Contacts of the helix formed by residues 15 - 23 (chain A) in PDB entry 4EEJ
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 ASN 15 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A ASN 4.1 1.2 + - - -
14A GLU* 1.3 81.8 - - + +
16A PHE* 1.3 64.6 + - - +
17A GLU* 3.2 3.8 - - - +
18A GLY* 3.2 19.8 + - - -
19A TRP* 3.1 16.8 + - - +
124A GLN* 2.9 25.8 + - - +
125A VAL 3.0 29.4 + - - +
126A CYS* 3.7 1.9 - - - +
127A ARG* 6.3 0.2 - - - +
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Residues in contact with PHE 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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13A ASN* 3.4 28.2 - - - +
14A GLU 3.3 3.0 - - - -
15A ASN* 1.3 76.3 - - - +
17A GLU* 1.3 62.9 + - - +
19A TRP* 3.3 27.6 + + - +
20A MET* 3.0 46.7 + - + +
33A ALA 3.5 20.2 - - - -
34A VAL* 3.5 19.1 - - + +
36A LEU 5.9 0.2 - - - -
38A GLN* 3.4 22.0 - - - -
119A LEU* 4.6 1.3 - - + -
126A CYS* 3.7 12.1 - - - -
128A GLN* 3.7 21.5 - - - -
201A RET 3.7 31.4 - - + -
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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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15A ASN* 3.2 2.1 - - - +
16A PHE* 1.3 80.6 - - - +
18A GLY* 1.3 60.1 + - - +
20A MET* 3.3 7.7 + - - +
21A LYS* 2.9 43.9 + - - +
27A PHE* 5.3 2.1 - - - -
30A ARG* 3.0 52.6 + - - +
34A VAL* 4.0 20.3 - - + +
35A ARG* 6.1 0.9 - - - +
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Residues in contact with GLY 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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15A ASN* 3.2 24.0 + - - -
17A GLU* 1.3 81.7 - - - +
19A TRP* 1.3 54.6 + - - +
21A LYS* 3.5 8.6 + - - +
22A ALA 2.9 22.9 + - - -
124A GLN* 3.5 23.8 - - - +
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Residues in contact with TRP 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 ASN 3.1 6.9 + - - +
16A PHE* 3.7 29.4 - + - +
18A GLY* 1.3 74.3 - - - +
20A MET* 1.4 82.9 + - + +
22A ALA* 3.2 4.2 + - - +
23A LEU* 3.1 46.2 + - + +
77A LEU* 4.6 5.4 - - + -
104A ARG* 5.8 2.2 - - - +
105A GLY 5.1 0.6 + - - -
119A LEU* 3.6 44.8 - - + +
120A THR 3.6 26.0 + - - +
121A CYS* 3.8 10.3 - - + +
124A GLN* 4.1 12.2 - - + +
126A CYS* 3.6 25.1 - - + +
201A RET 3.7 41.1 - - + -
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Residues in contact with MET 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 PHE* 3.0 45.5 + - + +
17A GLU* 3.9 6.7 - - - +
19A TRP* 1.4 94.9 - - + +
21A LYS* 1.3 63.9 + - - +
23A LEU* 3.2 4.4 + - - +
24A ASP 3.1 4.9 + - - -
25A ILE* 3.1 40.6 + - + +
30A ARG* 3.5 49.4 - - + +
33A ALA* 4.0 13.9 - - - -
34A VAL* 3.9 10.5 - - + +
201A RET 4.0 19.1 - - - -
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Residues in contact with LYS 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* 2.9 28.3 + - - +
18A GLY* 3.8 7.9 - - - +
20A MET* 1.3 78.4 - - - +
22A ALA* 1.3 56.9 + - - +
24A ASP* 2.9 25.8 + - - +
30A ARG* 3.1 44.1 - - - +
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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 GLY 2.9 17.4 + - - +
19A TRP 3.2 6.3 + - - +
21A LYS* 1.3 76.3 - - - +
23A LEU* 1.3 52.1 + - - +
24A ASP* 3.9 0.2 - - - +
101A LYS* 2.7 36.9 + - - +
121A CYS* 3.7 24.0 - - + +
122A GLY* 5.5 1.1 - - - -
123A ASP* 5.4 0.9 - - - +
124A GLN* 3.7 20.4 - - + -
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Residues in contact with LEU 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 TRP* 3.1 51.4 + - + +
20A MET 3.2 7.4 + - - +
22A ALA* 1.3 76.1 - - - +
24A ASP* 1.3 64.8 + - - +
25A ILE* 4.1 15.0 - - + -
77A LEU* 5.4 2.5 - - + -
78A ASP* 3.3 18.2 - - + +
80A ARG* 2.9 25.1 + - - +
101A LYS* 4.4 2.2 - - + +
104A ARG* 3.4 44.4 - - + +
121A CYS* 3.6 25.8 - - + -
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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