Contacts of the helix formed by residues 18 - 30 (chain A) in PDB entry 2I5B
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 ALA 18 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A ASP* 2.8 26.6 + - + +
17A GLY* 1.3 74.5 - - - -
19A GLY* 1.3 69.0 + - - +
21A GLN* 3.3 12.5 + - - +
22A ALA* 2.9 17.5 + - - -
212A HIS* 3.6 16.2 - - + +
213A GLY* 3.8 15.9 - - - -
216A CYS* 4.1 7.9 - - - -
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Residues in contact with GLY 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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10A ALA* 5.0 2.7 - - - -
11A GLY 3.3 15.7 - - - -
13A ASP* 4.2 3.3 - - - +
18A ALA* 1.3 80.6 - - - +
20A ILE* 1.3 64.2 + - - -
21A GLN* 4.6 0.2 - - - -
22A ALA* 3.0 1.2 + - - +
23A ASP* 2.8 32.5 + - - +
82A MET* 5.9 4.0 - - - -
216A CYS* 3.4 18.3 - - - -
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Residues in contact with ILE 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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8A THR* 3.9 17.3 - - + +
10A ALA* 3.4 42.4 - - + +
11A GLY 2.7 14.4 + - - +
12A SER* 4.3 0.2 - - - -
19A GLY* 1.3 70.7 - - - -
21A GLN* 1.3 75.9 + - + +
23A ASP* 3.6 2.5 - - - +
24A LEU* 2.8 45.3 + - + +
36A THR* 3.5 25.8 - - + -
37A ALA 5.0 0.2 - - - +
38A LEU* 3.4 31.9 - - + -
20B ILE* 5.3 6.3 - - + -
21B GLN* 6.1 0.2 - - - +
24B LEU* 4.8 3.1 - - + -
38B LEU* 6.0 1.3 - - + -
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Residues in contact with GLN 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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12A SER* 2.9 25.3 + - - -
13A ASP 2.8 37.6 + - - +
16A GLY* 3.5 26.0 - - - +
18A ALA 3.5 6.8 - - - +
19A GLY 3.0 0.4 + - - -
20A ILE* 1.3 85.1 + - - +
22A ALA* 1.3 66.7 + - - +
24A LEU* 3.9 0.3 - - - +
25A LYS* 2.9 36.5 + - - +
20B ILE* 6.1 0.2 - - - +
24B LEU* 4.2 24.5 - - + -
34B GLY 4.7 2.2 - - - +
36B THR* 2.9 25.0 + - + +
38B LEU* 5.1 0.4 - - - +
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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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17A GLY 3.2 24.4 - - - +
18A ALA* 2.9 16.3 + - - +
19A GLY 3.4 7.9 - - - +
21A GLN* 1.3 73.6 - - - +
23A ASP* 1.3 58.4 + - - +
25A LYS* 3.7 1.2 - - - +
26A THR* 2.8 36.3 + - - -
216A CYS* 3.9 12.6 - - + -
217A THR* 3.7 16.2 - - - +
220A ALA* 4.9 0.2 - - - -
262A HIS* 3.9 12.1 - - - -
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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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8A THR* 2.9 36.8 + - + -
10A ALA* 3.9 6.1 - - - +
19A GLY* 2.8 26.0 + - - +
20A ILE* 3.6 5.0 + - - +
22A ALA* 1.3 75.8 - - - +
24A LEU* 1.3 57.5 + - - +
26A THR* 3.2 0.9 + - - -
27A PHE* 2.8 40.6 + - + -
79A LYS* 2.6 34.8 + - - -
216A CYS* 3.3 12.8 - - - +
220A ALA* 3.4 9.1 - - + +
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Residues in contact with LEU 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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8A THR* 5.4 0.4 - - + -
20A ILE* 2.8 25.2 + - + +
21A GLN 4.0 1.8 - - - +
23A ASP* 1.3 72.6 - - - +
25A LYS* 1.3 54.4 + - - +
27A PHE* 3.1 6.8 + - + +
28A GLN* 2.8 37.2 + - - +
34A GLY* 3.8 36.6 - - - +
35A MET 4.3 0.7 - - - +
36A THR* 3.7 27.8 - - + -
