Contacts of the helix formed by residues 9 - 19 (chain A) in PDB entry 2ELL
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 9 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A GLY 4.3 0.5 - - - +
8A MET* 1.3 80.1 - - - +
10A MET* 1.3 71.6 + - - +
11A LYS* 3.5 0.4 - - + -
12A ARG* 3.2 23.6 + - + +
13A ARG* 3.0 14.2 + - - +
35A LYS* 3.2 14.9 - - - +
37A ASN* 3.8 14.7 + - - +
42A GLU* 3.6 15.0 - - - +
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Residues in contact with MET 10 (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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8A MET 3.5 1.5 + - - -
9A ASP* 1.3 69.8 - - - +
11A LYS* 1.3 65.5 + - - +
13A ARG* 2.7 18.1 + - - +
14A ILE* 2.8 35.2 + - + +
31A LEU* 4.2 19.1 - - + -
34A CYS* 3.2 36.8 - - - -
35A LYS 3.0 9.4 + - - +
36A SER* 3.3 33.7 - - - +
41A ILE* 4.8 15.9 - - + -
42A GLU* 3.5 10.6 + - + +
43A GLY* 4.4 10.3 - - - +
44A LEU* 4.5 2.5 - - + +
56A LEU* 4.6 13.7 - - + -
59A VAL* 4.8 1.8 - - + -
61A LEU* 5.0 1.6 - - + -
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Residues in contact with LYS 11 (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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10A MET* 1.3 73.4 - - - +
12A ARG* 1.3 64.2 + - + +
14A ILE* 3.7 5.4 - - + +
15A HIS* 3.0 24.5 + - + +
42A GLU* 2.8 47.2 + - - +
43A GLY* 3.8 19.7 - - - -
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Residues in contact with ARG 12 (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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8A MET* 3.7 23.7 - - + +
9A ASP* 3.2 33.5 + - + +
10A MET 3.0 0.4 + - - -
11A LYS* 1.3 79.6 - - + +
13A ARG* 1.3 60.9 + - - +
15A HIS* 3.4 9.2 - - - +
16A LEU* 3.1 23.6 - - - +
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Residues in contact with ARG 13 (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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1A GLY 4.7 17.2 + - - +
4A GLY* 4.5 7.3 - - - -
5A SER* 3.1 40.1 + - - +
8A MET* 3.8 30.0 - - + +
9A ASP 3.0 9.2 + - - +
10A MET* 2.7 16.3 + - - +
12A ARG* 1.3 68.2 - - - +
14A ILE* 1.3 58.7 + - + +
15A HIS 2.8 2.0 - - - -
16A LEU* 2.6 45.2 + - - +
17A GLU* 3.3 15.1 + - + +
31A LEU* 6.1 5.6 - - + -
32A ASP 4.5 12.2 + - - +
33A ASN* 3.7 15.6 + - - +
34A CYS* 5.0 10.5 - - + +
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Residues in contact with ILE 14 (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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10A MET* 2.8 28.3 + - + +
11A LYS* 3.7 6.3 - - + +
13A ARG* 1.3 73.5 - - + +
15A HIS* 1.3 56.6 + - - +
17A GLU* 3.2 9.8 + - - +
18A LEU* 3.0 50.2 + - + +
29A LEU* 5.0 2.2 - - + -
31A LEU* 3.7 24.2 - - + -
43A GLY* 3.2 17.0 - - - +
44A LEU* 3.0 36.6 - - - +
45A THR* 5.9 1.8 - - + -
48A PHE* 3.6 17.3 - - + -
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Residues in contact with HIS 15 (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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11A LYS* 3.0 12.1 + - + +
12A ARG* 3.4 12.8 - - - +
13A ARG 2.6 4.0 + - - -
14A ILE* 1.3 69.5 - - - +
16A LEU* 1.3 80.2 + - + +
17A GLU 2.9 3.0 + - - -
18A LEU* 3.0 12.8 + - - +
19A ARG* 3.0 50.2 + - + +
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Residues in contact with LEU 16 (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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1A GLY* 4.5 17.7 - - - +
8A MET* 3.6 30.7 - - + -
12A ARG 3.1 26.0 - - - +
13A ARG* 2.6 24.6 + - - +
15A HIS* 1.3 87.1 - - + +
17A GLU* 1.3 62.4 + - + +
19A ARG* 3.5 25.1 - - - +
20A ASN* 3.8 4.5 - - - +
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Residues in contact with GLU 17 (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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13A ARG* 3.3 19.7 + - + +
14A ILE* 3.2 12.5 + - - +
15A HIS 3.0 0.4 - - - -
16A LEU* 1.3 78.7 - - + +
18A LEU* 1.3 66.6 + - + +
19A ARG 3.0 1.8 - - - -
20A ASN* 2.5 34.8 + - - +
21A ARG* 5.4 0.5 - - - -
26A VAL* 6.1 1.0 - - - +
29A LEU* 3.2 37.4 - - + +
30A VAL 4.6 10.2 + - - +
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Residues in contact with LEU 18 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A ILE* 3.0 41.6 + - + +
15A HIS* 3.0 12.1 + - + +
17A GLU* 1.3 74.4 - - + +
19A ARG* 1.3 53.9 + - - +
20A ASN 2.5 18.9 + - - -
21A ARG* 2.6 28.3 + - - +
23A PRO* 3.6 47.6 - - + -
26A VAL* 5.4 4.0 - - + -
29A LEU* 5.6 0.7 - - + -
45A THR* 5.6 3.6 - - + -
47A GLU* 5.6 0.9 - - - +
48A PHE* 4.2 8.3 - - + -
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Residues in contact with ARG 19 (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 HIS* 3.0 44.6 + - + +
16A LEU* 3.5 23.3 - - - +
17A GLU 3.0 0.4 + - - -
18A LEU* 1.3 74.0 - - - +
20A ASN* 1.3 62.6 + - - +
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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