILE* 4.7 5.6 - - + -
169P LEU* 4.5 30.3 - - + -
306P PEK 3.8 51.0 - - + +
20T THR* 2.8 29.5 + - + +
21T PHE* 3.6 34.8 - - + -
24T ALA* 1.3 74.3 - - + +
26T PRO* 1.4 66.2 - - + +
28T VAL* 3.1 8.7 + - + +
29T ALA* 2.9 22.2 + - - +
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Residues in contact with PRO 26 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B CHD 4.4 7.2 - - + -
306P PEK 4.2 47.6 - - + +
21T PHE 3.2 28.9 - - - +
22T GLY* 3.8 13.9 - - - +
23T LEU 3.4 15.5 - - - +
25T LEU* 1.4 89.6 - - + +
27T SER* 1.3 56.5 + - - +
29T ALA* 3.1 10.1 + - + +
30T LEU* 2.9 34.8 + - - +
102T CDL 5.3 0.7 - - + -
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Residues in contact with SER 27 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135P SER* 4.4 6.5 - - - -
23T LEU 3.0 15.9 + - - -
24T ALA 3.1 9.8 + - - -
26T PRO* 1.3 76.3 - - - +
28T VAL* 1.3 62.0 + - - +
30T LEU* 3.4 6.4 + - - +
31T CYS* 3.1 29.6 + - - -
102T CDL 3.2 64.4 - - - +
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Residues in contact with VAL 28 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132P LEU* 3.8 2.3 - - + +
135P SER* 3.5 35.0 - - - +
136P VAL* 4.0 22.2 - - + +
139P ALA* 3.6 12.6 - - + -
169P LEU* 4.6 11.2 - - + -
172P TYR* 4.2 9.2 - - + -
306P PEK 4.8 7.6 - - + -
24T ALA 3.1 14.1 + - - +
25T LEU* 3.1 12.9 + - + +
27T SER* 1.3 77.1 - - - +
29T ALA* 1.3 52.9 - - - +
31T CYS 3.5 0.5 + - - -
32T THR* 2.5 46.1 + - - +
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Residues in contact with ALA 29 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306P PEK 4.8 16.2 - - + -
25T LEU 2.9 12.1 + - - +
26T PRO* 3.4 12.1 - - + +
28T VAL* 1.3 77.7 - - - +
30T LEU* 1.3 57.4 + - + +
32T THR* 3.3 7.1 + - - -
33T LEU* 2.9 28.1 + - - +
102T CDL 5.8 6.3 - - + -
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Residues in contact with LEU 30 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A ILE* 4.3 18.8 - - + -
306P PEK 4.6 12.1 - - + -
26T PRO 2.9 19.6 + - - +
27T SER* 3.7 5.2 - - - +
28T VAL 3.4 0.2 - - - -
29T ALA* 1.3 74.2 - - - +
31T CYS* 1.3 60.3 + - - +
33T LEU* 3.2 13.5 + - + +
34T ASN* 2.9 29.3 + - - +
102T CDL 3.5 102.8 - - + +
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Residues in contact with CYS 31 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131P LEU* 4.2 14.8 - - + -
132P LEU* 3.7 27.3 - - + +
135P SER* 3.8 12.6 - - - +
27T SER 3.1 14.3 + - - +
30T LEU* 1.3 77.3 - - - +
32T THR* 1.3 57.8 + - - +
34T ASN* 4.0 6.4 - - - +
35T SER* 3.0 33.8 + - - -
102T CDL 2.9 51.6 - - - -
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Residues in contact with THR 32 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132P LEU* 3.4 13.2 - - - +
172P TYR* 3.4 25.9 + - - +
306P PEK 4.2 14.4 - - + +
28T VAL* 2.5 27.5 + - - +
29T ALA* 3.5 9.1 - - - -
31T CYS* 1.3 75.3 - - - +
33T LEU* 1.3 64.9 + - - +
36T TRP* 3.1 40.3 + - + +
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Residues in contact with LEU 33 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ILE* 4.8 16.6 - - + -
29T ALA 2.9 13.4 + - - +
30T LEU* 3.3 22.7 - - + +
32T THR* 1.3 77.8 - - - +
34T ASN* 1.3 80.3 + - + +
36T TRP* 3.3 8.4 + - - +
37T LEU* 3.3 30.2 - - + +
102T CDL 3.8 54.1 - - + -
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Residues in contact with ASN 34 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127P LEU 3.4 16.3 - - - +
128P GLU* 4.9 0.9 - - - -
30T LEU 2.9 16.5 + - - +
31T CYS* 4.0 3.8 - - - +
33T LEU* 1.3 83.1 - - + +
35T SER* 1.3 64.2 + - - +
37T LEU* 3.0 21.1 - - - +
38T HIS* 3.1 26.5 + - - -
102T CDL 3.0 76.3 + - + +
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Residues in contact with SER 35 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127P LEU 4.9 0.2 + - - -
128P GLU* 3.2 36.2 + - - +
129P VAL* 3.7 8.6 + - - +
132P LEU* 3.8 17.9 - - - +
31T CYS* 3.0 21.0 + - - +
32T THR 4.2 1.6 - - - -
34T ASN* 1.3 74.8 + - - +
36T TRP* 1.3 67.9 + - - +
37T LEU 2.9 10.9 + - - -
38T HIS* 3.4 4.1 + - - +
39T SER* 3.3 24.4 + - - -
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Residues in contact with TRP 36 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129P VAL* 4.3 22.4 - - + -
132P LEU* 4.8 4.8 - - + +
172P TYR* 4.1 14.5 + + - -
176P LEU* 4.1 22.2 - - + +
179P SER* 4.8 13.9 - - - -
306P PEK 5.1 8.6 - - + +
32T THR* 3.1 35.1 + - + +
33T LEU* 3.4 5.6 - - - +
35T SER* 1.3 83.6 - - - +
37T LEU* 1.3 63.5 + - - +
39T SER* 3.9 24.9 - - - -
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Residues in contact with LEU 37 (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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78B LEU* 6.4 0.7 - - + -
33T LEU* 3.3 23.3 - - + +
34T ASN* 3.0 18.4 - - - +
35T SER 2.9 1.0 + - - -
36T TRP* 1.3 79.6 - - - +
38T HIS* 1.3 74.0 + - + +
39T SER* 3.2 8.6 + - - +
102T CDL 3.5 52.0 - - + -
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Residues in contact with HIS 38 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125P ASN* 5.9 0.4 - - - -
128P GLU* 3.6 40.1 - - + +
34T ASN* 3.1 22.0 + - - +
35T SER 3.4 2.4 + - - +
37T LEU* 1.3 93.0 + - + +
39T SER* 1.3 67.6 + - - +
42T ARG* 5.1 6.2 + - - -
102T CDL 3.0 103.7 + - + +
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Residues in contact with SER 39 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128P GLU* 5.2 3.6 - - - -
35T SER 3.3 16.4 + - - -
36T TRP* 3.9 25.7 - - - -
37T LEU 3.2 10.2 + - - -
38T HIS* 1.3 87.5 - - - +
40T GLY* 1.3 74.8 + - - +
42T ARG* 5.3 2.8 + - - +
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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