Contacts of the helix formed by residues 5 - 18 (chain E) in PDB entry 3VON
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 PRO 5 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4E LEU* 1.4 89.4 - - + +
6E ARG* 1.3 65.7 + - + +
7E ARG* 3.3 8.1 - - + +
8E ILE* 3.3 28.5 + - + +
9E ILE* 3.4 11.3 + - - +
33E ARG* 3.6 28.0 - - - +
60E GLU 5.7 1.3 - - - +
62E TYR 5.1 8.7 - - - +
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Residues in contact with ARG 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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4E LEU 5.0 2.5 - - - +
5E PRO* 1.3 70.3 - - + +
7E ARG* 1.3 65.2 + - - +
9E ILE* 3.4 20.2 + - + +
10E LYS* 3.0 24.7 + - - +
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Residues in contact with ARG 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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5E PRO* 3.3 6.6 - - + +
6E ARG* 1.3 78.9 - - - +
8E ILE* 1.3 56.7 + - + +
10E LYS* 3.3 16.4 + - - +
11E GLU* 2.8 55.9 + - + +
62E TYR* 3.2 23.1 + - - -
63E PRO* 3.6 36.4 - - + +
97E PRO* 2.9 20.6 + - - +
98E ALA 4.8 1.0 + - - -
99E LEU 2.9 27.7 + - - -
100E GLN* 3.6 7.9 + - - +
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Residues in contact with ILE 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 LEU* 4.1 18.8 - - + -
5E PRO* 3.3 25.9 + - + +
6E ARG 3.3 0.2 - - - -
7E ARG* 1.3 74.5 - - + +
9E ILE* 1.3 65.6 + - - +
11E GLU* 3.1 7.8 + - - +
12E THR* 2.9 37.5 + - - +
32E ALA* 4.3 13.0 - - + +
33E ARG* 3.6 38.1 - - - +
35E PHE* 5.3 0.7 - - + -
58E LEU* 4.1 31.2 - - + -
62E TYR* 4.1 19.7 - - + +
101E ILE* 5.8 0.7 - - + -
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Residues in contact with ILE 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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4E LEU* 3.4 43.5 - - + +
5E PRO 3.4 8.2 + - - +
6E ARG* 3.8 23.8 - - + +
8E ILE* 1.3 75.5 - - - +
10E LYS* 1.3 62.1 + - - +
12E THR* 3.7 5.4 + - - -
13E GLN* 3.3 25.0 + - + +
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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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6E ARG 3.0 17.9 + - - +
7E ARG* 3.5 14.6 - - - +
9E ILE* 1.3 77.0 - - - +
11E GLU* 1.3 65.1 + - - +
13E GLN* 3.4 5.9 + - - +
14E ARG* 2.9 55.0 + - + +
100E GLN* 4.7 10.5 + - - -
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Residues in contact with GLU 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 ARG* 2.8 43.8 + - + +
8E ILE* 3.1 6.0 + - - +
10E LYS* 1.3 84.0 - - - +
12E THR* 1.3 60.2 + - - +
14E ARG* 3.3 8.8 + - - +
15E LEU* 2.8 34.2 + - + +
62E TYR* 2.5 26.7 + - - -
100E GLN* 3.2 20.4 - - - +
101E ILE* 3.0 43.4 + - + +
102E ARG 4.6 0.7 + - - -
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Residues in contact with THR 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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8E ILE* 2.9 22.3 + - - +
9E ILE* 4.1 5.2 - - - -
11E GLU* 1.3 76.4 - - - +
13E GLN* 1.3 57.4 + - - +
15E LEU* 3.2 11.1 + - + +
16E LEU* 3.1 38.5 + - + +
27E PRO* 3.8 34.1 - - + -
32E ALA* 4.8 3.0 + - + +
35E PHE* 3.6 27.6 - - + -
101E ILE* 5.4 0.3 - - - +
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Residues in contact with GLN 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 ILE* 3.3 17.4 + - + +
10E LYS* 3.6 6.7 - - - +
11E GLU 3.3 0.4 - - - -
12E THR* 1.3 77.7 - - - +
14E ARG* 1.3 58.0 + - - +
16E LEU* 3.6 16.3 + - - +
17E ALA* 3.1 38.3 + - + +
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Residues in contact with ARG 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 41.4 + - + +
11E GLU* 3.6 9.2 - - - +
13E GLN* 1.3 76.7 - - - +
15E LEU* 1.3 57.0 + - - +
17E ALA* 4.5 4.9 - - - -
18E GLU* 3.0 54.4 + - - +
100E GLN* 4.5 18.0 + - - +
102E ARG* 3.0 27.6 + - - +
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Residues in contact with LEU 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 GLU* 2.8 19.1 + - + +
12E THR* 3.5 8.3 - - + +
13E GLN 3.2 0.4 - - - -
14E ARG* 1.3 78.4 - - - +
16E LEU* 1.3 62.9 + - + +
18E GLU 5.4 0.2 - - - +
19E PRO* 3.5 28.1 - - + +
20E VAL* 5.1 6.1 - - + +
25E ALA* 4.7 19.6 - - + +
35E PHE* 4.5 16.4 - - + -
101E ILE* 3.8 37.0 - - + -
102E ARG* 3.5 31.0 - - + +
105E LEU* 4.4 19.5 - - + -
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Residues in contact with LEU 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 THR* 3.1 25.5 + - + +
13E GLN* 3.6 18.1 + - - +
14E ARG 3.4 0.2 - - - -
15E LEU* 1.3 77.7 - - + +
17E ALA* 1.3 65.4 + - - +
18E GLU 3.6 0.2 + - - -
19E PRO* 3.7 13.4 - - - +
25E ALA 4.5 10.1 - - - +
26E GLU* 4.7 10.3 - - + -
27E PRO* 4.0 28.3 - - + -
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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 GLN* 3.1 26.3 + - + +
14E ARG* 4.1 5.6 - - - +
16E LEU* 1.3 79.3 - - - +
18E GLU* 1.3 65.4 + - + +
19E PRO* 3.8 3.8 - - - +
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Residues in contact with GLU 18 (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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14E ARG* 3.0 42.9 + - - +
15E LEU 3.8 2.7 - - - -
17E ALA* 1.3 82.3 - - + +
19E PRO* 1.3 64.0 - - - +
102E ARG* 2.9 35.1 + - - +
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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