Contacts of the helix formed by residues 15 - 20 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233C LEU* 3.9 15.3 - - + +
240C HIS* 4.5 0.2 + - - -
362C TYR 3.5 18.2 - - - +
363C ARG 2.6 28.3 + - - +
364C ASP* 2.9 26.2 + - - +
365C PRO* 3.7 10.5 - - - +
412C LEU* 5.1 1.8 - - - -
413C GLU* 2.7 55.3 + - + +
414C LEU* 3.8 2.2 - - - +
418C GLU* 2.9 37.4 + - - -
13D LEU* 4.2 6.9 - - + +
14D THR* 1.3 72.2 - - - +
16D TYR* 1.3 53.5 + - - +
17D ASN* 2.8 37.6 + - - +
18D VAL* 2.9 24.9 + - + +
19D ALA* 4.3 1.4 + - - +
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Residues in contact with TYR 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A VAL* 3.3 36.6 - - + +
77A GLY* 3.7 11.0 - - - -
78A PHE 2.6 29.4 + - - -
79A PRO* 3.4 10.7 - - - +
116A TYR* 3.3 55.1 - - + -
117A GLY 4.6 0.9 - - - -
118A ILE* 3.4 24.3 - - + +
233C LEU* 4.7 2.6 - - + +
234C LEU* 4.0 7.2 - - + -
14D THR* 2.9 50.4 + - + -
15D ARG* 1.3 70.7 - - - +
17D ASN* 1.3 60.7 + - - +
18D VAL 3.3 0.6 + - - -
19D ALA* 3.9 8.7 + - - +
20D LEU* 3.8 19.9 + - - +
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Residues in contact with ASN 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233C LEU* 3.1 41.3 - - - +
234C LEU* 3.8 12.8 - - + +
415C SER* 4.3 8.0 + - - -
418C GLU* 3.7 23.2 - - - +
15D ARG* 3.3 37.8 + - - +
16D TYR* 1.3 72.9 - - - +
18D VAL* 1.3 68.5 + - - +
20D LEU* 3.4 12.0 + - - +
21D GLU* 3.5 11.6 + - - +
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Residues in contact with VAL 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413C GLU* 3.4 53.8 - - + +
414C LEU 4.1 8.3 - - - +
415C SER* 4.0 19.3 - - - +
416C ARG* 5.6 2.8 + - - -
15D ARG* 2.9 31.3 + - + +
17D ASN* 1.3 80.6 - - - +
19D ALA* 1.3 61.4 + - - +
20D LEU 3.4 0.2 + - - -
21D GLU* 3.5 16.7 + - - +
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Residues in contact with ALA 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D ARG 4.3 1.6 + - - -
16D TYR* 3.9 6.7 + - - +
17D ASN 3.4 0.4 - - - -
18D VAL* 1.3 80.6 - - - +
20D LEU* 1.3 63.5 + - + +
21D GLU 3.4 4.7 + - - +
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Residues in contact with LEU 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A GLU* 3.9 38.1 - - - +
116A TYR* 3.6 32.3 - - + +
234C LEU* 4.2 9.9 - - + -
16D TYR 3.8 12.5 + - - +
17D ASN* 3.4 9.2 + - - +
18D VAL 3.3 0.6 - - - -
19D ALA* 1.3 80.2 - - + +
21D GLU* 1.3 62.6 + - - +
22D LYS* 3.5 7.3 + - - +
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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