Contacts of the helix formed by residues 29 - 33 (chain D) in PDB entry 5X11
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 GLU 29 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C TYR* 3.0 27.1 + - + -
25D TYR* 5.1 2.9 - - - -
28D GLU* 1.3 88.3 - - - +
30D LEU* 1.3 67.8 + - - +
31D GLY 3.0 1.9 + - - -
32D GLN* 3.2 25.1 + - + +
33D PHE* 4.4 1.0 - - - -
154D HIS* 3.0 45.8 + - + +
157D VAL* 3.6 31.2 - - + +
158D LEU* 4.8 12.8 - - + -
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Residues in contact with LEU 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C LEU* 3.6 37.0 - - + +
103C TYR* 3.6 49.1 - - + +
104C PHE* 4.6 2.2 - - + -
7D ALA* 5.4 0.2 - - + -
11D LEU* 4.2 15.9 - - + -
25D TYR 3.7 15.0 + - - +
26D PHE* 3.9 26.5 - - + -
28D GLU 3.4 0.4 - - - -
29D GLU* 1.3 82.8 - - - +
31D GLY* 1.3 58.0 + - - +
33D PHE* 2.9 27.2 + - + -
34D TRP* 2.9 16.1 + - + +
157D VAL* 4.7 7.6 - - + -
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Residues in contact with GLY 31 (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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92C GLU* 4.2 3.8 - - - +
93C THR* 2.6 32.9 + - - +
26D PHE 3.1 25.0 + - - -
27D LYS 4.9 0.9 - - - -
28D GLU 3.2 11.4 + - - -
29D GLU 3.0 2.0 - - - -
30D LEU* 1.3 78.0 - - - +
32D GLN* 1.3 59.6 + - - +
33D PHE 3.4 0.3 + - - -
34D TRP 3.5 4.9 - - - -
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Residues in contact with GLN 32 (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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92C GLU* 3.9 17.2 + - - +
94C VAL 3.0 24.6 + - - +
28D GLU 4.4 2.4 + - - +
29D GLU* 3.2 14.9 + - + +
30D LEU 3.0 1.4 + - - -
31D GLY* 1.3 77.6 - - - +
33D PHE* 1.3 78.0 - - + +
127D LYS* 3.6 23.4 + - - +
131D LEU* 4.1 24.3 - - + +
158D LEU* 6.3 0.2 - - + -
161D ALA* 3.9 17.9 - - + +
164D ARG* 3.0 28.6 + - - +
165D GLU* 5.2 0.7 - - - +
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Residues in contact with PHE 33 (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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93C THR* 4.0 5.4 - - - -
94C VAL 3.9 2.9 - - - -
95C LYS* 3.3 4.7 - - - -
96C ASP* 3.0 36.2 + - + +
99C MET* 3.5 39.9 - - + -
100C LEU* 5.0 1.3 - - - +
29D GLU 4.4 3.6 - - - -
30D LEU* 2.9 9.0 + - + +
32D GLN* 1.3 95.1 - - + +
34D TRP* 1.3 67.6 + - - +
157D VAL* 3.2 40.8 - - + -
160D LYS* 3.8 13.9 - - + -
161D ALA* 3.5 29.6 - - + -
164D ARG* 3.6 31.0 - - - -
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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