Contacts of the helix formed by residues 15 - 21 (chain J) in PDB entry 2I2X
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 ARG 15 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233I LEU* 3.6 16.3 - - + +
240I HIS* 4.2 1.0 + - - -
362I TYR 3.8 16.4 - - - +
363I ARG 2.9 28.9 + - - +
364I ASP* 3.0 25.4 + - - +
365I PRO* 3.7 9.6 - - - +
412I LEU* 4.8 4.0 - - - -
413I GLU* 2.9 45.1 + - + +
414I LEU* 3.9 5.7 - - - +
418I GLU* 2.9 38.6 + - - -
13J LEU* 4.4 6.4 - - + +
14J THR* 1.3 72.8 - - - +
16J TYR* 1.3 63.2 + - - +
17J ASN* 2.9 25.2 + - - +
18J VAL* 2.9 26.5 + - + +
19J ALA 4.3 0.9 + - - -
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Residues in contact with TYR 16 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233I LEU* 4.4 2.8 - - + +
234I LEU* 4.2 7.0 - - + -
14J THR* 2.9 48.8 + - + -
15J ARG* 1.3 70.4 - - - +
17J ASN* 1.3 60.8 + - - +
18J VAL 3.2 1.1 + - - -
19J ALA* 3.8 9.8 + - - +
20J LEU* 3.7 18.7 + - - +
74K VAL* 3.3 42.2 - - + +
77K GLY* 3.7 10.1 - - - -
78K PHE 2.7 28.4 + - - -
79K PRO* 3.5 9.5 - - - +
116K TYR* 3.3 55.5 - + + -
117K GLY 4.7 0.7 - - - -
118K ILE* 3.4 19.9 - - - +
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Residues in contact with ASN 17 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233I LEU* 3.2 35.8 - - - +
234I LEU* 3.8 14.4 - - + +
415I SER* 4.4 7.9 + - - -
418I GLU* 3.7 25.1 - - - +
15J ARG* 3.1 35.2 + - - +
16J TYR* 1.3 74.9 - - - +
18J VAL* 1.3 64.7 + - - +
20J LEU* 3.2 14.2 + - - +
21J GLU* 3.2 15.2 + - - +
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Residues in contact with VAL 18 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413I GLU* 3.5 55.6 - - + +
414I LEU 4.1 18.8 - - - +
415I SER* 4.1 10.7 - - - +
416I ARG* 5.2 3.1 + - - -
15J ARG* 2.9 21.7 + - + +
17J ASN* 1.3 89.2 - - - +
19J ALA* 1.3 61.6 + - - +
20J LEU 3.3 0.5 + - - -
21J GLU* 3.5 15.2 + - - +
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Residues in contact with ALA 19 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15J ARG 4.3 1.2 + - - -
16J TYR* 3.8 8.3 + - - +
17J ASN 3.5 0.4 - - - -
18J VAL* 1.3 79.7 - - - +
20J LEU* 1.3 64.3 + - + +
21J GLU 3.4 4.2 + - - +
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Residues in contact with LEU 20 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234I LEU* 4.3 11.4 - - + -
16J TYR 3.7 12.1 - - - +
17J ASN* 3.2 9.8 + - - +
19J ALA* 1.3 81.6 - - + +
21J GLU* 1.3 65.4 + - - +
22J LYS* 3.3 9.0 + - - +
115K GLU* 3.8 33.4 - - + +
116K TYR* 3.5 33.4 - - + +
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Residues in contact with GLU 21 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415I SER* 3.4 11.2 - - - -
416I ARG* 2.8 66.5 + - - +
417I PHE* 2.7 37.8 + - - +
17J ASN 3.2 10.6 + - - +
18J VAL 3.8 12.1 - - - +
19J ALA 3.4 5.5 - - - +
20J LEU* 1.3 78.1 - - - +
22J LYS* 1.3 67.3 + - - +
23J ALA 3.9 0.2 + - - -
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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