Contacts of the helix formed by residues 53 - 67 (chain B) in PDB entry 2DPD
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 ASN 53 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A THR* 4.2 8.2 - - + +
38B LEU* 3.7 9.7 - - - +
42B ARG* 3.6 11.0 - - - +
51B LYS 3.9 0.6 + - - -
52B PRO* 1.3 75.3 - - - +
54B HIS* 1.3 65.1 + - - +
55B THR* 2.8 18.2 + - + +
56B GLU* 2.7 34.8 + - - +
57B VAL* 3.5 14.0 + - - +
14E G 2.9 54.2 + - + +
15E T 4.2 7.6 - - + +
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Residues in contact with HIS 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B LEU* 4.5 14.8 - - + -
38B LEU* 3.7 25.5 - - + +
42B ARG* 4.3 3.4 + - - +
53B ASN* 1.3 78.1 - - - +
55B THR* 1.3 86.4 + - + +
57B VAL* 3.1 8.0 + - - +
58B TYR* 2.9 45.7 + + + -
4D T 4.3 11.9 + - + +
5D G 3.3 29.6 + - - -
15E T 5.2 0.4 - - + -
16E T 4.0 24.4 + - + -
17E C 4.8 2.9 + - - -
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Residues in contact with THR 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B ASN* 2.9 15.7 - - - +
54B HIS* 1.3 92.3 - - + +
56B GLU* 1.3 63.7 + - - +
58B TYR* 3.8 8.0 - - - +
59B ARG* 3.1 45.2 + - - +
5D G 6.0 0.4 - - - -
6D A 4.5 8.3 - - - -
7D A 4.4 2.3 + - - -
14E G 3.9 1.5 + - - +
15E T 3.0 44.4 + - + +
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Residues in contact with GLU 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B GLN* 3.6 24.9 - - + +
16B ARG* 4.1 13.5 + - - +
19B LEU* 3.8 12.6 - - + -
52B PRO* 5.6 0.2 - - + -
53B ASN* 2.7 26.0 + - - +
55B THR* 1.3 71.9 + - - +
57B VAL* 1.3 66.2 + - - +
59B ARG* 3.0 38.0 + - - +
60B SER* 3.0 24.3 + - - +
12E A 5.3 0.3 - - - +
13E T 3.4 35.3 + - - +
14E G 3.9 17.5 - - - +
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Residues in contact with VAL 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LEU* 4.0 18.6 - - + +
23B MET* 3.4 7.1 - - + +
34B GLY* 3.8 29.4 - - - +
37B LEU* 3.8 31.2 - - + -
38B LEU* 4.1 21.8 - - + -
41B LEU* 4.8 4.9 - - + -
52B PRO* 5.2 1.1 - - + -
53B ASN 3.5 12.4 + - - +
54B HIS* 3.1 11.6 + - - +
56B GLU* 1.3 78.8 - - - +
58B TYR* 1.3 57.9 + - + +
60B SER* 3.4 0.6 + - - -
61B LEU* 2.9 28.9 + - + +
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Residues in contact with TYR 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B GLY* 3.7 25.4 - - - -
35B LEU* 3.1 24.8 - - + +
54B HIS* 2.9 34.8 + + - +
55B THR* 4.1 6.5 - - - +
56B GLU 3.2 0.2 - - - -
57B VAL* 1.3 77.8 - - + +
59B ARG* 1.3 57.1 + - - +
61B LEU* 3.6 8.5 + - + +
62B HIS* 2.9 46.3 + + + -
88B TYR* 4.6 3.1 - - - -
3D A 3.4 3.6 - - - +
4D T 2.4 70.7 + + + +
5D G 3.8 32.8 - + + -
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Residues in contact with ARG 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ARG* 6.0 1.3 - - + -
55B THR* 3.1 22.4 + - - +
56B GLU* 3.0 33.8 + - - +
58B TYR* 1.3 72.7 - - - +
60B SER* 1.3 66.9 + - - +
62B HIS* 2.9 18.6 + - - +
63B GLU* 3.0 26.0 + - + +
7D A 5.1 2.2 - - - +
8D C 4.7 4.8 - - - +
13E T 3.3 45.6 + - - +
14E G 2.8 50.3 + - - -
