Contacts of the helix formed by residues 53 - 67 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A LEU* 3.7 7.7 - - - +
42A ARG* 3.7 10.3 - - - +
51A LYS 3.8 1.0 + - - +
52A PRO* 1.3 76.4 - - - +
54A HIS* 1.3 65.5 - - - +
55A THR* 3.0 18.4 - - + +
56A GLU* 2.8 27.3 + - - +
57A VAL* 3.5 13.5 + - - +
9B THR* 4.2 9.4 - - + +
14D G 2.9 42.0 + - - +
15D T 3.9 18.4 - - + +
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Residues in contact with HIS 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A LEU* 4.6 13.5 - - + -
38A LEU* 3.6 26.2 - - + +
42A ARG* 4.3 3.8 + - - +
53A ASN* 1.3 76.9 - - + +
55A THR* 1.3 85.6 + - + +
57A VAL* 3.0 9.3 + - - +
58A TYR* 2.9 45.7 + + + -
15D T 5.3 0.2 - - + -
16D T 3.8 24.0 + - + -
17D C 4.8 2.4 + - - -
4E T 4.4 10.6 + - + -
5E G 3.4 26.8 + - - -
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Residues in contact with THR 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A ASN* 3.0 7.2 - - - +
54A HIS* 1.3 92.0 - - + +
56A GLU* 1.3 59.1 + - - +
58A TYR* 3.4 8.3 + - - +
59A ARG* 3.0 50.1 + - - +
15D T 2.9 53.4 + - + +
5E G 6.0 0.4 - - - -
6E A 4.1 13.0 - - - -
7E A 4.5 1.2 + - - -
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Residues in contact with GLU 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A GLN* 3.6 24.2 - - - +
16A ARG* 3.9 15.1 + - - +
19A LEU* 3.7 13.0 - - + -
52A PRO* 5.6 0.2 - - + -
53A ASN* 2.8 23.0 + - - +
55A THR* 1.3 74.4 + - - +
57A VAL* 1.3 65.9 + - - +
59A ARG* 3.1 35.9 + - - +
60A SER* 2.9 26.3 + - - -
12D A 5.3 0.7 - - - +
13D T 3.5 39.0 + - - +
14D G 3.9 9.9 - - - +
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Residues in contact with VAL 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A LEU* 4.3 13.9 - - + -
23A MET* 3.5 7.1 - - + +
34A GLY* 3.8 28.9 - - - +
37A LEU* 3.6 33.4 - - + -
38A LEU* 4.1 20.6 - - + -
41A LEU* 4.7 6.1 - - + -
52A PRO* 5.1 1.8 - - + -
53A ASN 3.5 12.1 + - - +
54A HIS* 3.0 11.1 + - - +
56A GLU* 1.3 78.4 - - - +
58A TYR* 1.3 59.5 + - + +
59A ARG 3.3 0.2 + - - -
60A SER* 3.5 4.4 + - - -
61A LEU* 3.0 28.9 + - + +
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Residues in contact with TYR 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A GLY* 3.7 23.3 - - - -
35A LEU* 3.0 22.2 - - + +
54A HIS* 2.9 33.7 + + - +
55A THR* 3.9 7.0 - - - +
56A GLU 3.3 0.2 - - - -
57A VAL* 1.3 76.3 - - + +
59A ARG* 1.3 60.1 + - - +
61A LEU* 3.6 9.8 + - + +
62A HIS* 2.8 44.5 + + + -
88A TYR* 5.7 1.6 - + - -
3E A 3.6 6.2 - - - +
4E T 2.7 68.1 + + + -
5E G 3.7 32.1 - + + -
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Residues in contact with ARG 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ARG* 6.0 1.3 - - + -
55A THR* 3.0 26.0 + - - +
56A GLU* 3.1 31.4 + - - +
58A TYR* 1.3 73.5 - - - +
60A SER* 1.3 66.7 + - - +
62A HIS* 3.0 18.2 + - - +
63A GLU* 3.0 27.8 + - + +
13D T 3.4 37.8 + - - +
14D G 2.6 54.1 + - - -
7E A 4.7 3.4 - - - +
8E C 4.6 4.6 - - - +
