Contacts of the helix formed by residues 3 - 17 (chain E) in PDB entry 5D3E
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 ASP 3 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2E VAL* 1.3 80.8 - - - +
4E ARG* 1.3 82.9 + - - +
5E GLU* 3.1 30.9 + - - +
6E GLN* 3.1 17.6 + - + +
7E LEU* 3.0 20.8 + - - +
77F LYS* 3.8 17.6 + - - +
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Residues in contact with ARG 4 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2E VAL 3.9 1.0 + - - -
3E ASP* 1.3 83.1 + - - +
5E GLU* 1.3 63.0 + - - +
7E LEU* 3.1 9.7 + - - +
8E VAL* 3.1 22.1 + - + +
30E VAL* 3.8 22.4 + - + +
33E LEU* 3.5 36.7 - - + +
35E GLU* 3.2 37.8 + - - +
36E PRO 3.6 16.4 + - - -
37E LEU* 3.9 3.6 - - - +
41E GLU* 2.5 43.0 + - - -
77J LYS* 4.2 17.9 - - - +
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Residues in contact with GLU 5 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E ASP* 3.1 24.5 + - - +
4E ARG* 1.3 82.4 - - - +
6E GLN* 1.3 75.6 + - - +
8E VAL* 3.3 8.9 + - - +
9E GLN* 2.9 46.4 + - - +
12E ARG* 5.0 0.3 + - - -
77F LYS* 4.0 12.6 + - - -
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Residues in contact with GLN 6 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2E VAL* 4.5 9.0 - - + -
3E ASP* 3.1 32.6 + - + +
5E GLU* 1.3 100.2 + - - +
7E LEU* 1.3 56.4 + - - +
9E GLN* 2.8 30.2 + - - +
10E LYS* 3.0 29.6 + - - +
77F LYS* 3.6 37.6 + - + +
78F LYS 4.8 0.6 - - - +
81F MET* 3.4 30.0 - - + +
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Residues in contact with LEU 7 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2E VAL* 3.8 30.1 - - + +
3E ASP 3.0 17.7 + - - +
4E ARG* 3.3 13.2 - - - +
6E GLN* 1.3 74.1 - - - +
8E VAL* 1.3 66.4 + - - +
10E LYS* 2.9 20.3 + - + +
11E ALA* 2.9 20.4 + - - +
26E ALA* 3.9 12.1 - - - +
27E MET* 4.3 1.8 - - - -
29E ASN* 3.6 43.7 - - + +
30E VAL* 3.5 23.3 - - + +
33E LEU* 4.6 7.4 - - + -
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Residues in contact with VAL 8 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E ARG* 3.1 16.0 + - + +
5E GLU* 3.7 9.9 - - - +
7E LEU* 1.3 75.1 - - - +
9E GLN* 1.3 62.2 - - - +
11E ALA* 3.0 3.3 + - - +
12E ARG* 2.9 56.3 + - - +
27E MET* 3.6 19.1 - - + -
30E VAL* 4.0 9.0 - - + -
41E GLU* 3.5 31.6 - - + +
44E LEU* 4.0 16.2 - - + -
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Residues in contact with GLN 9 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E GLU* 2.9 40.4 + - - +
6E GLN* 2.8 34.8 + - - +
8E VAL* 1.3 77.4 - - - +
10E LYS* 1.3 61.0 + - - +
12E ARG* 3.3 23.1 + - - +
13E LEU* 3.0 24.8 + - - +
75F ASN* 5.6 3.4 - - - +
78F LYS* 4.4 24.9 - - + +
81F MET* 3.5 22.9 - - + +
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Residues in contact with LYS 10 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2E VAL* 4.1 22.6 - - - +
6E GLN* 3.0 16.3 + - - +
7E LEU* 2.9 22.5 + - + +
9E GLN* 1.3 74.8 - - - +
11E ALA* 1.3 58.9 + - - +