20B ILE* 4.8 2.0 - - + -
21B GLN* 4.0 22.0 - - + +
24B LEU* 3.7 35.4 - - + -
25B LYS* 4.4 15.2 - - + +
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Residues in contact with LYS 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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16A GLY 2.8 27.9 + - - +
21A GLN* 2.9 29.5 + - - +
22A ALA 3.7 3.1 - - - +
24A LEU* 1.3 77.1 - - + +
26A THR* 1.3 62.2 + - - +
28A GLN* 3.4 1.1 + - - -
29A GLU* 3.0 29.3 + - - +
262A HIS* 4.0 23.8 - - + +
24B LEU* 4.3 16.4 - - + +
28B GLN* 3.3 37.8 - - + +
33B TYR* 3.5 18.8 - - + +
34B GLY 2.9 40.4 + - - +
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Residues in contact with THR 26 (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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22A ALA 2.8 27.5 + - - -
23A ASP 3.6 3.6 - - - -
25A LYS* 1.3 69.1 - - - +
27A PHE* 1.3 65.8 + - - +
29A GLU* 3.2 11.8 + - - +
30A LYS* 3.2 16.9 + - + +
217A THR* 3.5 10.4 - - - +
220A ALA* 3.6 10.6 - - + +
221A ALA* 3.5 36.3 - - + +
224A ALA* 5.2 0.2 - - + -
242A PHE* 3.8 25.8 - - + -
262A HIS* 3.3 16.8 - - - -
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Residues in contact with PHE 27 (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 ALA* 3.8 31.2 - - + -
7A LEU 4.5 1.1 - - - -
8A THR* 4.3 21.5 - - + -
23A ASP* 2.8 27.6 + - + +
24A LEU* 3.5 8.3 - - + +
26A THR* 1.3 72.3 - - - +
28A GLN* 1.3 61.4 + - - +
30A LYS 3.2 3.8 + - - -
31A ASN 3.1 4.3 + - - -
32A VAL* 2.8 41.9 + - + +
34A GLY* 3.8 21.3 - - - -
79A LYS* 4.4 16.6 - - + -
220A ALA* 3.3 34.3 - - + -
223A THR* 3.9 18.8 - - + -
224A ALA* 3.8 15.7 - - + -
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Residues in contact with GLN 28 (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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3A MET* 5.5 8.4 - - - +
24A LEU 2.8 17.3 + - - +
25A LYS 3.8 3.6 - - - +
27A PHE* 1.3 75.3 - - - +
29A GLU* 1.3 65.5 + - - +
31A ASN* 2.8 18.4 + - - +
32A VAL 3.9 8.8 + - - +
33A TYR* 5.3 1.6 - - - -
25B LYS* 3.4 53.9 + - + +
28B GLN* 4.5 12.1 - - + -
29B GLU* 2.8 34.8 + - - +
262B HIS* 3.9 5.7 + - - +
263B SER* 3.8 21.8 + - - +
266B ARG* 4.1 3.6 + - - -
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Residues in contact with GLU 29 (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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25A LYS 3.0 19.3 + - - +
26A THR 3.6 7.0 - - - +
28A GLN* 1.3 74.7 - - - +
30A LYS* 1.3 59.6 + - - +
242A PHE* 4.0 16.9 - - + -
262A HIS* 3.5 20.2 - - + +
263A SER* 3.6 11.8 - - - -
266A ARG* 2.6 55.8 + - - +
28B GLN* 2.7 28.6 + - - +
266B ARG* 3.3 22.1 + - - +
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Residues in contact with LYS 30 (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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26A THR* 3.2 14.2 + - + +
27A PHE 3.2 2.4 + - - +
28A GLN 3.0 0.6 - - - -
29A GLU* 1.3 77.2 - - - +
31A ASN* 1.3 69.4 + - - +
32A VAL* 3.2 3.1 + - - +
221A ALA* 4.2 17.3 - - - +
224A ALA* 3.9 24.9 - - + -
225A GLU* 3.0 28.7 + - - +
228A LYS* 2.7 37.3 + - + +
238A ALA* 4.7 11.9 + - - +
242A PHE* 3.6 39.1 - - + -
265A LEU* 4.6 9.9 - - - +
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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