Contacts of the helix formed by residues 7 - 18 (chain E) in PDB entry 3J41
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 GLU 7 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6E GLU* 1.3 96.9 + - - +
8E GLN* 1.3 58.7 + - - +
10E ALA* 2.9 27.6 + - - +
11E GLU* 3.0 22.6 + - - +
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Residues in contact with GLN 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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6E GLU* 4.2 7.8 - - - +
7E GLU* 1.3 79.2 + - - +
9E ILE* 1.3 70.2 + - + +
11E GLU* 3.9 8.1 - - - -
12E PHE* 2.9 56.5 + - + +
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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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6E GLU* 2.9 44.2 + - + +
8E GLN* 1.3 85.1 - - + +
10E ALA* 1.3 57.4 + - - +
12E PHE* 4.2 4.2 - - - -
13E LYS* 3.3 40.0 + - - +
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Residues in contact with ALA 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 GLU* 3.9 3.2 + - + +
7E GLU* 2.9 14.1 + - - +
9E ILE* 1.3 76.0 - - - +
11E GLU* 1.3 62.8 + - - +
13E LYS* 2.9 22.3 + - - +
14E GLU* 3.0 16.8 + - - +
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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 GLU* 3.0 24.2 + - - +
8E GLN* 4.0 9.0 - - - +
10E ALA* 1.3 78.3 - - - +
12E PHE* 1.3 63.4 + - + +
13E LYS 3.1 1.6 + - - -
14E GLU* 4.0 0.6 - - - +
15E ALA* 2.9 36.2 + - + +
143E GLN* 4.3 20.6 - - - +
146E THR* 5.9 0.4 - - + -
148E LYS* 2.7 45.9 + - + +
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Residues in contact with PHE 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 GLN* 2.9 43.9 + - + +
9E ILE* 4.2 7.0 - - - +
11E GLU* 1.3 79.1 - - + +
13E LYS* 1.3 58.5 + - - +
15E ALA* 4.6 3.6 - - - -
16E PHE* 4.2 10.1 - - - +
65E PHE* 4.7 5.4 - - - -
69E LEU* 3.8 48.2 - - + +
72E MET* 6.5 0.7 - - + -
73E ALA* 5.7 5.2 - - + -
142E VAL* 4.5 22.2 - - + -
143E GLN* 4.6 9.9 - - - -
146E THR* 4.3 22.7 - - + -
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Residues in contact with LYS 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 32.8 + - - +
10E ALA* 2.9 15.8 + - - +
12E PHE* 1.3 79.5 + - - +
14E GLU* 1.3 59.5 + - + +
15E ALA 3.4 0.2 - - - -
16E PHE* 3.1 7.6 + - - +
17E SER* 2.9 28.3 + - - -
65E PHE* 4.1 27.8 - - + -
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Residues in contact with GLU 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 ALA 3.0 13.7 + - - +
13E LYS* 1.3 72.9 - - + +
15E ALA* 1.3 55.7 + - - +
16E PHE 3.0 4.0 + - - -
17E SER* 3.1 22.5 + - - -
18E LEU* 2.9 36.4 + - + +
148E LYS* 3.9 26.2 - - + -
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Residues in contact with ALA 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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241B ARG* 3.2 23.8 + - - +
11E GLU* 2.9 20.4 + - + +
12E PHE* 4.6 3.6 - - - -
14E GLU* 1.3 74.5 - - - +
16E PHE* 1.3 54.8 + - - -
18E LEU* 4.7 7.5 - - - +
19E PHE* 5.1 2.3 - - - -
68E PHE* 3.5 14.0 - - - -
69E LEU* 6.4 1.6 - - + -
146E THR* 3.7 28.7 - - + -
148E LYS* 4.1 21.3 - - + +
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Residues in contact with PHE 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 PHE 4.2 8.5 + - - +
13E LYS 3.1 9.4 + - - +
14E GLU 3.1 0.4 - - - -
15E ALA* 1.3 77.3 - - - +
17E SER* 1.3 54.8 + - - +
18E LEU 3.2 1.6 - - - -
19E PHE* 2.9 27.3 + - - +
20E ASP* 3.0 40.3 + - + +
25E GLY 3.5 21.8 - - - -
26E THR 4.1 0.4 - - - -
27E ILE* 3.7 20.2 - - + -
63E ILE 3.9 2.2 - - - -
65E PHE* 3.2 68.0 - + + -
68E PHE* 3.6 39.7 - + + -
69E LEU* 5.8 2.0 - - + -
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Residues in contact with SER 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 LYS* 2.9 16.4 + - - -
14E GLU* 3.1 28.2 + - - -
16E PHE* 1.3 77.4 - - - +
18E LEU* 1.3 54.0 + - - +
19E PHE 3.0 6.9 + - - -
20E ASP 3.0 26.3 + - - +
21E LYS* 3.6 6.6 + - - +
65E PHE* 5.7 3.1 - - - -
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Residues in contact with LEU 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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241B ARG* 4.3 21.8 - - - +
14E GLU* 2.9 20.2 + - + +
15E ALA* 4.7 4.0 - - - -
16E PHE 4.7 0.4 - - - +
17E SER* 1.3 73.8 - - - +
19E PHE* 1.3 72.5 + - + +
21E LYS* 4.0 16.2 + - - +
147E ALA 4.9 9.9 - - - +
148E LYS* 5.2 10.5 - - + -
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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