Contacts of the helix formed by residues 10 - 25 (chain A) in PDB entry 2LI5
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 10 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A LYS* 4.9 2.1 - - - +
9A TYR* 1.4 97.6 - - + +
11A PHE* 1.3 67.2 + - - +
12A GLU* 4.4 9.0 - - + +
13A LYS* 3.1 35.3 - - + +
14A ARG* 3.5 4.2 + - - +
598B PRO* 4.1 38.8 - - + +
609B GLN* 4.6 16.4 - - + -
610B GLU* 6.0 0.7 - - + +
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Residues in contact with PHE 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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6A LYS* 6.3 5.1 - - - +
10A PRO* 1.3 71.1 - - - +
12A GLU* 1.3 79.0 + - + +
13A LYS 2.6 5.4 + - - -
14A ARG* 2.5 32.6 + - - +
15A LYS* 3.0 34.6 + - + -
101A LYS* 3.6 24.9 - - + -
102A ASP* 3.1 58.8 - - + -
106A TYR* 5.6 2.0 - - - -
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Residues in contact with GLU 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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10A PRO* 3.5 8.4 - - + +
11A PHE* 1.3 93.9 - - + +
13A LYS* 1.3 65.3 + - - +
15A LYS* 3.3 29.6 + - + +
16A ALA* 3.1 25.1 + - - +
598B PRO 5.5 2.9 - - - +
599B HIS* 5.8 3.1 - - - -
600B MET* 5.8 3.8 + - - +
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Residues in contact with LYS 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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9A TYR* 3.4 38.1 - - + -
10A PRO* 3.1 25.5 + - + +
11A PHE 2.6 4.9 + - - -
12A GLU* 1.3 79.4 + - - +
14A ARG* 1.3 57.3 - - - +
16A ALA* 3.3 8.5 + - - +
17A GLU* 2.9 25.7 + - - +
609B GLN* 3.8 36.8 - - + +
610B GLU 6.0 0.7 - - - +
611B VAL* 6.3 1.6 - - + -
618B VAL* 5.5 10.4 - - + +
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Residues in contact with ARG 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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5A PHE* 3.1 26.9 - - - -
6A LYS* 4.6 10.5 - - + -
9A TYR* 3.9 18.6 - - - -
10A PRO 3.5 3.5 + - - +
11A PHE* 2.5 17.4 + - + +
13A LYS* 1.3 69.5 - - - +
15A LYS* 1.3 58.2 + - - +
16A ALA 3.0 1.3 - - - -
17A GLU* 2.5 29.7 + - - +
18A SER 2.8 12.3 + - - -
32A ILE* 2.8 37.9 - - - +
48A LYS* 3.4 7.7 - - - +
102A ASP* 4.2 11.0 - - + -
104A PHE* 2.6 94.6 - - + +
106A TYR* 4.4 14.0 + - - +
618B VAL* 5.3 0.2 - - - +
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Residues in contact with LYS 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 PHE* 3.0 30.0 + - + -
12A GLU* 3.3 34.1 + - - +
14A ARG* 1.3 78.0 - - - +
16A ALA* 1.3 64.1 - - - +
18A SER* 2.8 15.4 + - - -
19A GLU* 2.9 24.3 + - + +
101A LYS 4.3 3.4 - - - +
102A ASP* 3.3 32.4 + - - +
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Residues in contact with ALA 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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12A GLU 3.1 16.8 + - - +
13A LYS* 3.4 10.5 - - - +
14A ARG 3.0 0.6 - - - -
15A LYS* 1.3 84.5 - - + +
17A GLU* 1.3 63.7 + - - +
19A GLU* 3.2 15.4 - - - +
20A ARG* 3.2 23.7 - - - +
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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 LYS 2.9 12.5 + - - +
14A ARG* 2.5 21.0 + - + +
16A ALA* 1.3 67.7 - - - +
18A SER* 1.3 54.4 + - - -
19A GLU 3.0 4.5 - - - -
20A ARG* 2.9 24.0 + - - +
21A ILE* 2.8 32.4 + - + +
24A ARG* 3.6 18.4 + - - -
104A PHE* 3.3 25.1 - - + -
617B ASP 4.0 0.3 - - - +
618B VAL* 2.8 52.5 - - + +
619B PHE* 3.7 10.1 - - + -