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Residues in contact with SER 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ARG* 3.8 13.7 - - - +
19B LEU* 3.4 21.4 - - - +
20B LYS* 3.7 27.8 - - - +
23B MET* 3.3 22.7 - - - -
56B GLU 3.0 12.5 + - - -
57B VAL 3.6 1.3 - - - -
59B ARG* 1.3 77.3 - - - +
61B LEU* 1.3 66.5 + - - +
63B GLU* 3.3 9.8 + - - +
64B LEU* 3.2 16.1 + - - +
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Residues in contact with LEU 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B MET* 2.4 60.8 - - + -
33B TYR 4.7 1.1 - - - -
34B GLY* 3.9 24.9 - - - +
37B LEU* 5.4 1.3 - - + -
57B VAL* 2.9 19.0 + - + +
58B TYR* 3.8 9.0 - - + +
59B ARG 3.1 0.2 - - - -
60B SER* 1.3 75.8 - - - +
62B HIS* 1.3 64.0 + - - +
64B LEU* 3.2 10.9 + - + +
65B LEU* 3.0 24.0 + - - +
70B LEU* 5.5 2.9 - - + -
88B TYR* 3.0 54.7 - - + +
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Residues in contact with HIS 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B TYR* 2.9 29.8 + + + +
59B ARG* 2.9 12.1 + - - +
61B LEU* 1.3 73.9 - - - +
63B GLU* 1.3 57.8 + - - +
65B LEU* 3.1 22.3 - - + +
66B ASP* 2.9 38.4 + - - +
72B GLN* 4.5 2.5 - - - -
88B TYR* 3.8 14.6 + - - -
5D G 2.9 52.4 + - + -
6D A 4.9 5.2 + - - -
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Residues in contact with GLU 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ARG* 3.3 30.8 + - - +
20B LYS* 2.8 37.7 + - - +
59B ARG* 3.0 23.7 + - + +
60B SER* 3.5 6.9 - - - +
62B HIS* 1.3 72.4 - - - +
64B LEU* 1.3 51.8 + - - +
65B LEU 2.8 3.8 + - - -
66B ASP* 2.6 30.7 + - - +
67B ASP* 2.6 27.4 + - - +
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Residues in contact with LEU 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B LYS* 3.6 37.7 - - + +
23B MET* 4.0 24.2 - - + -
24B ILE* 3.7 26.5 - - + -
60B SER 3.2 4.9 + - - +
61B LEU* 3.2 11.1 + - + +
63B GLU* 1.3 76.9 - - - +
65B LEU* 1.3 58.3 + - - +
67B ASP* 4.0 7.6 + - - +
69B ILE* 3.0 52.8 + - + -
70B LEU* 3.0 34.2 + - + -
99B TYR* 4.4 4.3 - - + -
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Residues in contact with LEU 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B LEU 3.0 14.6 + - - +
62B HIS* 3.1 21.1 - - + +
63B GLU 2.8 1.2 + - - -
64B LEU* 1.3 76.3 - - - +
66B ASP* 1.3 61.0 + - - +
68B GLY* 2.6 27.7 + - - -
70B LEU* 3.1 31.2 - - + +
71B LYS* 3.7 12.6 - - - +
72B GLN* 3.6 33.0 - - + +
88B TYR* 3.9 17.9 - - + -
91B LYS* 5.3 0.9 - - - +
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Residues in contact with ASP 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B HIS* 2.9 25.2 + - - +
63B GLU* 2.6 14.7 + - - +
65B LEU* 1.3 77.6 - - - +
67B ASP* 1.3 62.3 + - - +
68B GLY* 3.3 1.0 + - - -
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Residues in contact with ASP 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B LYS* 3.9 18.0 + - - +
63B GLU* 2.6 30.1 + - - +
64B LEU* 4.2 2.6 + - - +
66B ASP* 1.3 76.4 - - - +
68B GLY* 1.3 61.6 + - - +
69B ILE* 3.2 27.9 + - + +
95B ALA* 5.3 2.8 - - - +
99B TYR* 5.9 1.4 - - - -
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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