Contacts of the helix formed by residues 25 - 34 (chain L) 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 THR 25 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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416K ARG* 6.0 6.7 - - - +
23L ALA 3.6 3.0 + - - +
24L LEU* 1.3 73.4 - - - +
26L PRO* 1.3 72.9 - - + +
27L GLU* 2.9 21.5 + - - +
28L GLU* 2.7 51.0 + - - +
29L ALA* 3.0 11.9 + - - +
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Residues in contact with PRO 26 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417K PHE* 4.1 20.2 - - + -
24L LEU 4.3 2.2 - - - +
25L THR* 1.3 86.7 - - + +
27L GLU* 1.3 73.4 + - - +
29L ALA* 3.4 1.6 + - + +
30L ALA 3.1 18.9 + - - -
48L PHE* 3.5 14.9 - - + -
87L LEU* 4.4 0.9 - - - +
92L VAL* 3.6 33.1 - - + +
93L ILE* 3.9 19.7 - - + -
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Residues in contact with GLU 27 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420K LYS* 4.8 17.2 + - - +
25L THR* 3.0 22.4 + - - +
26L PRO* 1.3 90.7 - - - +
28L GLU* 1.3 61.9 - - + +
30L ALA* 3.7 3.8 + - - +
31L GLU* 3.3 22.0 + - - +
34L TYR* 5.0 1.4 + - - -
48L PHE* 4.4 17.9 - - + -
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Residues in contact with GLU 28 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23L ALA 4.5 1.4 - - - +
24L LEU* 3.4 22.2 - - + +
25L THR* 2.7 45.7 + - - +
27L GLU* 1.3 75.8 - - + +
29L ALA* 1.3 64.9 + - - +
30L ALA 3.3 0.2 - - - -
31L GLU* 3.2 16.3 + - - +
32L GLU* 3.3 18.2 + - - +
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Residues in contact with ALA 29 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24L LEU* 3.7 19.9 - - + +
25L THR 3.0 14.7 + - - +
26L PRO 3.8 4.7 - - - +
28L GLU* 1.3 76.6 - - - +
30L ALA* 1.3 65.6 + - - +
31L GLU 3.4 0.5 + - - -
32L GLU* 3.5 13.0 + - - +
33L LEU* 3.6 18.0 + - - +
87L LEU* 3.9 22.0 - - + -
92L VAL* 4.5 11.4 - - + -
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Residues in contact with ALA 30 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26L PRO 3.1 17.1 + - - +
27L GLU 3.7 5.6 - - - +
29L ALA* 1.3 77.3 - - - +
31L GLU* 1.3 55.6 + - - +
33L LEU* 2.9 18.2 + - - +
34L TYR* 2.9 46.5 + - + +
48L PHE* 3.7 22.0 - - + -
83L VAL* 4.3 5.8 - - + +
87L LEU* 4.0 9.5 - - + +
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Residues in contact with GLU 31 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27L GLU 3.3 11.8 + - - +
28L GLU* 3.2 14.8 + - - +
29L ALA 3.2 0.6 - - - -
30L ALA* 1.3 79.6 - - - +
32L GLU* 1.3 62.3 + - + +
33L LEU 3.1 1.0 + - - -
34L TYR* 3.2 31.1 + - - +
41L TYR* 3.0 36.7 + - - -
45L LYS* 4.9 5.4 + - - -
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Residues in contact with GLU 32 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24L LEU* 3.6 26.7 - - + +
28L GLU 3.3 10.3 + - - +
29L ALA* 3.6 9.7 - - - +
31L GLU* 1.3 76.1 - - + +
33L LEU* 1.3 64.3 + - + +
34L TYR 5.1 0.4 - - - -
36L LYS* 4.4 10.7 + - - -
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Residues in contact with LEU 33 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29L ALA 3.6 8.9 + - - +
30L ALA 2.9 9.3 + - - +
32L GLU* 1.3 83.9 - - + +
34L TYR* 1.3 66.2 + - - +
35L PRO* 3.5 6.4 - - - +
36L LYS* 4.6 5.1 + - - +
83L VAL* 3.8 25.6 - - + +
86L ARG* 3.4 59.5 - - + +
87L LEU* 3.9 25.8 - - + -
90L GLU* 5.3 1.3 - - - +
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Residues in contact with TYR 34 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27L GLU 5.0 1.7 + - - -
30L ALA* 2.9 35.2 + - + +
31L GLU* 3.2 40.9 + - - +
32L GLU 4.9 0.3 - - - +
33L LEU* 1.3 76.7 - - - +
35L PRO* 1.4 70.9 - - + +
36L LYS* 3.3 19.6 + - - +
41L TYR* 4.0 25.1 - + + -
44L ALA* 3.7 24.9 - - + -
45L LYS* 3.6 37.9 - - + +
48L PHE* 3.1 38.4 - - + +
83L VAL* 4.6 11.7 - - + -
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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