Contacts of the helix formed by residues 19 - 27 (chain A) in PDB entry 3CEI
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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11A LYS 4.0 2.2 - - - -
15A GLY 4.9 3.4 - - - -
18A LEU* 1.3 73.6 - - - +
20A PRO* 1.3 76.5 - - - +
21A VAL* 3.6 9.0 + - - +
22A ALA* 3.1 22.2 + - - +
23A PHE* 3.2 14.4 + - - -
164A ILE* 4.4 1.7 - - - +
165A ASP* 2.8 29.7 + - - -
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Residues in contact with PRO 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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11A LYS* 3.5 34.6 - - + +
12A ASP* 3.9 19.5 - - + -
18A LEU 4.8 0.4 - - - +
19A SER* 1.3 88.1 - - - +
21A VAL* 1.3 59.7 + - + +
23A PHE* 3.1 5.5 + - - +
24A ASP* 2.9 33.1 + - - +
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Residues in contact with VAL 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* 3.2 8.4 + - - +
20A PRO* 1.3 75.5 - - + +
22A ALA* 1.3 68.4 + - - +
24A ASP* 2.8 26.3 + - - +
25A PHE* 3.0 38.5 + - + -
164A ILE* 4.5 13.9 - - + -
167B LYS* 5.2 3.8 - - - -
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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 LEU* 4.4 13.7 - - + -
19A SER* 3.1 15.9 + - - +
21A VAL* 1.3 77.4 - - - +
23A PHE* 1.3 59.5 + - + +
25A PHE* 3.4 1.4 + - - +
26A HIS* 2.8 33.8 + - + +
161A ALA 5.7 1.8 - - - +
164A ILE* 4.0 21.0 - - + +
165A ASP* 3.2 28.9 - - - +
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Residues in contact with PHE 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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7A LEU* 3.8 15.9 - - + -
9A PHE* 3.4 30.7 - + - -
11A LYS* 3.3 44.7 + - + -
14A MET* 3.6 22.2 - - + -
18A LEU* 3.7 33.7 - - + -
19A SER 3.2 18.0 + - - -
20A PRO 3.1 7.5 + - - +
21A VAL 3.0 0.4 - - - -
22A ALA* 1.3 78.4 - - + +
24A ASP* 1.3 66.5 + - - +
26A HIS* 4.5 0.7 - - + +
27A HIS* 2.9 24.7 + - - +
28A GLY 3.2 4.9 + - - -
77A TRP* 3.5 31.9 - + - -
80A LEU* 5.0 0.7 - - + -
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Residues in contact with ASP 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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11A LYS* 2.9 30.1 + - - +
20A PRO* 2.9 21.4 + - - +
21A VAL* 2.8 21.6 + - + +
23A PHE* 1.3 75.5 - - - +
25A PHE* 1.3 64.9 + - + +
28A GLY* 2.9 27.1 - - - -
29A LYS* 3.3 10.4 + - - +
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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 VAL* 3.0 39.0 + - + -
22A ALA 3.9 4.0 - - - +
24A ASP* 1.3 81.2 - - + +
26A HIS* 1.3 62.1 + - - +
29A LYS* 3.0 34.8 + - + +
30A HIS* 2.9 30.0 + - - -
164A ILE* 3.9 14.4 - - + -
163B TYR* 4.0 13.2 - - - +
167B LYS* 3.5 34.5 - - + -
168B ASN* 3.3 32.1 - - - -
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Residues in contact with HIS 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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18A LEU* 6.0 2.4 - - - +
22A ALA* 2.8 24.2 + - + +
23A PHE* 4.5 0.9 - - + +
25A PHE* 1.3 72.2 - - - +
27A HIS* 1.3 57.4 + - - +
30A HIS* 3.2 14.2 - - + +
31A HIS* 2.9 26.3 + - - +
73A HIS* 2.8 15.5 + + - -
76A TYR* 3.9 17.7 + + - -
77A TRP* 3.5 18.2 - + + -
156A ASP* 2.8 18.6 + - - -
160A HIS* 3.0 20.8 + + - +
161A ALA* 3.5 29.2 + - + +
500A FE 2.1 26.2 - - - -
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Residues in contact with HIS 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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4A LEU* 3.5 36.3 - - + +
5A ARG 2.8 27.2 + - - -
6A GLU* 5.1 1.1 - - - -
7A LEU* 3.5 45.2 + - + +
11A LYS* 4.8 8.9 + - - -
23A PHE 2.9 11.4 + - - +
26A HIS* 1.3 77.9 - - - +
28A GLY* 1.3 69.0 + - - +
31A HIS* 3.2 8.5 - + - +
32A GLN 3.1 22.3 + - - -
77A TRP* 3.7 27.4 - + + -
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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