Contacts of the helix formed by residues 16 - 33 (chain A) in PDB entry 2EIT
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 THR 16 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A GLU* 4.8 1.3 + - - +
15A GLN* 1.3 84.6 - - + +
17A GLU* 1.3 65.2 + - - +
18A GLU* 3.3 21.6 + - - +
19A ALA* 3.3 22.7 + - - +
20A ARG* 3.1 25.1 + - - +
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Residues in contact with GLU 17 (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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16A THR* 1.3 73.4 - - - +
18A GLU* 1.3 69.9 + - - +
20A ARG* 3.3 16.1 + - - +
21A ARG* 2.8 87.7 + - - +
24A ARG* 4.2 13.2 + - - -
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Residues in contact with GLU 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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16A THR* 3.3 23.3 + - - +
17A GLU* 1.3 94.3 + - + +
19A ALA* 1.3 56.9 + - - +
21A ARG* 3.4 11.8 + - - +
22A ALA* 3.0 29.2 + - - +
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Residues in contact with ALA 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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12A GLU* 3.3 37.0 - - + +
14A PHE* 3.7 15.3 - - + -
16A THR* 3.2 19.3 + - - +
18A GLU* 1.3 77.3 - - - +
20A ARG* 1.3 59.3 + - - +
22A ALA* 3.4 5.5 + - - +
23A MET* 3.0 30.7 + - - +
114A ARG* 4.8 4.6 - - - +
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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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14A PHE* 3.1 31.8 + - + +
15A GLN* 4.3 22.4 + - - +
16A THR 3.1 14.4 + - - +
17A GLU* 3.7 19.2 + - - +
19A ALA* 1.3 76.4 - - - +
21A ARG* 1.3 57.8 + - - +
23A MET* 3.3 1.2 + - - +
24A ARG* 2.8 67.8 + - - +
128A TRP* 4.5 14.1 - - + -
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Residues in contact with ARG 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 59.5 + - - +
18A GLU* 3.7 10.6 - - - +
20A ARG* 1.3 76.1 - - - +
22A ALA* 1.3 61.4 + - - +
24A ARG* 3.9 8.1 - - - +
25A GLU* 3.0 24.1 + - - +
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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 GLU 3.0 17.4 + - - +
19A ALA* 3.8 6.5 - - - +
20A ARG 3.3 0.2 - - - -
21A ARG* 1.3 74.8 - - - +
23A MET* 1.3 58.2 + - - +
25A GLU* 3.4 6.8 + - - +
26A ALA* 3.0 28.2 + - - +
114A ARG* 4.1 24.4 - - + +
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Residues in contact with MET 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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14A PHE* 3.5 20.2 - - + -
19A ALA 3.0 17.9 + - - +
20A ARG 3.8 3.4 - - - +
22A ALA* 1.3 74.1 - - - +
24A ARG* 1.3 59.8 + - - +
26A ALA* 3.2 1.6 + - - -
27A LEU* 2.8 44.4 + - + +
114A ARG* 4.1 18.1 - - - +
117A GLU* 3.9 36.6 - - + +
118A ALA* 4.2 4.3 - - - +
121A VAL* 4.1 18.4 - - + -
128A TRP* 3.5 47.8 - - + +
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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* 4.2 15.4 + - - -
20A ARG* 2.8 67.6 + - - +
21A ARG* 3.9 8.7 - - - +
23A MET* 1.3 73.2 - - - +
25A GLU* 1.3 56.4 + - - +
27A LEU* 3.4 7.9 + - + +
28A ARG* 2.9 65.0 + - - +
128A TRP* 4.2 19.3 - - + -
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Residues in contact with GLU 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 ARG 3.0 16.9 + - - +
22A ALA* 3.8 6.1 - - - +