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Residues in contact with SER 18 (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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14A ARG 2.8 8.1 + - - -
15A LYS 2.8 15.4 + - - -
17A GLU* 1.3 74.1 - - - +
19A GLU* 1.3 62.8 + - - +
21A ILE* 3.7 10.2 - - - +
22A ALA* 3.2 24.3 + - - +
30A PRO* 5.5 2.0 - - - -
95A TYR* 5.0 4.9 - - - -
102A ASP 2.6 26.8 + - - -
103A GLY* 4.3 8.3 - - - -
104A PHE* 3.3 23.4 - - - -
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Residues in contact with GLU 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 LYS* 2.9 28.4 + - + +
16A ALA* 3.2 16.2 - - - +
17A GLU 3.0 0.4 - - - -
18A SER* 1.3 80.5 - - - +
20A ARG* 1.3 58.8 - - + +
22A ALA* 4.1 10.3 - - - +
23A ASP* 4.5 5.4 + - - +
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Residues in contact with ARG 20 (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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16A ALA* 3.2 20.4 - - - +
17A GLU* 2.9 24.6 + - - +
19A GLU* 1.3 80.2 - - + +
21A ILE* 1.3 54.1 + - - +
22A ALA 2.8 5.6 - - - -
23A ASP* 2.7 29.1 + - - +
24A ARG* 2.9 31.9 + - - +
617B ASP* 3.3 30.6 + - - +
618B VAL* 4.2 10.5 - - - +
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Residues in contact with ILE 21 (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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17A GLU* 2.8 26.3 + - + +
18A SER* 3.5 6.7 + - - +
20A ARG* 1.3 75.5 - - - +
22A ALA* 1.3 58.2 + - - +
23A ASP 3.2 0.2 - - - -
24A ARG* 3.6 29.6 - - - +
25A PHE* 2.8 42.7 + - + +
28A ARG* 5.5 0.2 - - + -
30A PRO* 4.3 22.0 - - + -
50A LEU* 4.0 24.0 - - + -
104A PHE* 3.3 35.4 - - + -
619B PHE* 4.5 4.0 - - + -
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Residues in contact with ALA 22 (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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18A SER 3.2 16.9 + - - +
19A GLU* 4.1 9.0 - - - +
20A ARG 2.8 0.6 - - - -
21A ILE* 1.3 79.7 - - - +
23A ASP* 1.3 58.8 + - + +
24A ARG 3.3 0.4 - - - -
25A PHE 4.6 3.1 - - - -
26A PRO* 3.8 22.9 - - - +
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Residues in contact with ASP 23 (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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19A GLU 4.5 3.3 + - - +
20A ARG* 2.7 14.9 + - - +
22A ALA* 1.3 78.4 - - - +
24A ARG* 1.3 62.9 + - - +
26A PRO* 5.1 2.4 - - - +
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Residues in contact with ARG 24 (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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17A GLU* 3.6 24.2 + - - -
20A ARG* 2.9 29.1 + - - +
21A ILE* 3.8 17.6 - - - +
23A ASP* 1.3 83.0 - - - +
25A PHE* 1.3 102.9 - - + +
26A PRO* 3.6 7.6 - - - +
617B ASP* 4.5 19.0 + - - -
619B PHE* 4.0 23.2 - - - +
624B ASP* 4.0 9.1 + - - -
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Residues in contact with PHE 25 (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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21A ILE* 2.8 34.4 + - + +
22A ALA* 4.8 0.2 - - - -
24A ARG* 1.3 122.7 - - + +
26A PRO* 1.4 66.8 - - - +
27A ASN 3.3 2.0 - - - +
28A ARG* 3.3 55.0 + - + +
30A PRO* 6.0 0.2 - - - +
50A LEU* 5.1 3.8 - - + -
624B ASP* 4.4 17.3 - - - -
625B GLU* 4.8 18.8 - - + -
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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