Contacts of the helix formed by residues 19 - 28 (chain A) in PDB entry 2EYY
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 SER 19 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A LEU* 1.3 84.1 - - - +
20A ARG* 1.3 54.2 + - - +
21A GLN* 2.5 25.4 + - - -
22A GLU* 2.4 39.6 + - - +
41A SER* 6.0 1.8 - - - -
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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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18A LEU* 3.9 2.8 + - - +
19A SER* 1.3 70.7 - - - +
21A GLN* 1.3 59.8 + - + +
23A ALA* 3.8 3.7 - - - +
24A VAL* 2.7 47.1 + - - +
38A ARG* 5.5 0.6 - - - +
56A ARG* 4.7 21.7 - - - +
57A VAL 4.4 10.5 + - - -
58A SER* 4.9 1.4 - - - +
59A HIS* 3.2 54.9 + - + +
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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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19A SER* 2.5 21.8 + - - +
20A ARG* 1.3 87.1 - - + +
22A GLU* 1.3 59.9 + - + +
24A VAL* 3.5 7.2 - - - +
25A ALA* 2.6 36.8 + - + +
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Residues in contact with GLU 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 LEU* 3.3 33.7 - - + +
19A SER* 2.4 28.7 + - - +
21A GLN* 1.3 71.4 - - + +
23A ALA* 1.3 66.4 + - - +
25A ALA* 2.9 18.4 + - + +
26A LEU* 3.0 21.4 + - + +
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Residues in contact with ALA 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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18A LEU* 3.4 17.5 - - + +
19A SER 3.3 2.0 + - - -
20A ARG 3.8 6.5 - - - +
22A GLU* 1.3 77.8 - - - +
24A VAL* 1.3 52.7 + - - +
26A LEU* 3.0 18.0 - - - +
27A LEU* 2.5 39.8 + - - +
36A LEU* 3.4 27.8 - - + -
38A ARG* 3.7 9.0 - - + +
50A SER* 4.2 7.4 - - - +
59A HIS* 4.5 1.1 - - - +
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Residues in contact with VAL 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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20A ARG* 2.7 38.5 + - - +
21A GLN* 3.5 7.6 - - - +
23A ALA* 1.3 73.4 - - - +
25A ALA* 1.3 68.1 + - - +
28A GLN* 3.0 34.8 + - + +
56A ARG* 5.1 6.1 - - + -
57A VAL* 3.1 55.4 - - + +
59A HIS* 4.2 2.7 - - + -
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Residues in contact with ALA 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 GLN* 2.6 22.4 + - + +
22A GLU* 3.0 14.4 - - + +
24A VAL* 1.3 78.0 - - - +
26A LEU* 1.3 58.7 + - - +
28A GLN* 4.6 2.9 - - - +
29A GLY* 4.0 8.7 + - - -
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Residues in contact with LEU 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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15A TRP* 4.9 0.9 - - + +
18A LEU* 5.2 0.7 - - + -
22A GLU* 3.0 33.8 + - + +
23A ALA* 3.0 22.4 - - - +
25A ALA* 1.3 75.0 - - - +
27A LEU* 1.3 52.6 + - - +
29A GLY* 2.7 21.6 + - - -
30A GLN* 2.5 26.4 + - - +
36A LEU* 3.6 14.8 - - + -
38A ARG* 4.0 13.5 - - - +
118A VAL* 3.1 38.6 - - + -
120A ARG* 4.2 36.6 - - + +
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Residues in contact with LEU 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ALA 2.5 17.8 + - - +
24A VAL 3.6 3.1 - - - +
26A LEU* 1.3 71.3 - - - +
28A GLN* 1.3 54.0 + - - +
30A GLN* 2.7 37.6 + - - +
31A ARG 4.8 0.7 - - - +
34A VAL* 4.0 16.9 - - + +
35A PHE* 4.1 1.6 - - - -
36A LEU* 3.5 32.8 - - + +
50A SER* 3.5 22.0 - - - +
52A SER* 3.9 8.7 - - - +
57A VAL* 3.1 42.0 - - + -
118A VAL* 3.3 30.5 - - + -
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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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24A VAL* 3.0 21.1 + - + +
25A ALA* 4.6 3.1 - - - +
27A LEU* 1.3 75.3 - - - +
29A GLY* 1.3 60.9 + - - +
30A GLN 3.1 9.9 + - - +
52A SER* 4.5 13.5 - - - +
55A SER* 2.5 34.4 + - - +
56A ARG* 4.4 3.6 - - - +
57A VAL* 4.4 8.4 - - + +
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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