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Residues in contact with SER 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ARG* 3.8 12.6 - - - +
19A LEU* 3.5 22.1 - - - +
20A LYS* 3.6 26.7 - - - +
23A MET* 3.3 24.2 - - - -
56A GLU* 2.9 13.5 + - - +
57A VAL 3.6 1.3 - - - -
59A ARG* 1.3 77.1 - - - +
61A LEU* 1.3 62.7 + - - +
63A GLU* 3.4 11.5 + - - +
64A LEU* 3.2 18.4 + - - +
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Residues in contact with LEU 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A MET* 2.8 52.0 - - + -
33A TYR 4.7 1.6 - - - -
34A GLY* 3.9 27.4 - - - +
37A LEU* 5.3 1.3 - - + -
57A VAL* 3.0 21.9 + - + +
58A TYR* 3.7 13.0 - - + +
60A SER* 1.3 75.5 - - - +
62A HIS* 1.3 64.9 + - + +
64A LEU* 3.2 12.9 + - + +
65A LEU* 3.1 22.9 + - - +
70A LEU* 5.3 3.1 - - + -
88A TYR* 3.7 45.7 - - + +
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Residues in contact with HIS 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A TYR* 2.8 31.0 + - + +
59A ARG* 3.0 7.0 + - - +
61A LEU* 1.3 74.2 - - + +
63A GLU* 1.3 61.0 + - - +
65A LEU* 3.1 19.9 - - + +
66A ASP* 2.9 36.9 + - - +
72A GLN* 4.6 0.4 - - - -
88A TYR* 3.9 15.6 + - - -
5E G 2.8 58.3 + - - -
6E A 5.0 6.2 + - - -
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Residues in contact with GLU 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ARG* 3.3 31.4 + - - +
20A LYS* 2.9 35.8 + - - +
59A ARG* 3.0 25.3 + - - +
60A SER* 3.5 6.6 - - - +
62A HIS* 1.3 71.2 - - + +
64A LEU* 1.3 52.6 + - - +
65A LEU 2.9 3.4 - - - -
66A ASP* 2.7 14.2 + - - +
67A ASP* 2.6 41.7 + - - +
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Residues in contact with LEU 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A LYS* 3.6 37.0 - - + +
23A MET* 4.0 24.7 - - + -
24A ILE* 3.7 26.5 - - + -
60A SER 3.2 5.1 + - - +
61A LEU* 3.2 11.5 + - + +
63A GLU* 1.3 76.7 - - - +
65A LEU* 1.3 57.4 + - - +
67A ASP* 4.0 6.9 + - - +
68A GLY 3.4 0.3 + - - -
69A ILE* 2.9 51.5 + - + -
70A LEU* 3.0 34.6 + - + -
99A TYR* 4.4 4.3 - - + -
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Residues in contact with LEU 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A LEU 3.1 15.0 + - - +
62A HIS* 3.1 22.0 - - + +
63A GLU 2.8 1.0 + - - -
64A LEU* 1.3 77.0 - - - +
66A ASP* 1.3 60.6 + - - +
68A GLY* 2.6 28.6 + - - -
70A LEU* 3.3 29.4 - - + +
71A LYS* 3.7 11.0 - - - -
72A GLN* 3.5 36.8 - - + +
88A TYR* 3.7 21.5 - - + +
91A LYS* 5.3 0.7 - - - +
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Residues in contact with ASP 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A HIS* 2.9 24.6 + - - +
63A GLU* 2.7 14.8 + - - +
65A LEU* 1.3 76.7 - - - +
67A ASP* 1.3 62.9 + - - +
68A GLY* 3.3 1.0 + - - -
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Residues in contact with ASP 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LYS* 4.0 19.8 + - - +
63A GLU* 2.6 28.2 + - - +
64A LEU* 4.3 3.0 + - - +
66A ASP* 1.3 75.8 - - - +
68A GLY* 1.3 62.4 + - - +
69A ILE* 3.3 26.9 + - + +
95A ALA* 5.3 3.1 - - - +
99A 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