Contacts of the helix formed by residues 5 - 19 (chain D) in PDB entry 1E8O
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 5 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4D LEU* 1.3 75.9 - - - +
6D SER* 1.3 81.2 + - - +
7D GLU* 2.5 13.6 + - - +
8D GLN* 2.9 21.0 + - + +
9D PHE 3.4 3.2 + - - -
69D THR* 4.2 1.8 - - - -
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Residues in contact with SER 6 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D GLU* 1.3 78.8 - - - +
7D GLU* 1.3 68.1 + - - +
9D PHE* 3.6 11.6 - - - +
10D LEU* 3.8 11.1 + - - +
69D THR* 3.8 13.4 + - - -
70D VAL 5.4 0.9 + - - -
75D GLU* 2.9 36.0 + - - -
79D PHE* 4.0 20.4 - - - -
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Residues in contact with GLU 7 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D GLU* 2.5 14.0 + - + +
6D SER* 1.3 74.4 - - - +
8D GLN* 1.3 61.1 + - - +
9D PHE 2.5 0.5 + - - -
10D LEU* 2.5 46.8 + - + +
11D THR* 3.8 15.7 + - + +
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Residues in contact with GLN 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D LEU* 3.2 38.5 - - + +
5D GLU* 2.9 16.3 + - + +
7D GLU* 1.3 80.2 - - - +
9D PHE* 1.3 64.5 + - - +
11D THR* 2.6 32.0 + - - -
12D GLU* 3.0 27.8 + - + +
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Residues in contact with PHE 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D LEU* 3.5 14.5 - - + +
5D GLU 3.4 2.0 + - - +
6D SER 3.6 9.9 - - - +
7D GLU 2.5 4.2 + - - -
8D GLN* 1.3 76.9 - - - +
10D LEU* 1.3 68.5 + - + +
12D GLU* 3.8 1.4 - - - +
13D LEU* 2.9 45.7 + - + +
28D ILE* 5.9 1.6 - - + -
58D LEU* 3.7 38.1 - - + -
59D ARG 4.7 0.4 - - - -
60D ALA* 4.2 15.7 - - + -
67D ILE* 3.8 24.4 - - + +
68D SER* 3.6 38.8 - - - -
69D THR* 3.6 20.2 - - + +
79D PHE* 4.2 3.4 - + - -
83D TYR* 4.4 5.2 - + - -
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Residues in contact with LEU 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D SER 3.8 2.9 - - - +
7D GLU* 2.5 23.1 + - + +
9D PHE* 1.3 75.6 - - + +
11D THR* 1.3 58.6 + - + +
13D LEU* 3.2 4.2 + - + +
14D THR* 2.8 32.4 + - - -
79D PHE* 3.4 45.5 - - + -
82D ALA* 3.9 26.5 - - + -
83D TYR* 4.0 22.0 - - + +
86D LEU* 3.5 19.0 - - + +
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Residues in contact with THR 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D GLU* 3.8 19.7 + - + +
8D GLN* 2.6 29.5 + - - -
10D LEU* 1.3 73.1 - - + +
12D GLU* 1.3 74.1 + - - +
14D THR* 3.3 9.5 + - - -
15D ARG* 3.2 32.3 + - - +
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Residues in contact with GLU 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D LEU* 3.3 27.8 - - + +
8D GLN* 3.0 27.0 + - + +
9D PHE 3.8 2.9 - - - +
11D THR* 1.3 83.4 + - - +
13D LEU* 1.3 64.9 + - - +
15D ARG* 3.1 42.6 + - - +
16D LEU* 3.1 15.3 + - - +
65D LYS* 3.5 26.5 - - - +
67D ILE* 3.7 24.9 - - + -
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Residues in contact with LEU 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D PHE* 2.9 28.3 + - + +
10D LEU* 3.4 5.6 - - + +
12D GLU* 1.3 73.7 - - - +
14D THR* 1.3 69.1 + - - +
16D LEU* 3.0 20.3 + - + +
17D PHE* 3.3 29.3 + - + -
26D VAL* 4.9 1.3 - - + -
28D ILE* 4.5 9.2 - - + -
60D ALA* 3.6 30.1 - - + -
67D ILE* 3.8 6.0 - - + +
83D TYR* 4.0 24.7 - - + -
86D LEU* 3.3 29.2 - - + -
87D LEU* 4.5 3.1 - - + -
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Residues in contact with THR 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D LEU 2.8 23.2 + - - -
11D THR* 3.3 9.8 + - - -
13D LEU* 1.3 73.8 - - - +
15D ARG* 1.3 65.4 + - - +
17D PHE* 3.1 17.0 + - - +
18D GLN* 3.1 32.0 + - - +
86D LEU* 3.6 16.6 - - - +
90D ASN* 4.1 18.4 - - - +
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Residues in contact with ARG 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D THR* 3.2 19.6 + - - +
12D GLU* 3.1 38.8 + - - +
13D LEU 3.0 0.6 - - - -
14D THR* 1.3 79.2 - - - +
16D LEU* 1.3 53.3 + - + +
18D GLN* 2.6 23.2 + - + +
19D LYS* 2.6 40.3 + - + +
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Residues in contact with LEU 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D GLU 3.1 16.9 + - - +
13D LEU* 3.0 13.5 + - + +
15D ARG* 1.3 77.4 - - + +
17D PHE* 1.3 59.5 + - - +
19D LYS* 3.6 11.7 + - + +
20D CYS* 3.3 24.9 + - - +
26D VAL* 3.6 18.1 - - + +
60D ALA* 3.9 17.5 - - + +
61D THR* 3.7 39.0 - - - +
62D ASP* 3.9 26.8 - - + +
65D LYS* 4.6 20.2 - - + +
67D ILE* 4.5 9.0 - - + -
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Residues in contact with PHE 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C TYR* 3.6 40.8 - + + -
33C HIS* 5.6 1.4 - - - +
13D LEU* 3.3 47.3 + - + -
14D THR 3.1 3.9 + - - +
15D ARG 2.8 2.2 + - - -
16D LEU* 1.3 75.1 - - - +
18D GLN* 1.3 59.5 + - - +
20D CYS* 3.2 3.3 + - - +
21D ARG* 3.1 33.9 + - - +
26D VAL* 3.7 26.7 - - + -
28D ILE* 4.1 15.5 - - + -
86D LEU* 3.9 11.7 - - + -
87D LEU* 4.2 9.6 - - + -
90D ASN* 3.5 38.4 - - + +
91D MET* 4.1 12.6 - - + -
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Residues in contact with GLN 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D THR* 3.3 31.7 - - + +
15D ARG* 2.6 26.0 + - - +
17D PHE* 1.3 73.4 - - - +
19D LYS* 1.3 53.6 + - - +
20D CYS 3.2 3.6 + - - -
21D ARG* 3.9 16.1 + - - +
90D ASN* 4.4 6.9 + - - +
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Residues in contact with LYS 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D ARG* 2.6 23.0 + - + +
16D LEU* 3.7 11.0 - - + +
17D PHE 3.2 0.2 - - - -
18D GLN* 1.3 71.1 - - - +
20D CYS* 1.3 65.2 + - - +
23D SER 4.7 0.2 - - - +
62D ASP* 3.4 26.7 + - - +
64D LYS* 4.3 17.6 - - - +
65D LYS* 4.6 13.4 - - + +
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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