13E LEU* 3.5 4.0 - - + +
14E ALA* 2.9 31.7 + - + +
22E ASP* 5.7 4.0 - - + +
26E ALA* 4.4 13.9 - - + -
81F MET* 4.1 22.2 - - - +
85F TYR* 5.2 19.5 - - + -
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Residues in contact with ALA 11 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E LEU 2.9 6.2 + - - +
8E VAL 3.0 4.2 + - - +
10E LYS* 1.3 78.2 - - - +
12E ARG* 1.3 63.6 + - - +
14E ALA* 3.1 3.6 + - - +
15E GLU* 2.9 24.0 + - - +
23E MET* 3.7 18.6 - - + +
26E ALA* 4.1 8.7 - - + +
27E MET* 3.4 45.8 - - + -
44E LEU* 4.4 6.7 - - + -
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Residues in contact with ARG 12 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E GLU 5.0 0.4 + - - -
8E VAL* 2.9 40.7 + - - +
9E GLN* 3.8 31.4 - - - +
11E ALA* 1.3 75.8 - - - +
13E LEU* 1.3 63.5 + - - +
15E GLU* 3.4 12.6 + - - +
16E GLN* 3.2 27.0 + - - +
40E GLU* 2.4 44.5 + - - +
44E LEU* 4.3 16.6 - - + +
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Residues in contact with LEU 13 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E GLN 3.0 15.1 + - - +
10E LYS* 3.5 5.6 - - - +
12E ARG* 1.3 74.9 - - - +
14E ALA* 1.3 61.1 + - - +
16E GLN* 2.9 23.5 + - + +
17E ALA* 2.9 12.8 + - - +
63F ILE* 3.7 22.5 - - + +
66F ILE* 4.2 22.2 - - + -
81F MET* 3.7 33.7 - - + -
82F VAL* 4.0 31.9 - - + -
85F TYR* 3.7 22.0 - - + -
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Residues in contact with ALA 14 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E LYS* 2.9 18.4 + - + +
11E ALA 3.6 3.6 - - - +
13E LEU* 1.3 76.6 - - - +
15E GLU* 1.3 61.4 + - - +
17E ALA* 3.3 1.9 + - - +
18E GLU 3.1 3.3 + - - -
19E ARG 2.8 44.8 + - - +
22E ASP* 3.8 3.4 - - + -
23E MET* 3.7 16.8 - - + +
85F TYR* 3.3 28.0 - - + +
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Residues in contact with GLU 15 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E ALA 2.9 12.8 + - - +
12E ARG* 3.6 12.6 - - - +
13E LEU 3.1 0.2 - - - -
14E ALA* 1.3 77.1 - - - +
16E GLN* 1.3 70.5 + - + +
18E GLU* 3.1 18.4 + - - +
20E TYR* 4.2 16.1 + - + +
23E MET* 3.7 29.8 - - + -
44E LEU* 3.9 16.9 - - - +
47E VAL* 3.8 18.4 - - - +
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Residues in contact with GLN 16 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E ARG* 3.2 16.7 - - + +
13E LEU* 2.9 8.9 + - + +
15E GLU* 1.3 87.0 - - - +
17E ALA* 1.3 57.2 + - - +
18E GLU* 3.0 12.1 + - - +
62F VAL* 3.8 31.0 - - + +
63F ILE* 5.4 0.7 - - + -
66F ILE* 4.0 24.6 - - + +
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Residues in contact with ALA 17 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E LEU 2.9 12.0 + - - +
14E ALA 3.3 4.4 + - - +
16E GLN* 1.3 75.4 - - - +
18E GLU* 1.3 67.1 - - - +
19E ARG* 3.3 15.2 + - - -
59F SER* 2.5 46.2 + - - +
62F VAL* 4.5 5.8 - - - +
63F ILE* 4.0 20.4 - - + -
85F TYR* 4.4 3.4 - - + -
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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