24A ARG* 1.3 76.8 - - - +
26A ALA* 1.3 57.3 + - - +
28A ARG* 3.3 17.8 + - - +
29A ARG* 2.8 73.9 + - - +
32A GLU* 5.6 0.5 - - - +
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Residues in contact with ALA 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 3.0 17.5 + - - +
23A MET* 3.2 5.8 + - - +
25A GLU* 1.3 76.1 - - - +
27A LEU* 1.3 58.3 + - - +
29A ARG* 3.4 5.6 + - - +
30A VAL* 3.0 34.8 + - - +
114A ARG* 3.5 41.5 - - + +
115A GLU* 4.0 4.5 - - - +
118A ALA* 3.7 3.6 - - + -
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Residues in contact with LEU 27 (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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23A MET* 2.8 30.5 + - + +
24A ARG* 3.8 6.3 - - + +
26A ALA* 1.3 71.8 - - - +
28A ARG* 1.3 59.2 + - + +
30A VAL 3.4 0.2 + - - -
31A ARG* 2.9 31.9 + - - +
118A ALA* 3.7 25.1 - - + -
121A VAL* 3.8 23.3 - - + -
122A TYR* 3.4 32.9 - - + +
128A TRP* 3.5 39.9 - - + +
355A GLU* 4.3 7.2 - - + +
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Residues in contact with ARG 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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24A ARG* 2.9 52.7 + - - +
25A GLU* 3.6 21.7 + - - +
27A LEU* 1.3 78.0 - - + +
29A ARG* 1.3 55.4 + - - +
31A ARG* 3.7 5.4 - - - +
32A GLU* 2.9 48.3 + - - +
122A TYR* 5.5 0.2 - - - -
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Residues in contact with ARG 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 GLU* 2.8 55.2 + - - +
26A ALA* 3.9 5.4 - - - +
27A LEU 3.3 0.2 - - - -
28A ARG* 1.3 76.6 - - + +
30A VAL* 1.3 63.6 + - + +
32A GLU* 3.2 16.5 + - - +
33A GLU* 3.2 23.2 + - - +
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Residues in contact with VAL 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 ALA 3.0 21.2 + - - +
27A LEU 3.9 3.1 - - - +
29A ARG* 1.3 76.6 - - + +
31A ARG* 1.3 63.1 + - - +
33A GLU* 3.0 27.3 + - - +
34A PHE* 3.3 16.6 + - + -
65A VAL* 5.6 3.4 - - + -
115A GLU* 3.7 13.7 - - + +
118A ALA* 3.6 17.5 - - + -
119A THR* 3.7 31.9 - - + +
122A TYR* 3.7 20.6 - - + -
218A LYS* 4.1 9.0 - - - +
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Residues in contact with ARG 31 (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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27A LEU 2.9 18.8 + - - +
28A ARG* 3.7 6.1 - - - +
30A VAL* 1.3 76.8 - - - +
32A GLU* 1.3 63.3 + - + +
33A GLU 3.2 1.2 + - - -
34A PHE* 3.2 56.9 + - - +
63A GLU* 3.7 26.2 + - - +
122A TYR* 3.9 21.0 - - + +
355A GLU* 5.4 2.7 - - - +
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Residues in contact with GLU 32 (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 GLU* 5.6 0.3 - - - +
28A ARG* 2.9 37.0 + - - +
29A ARG* 3.2 17.8 + - - +
31A ARG* 1.3 77.2 - - + +
33A GLU* 1.3 56.8 + - - +
34A PHE 3.5 2.5 + - - +
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Residues in contact with GLU 33 (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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29A ARG 3.2 9.6 + - - +
30A VAL* 3.0 20.4 + - - +
32A GLU* 1.3 77.3 - - - +
34A PHE* 1.3 66.5 + - - +
36A ARG* 2.9 58.0 + - + +
38A TYR* 3.7 6.4 + - - +
65A VAL 4.2 1.6 - - - +
115A GLU* 4.7 2.6 - - - +
218A LYS* 2.8 29.4 + - - -
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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