Contacts of the helix formed by residues 25 - 34 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416G ARG* 5.3 11.9 - - - +
23H ALA 5.0 2.5 - - - +
24H LEU* 1.3 75.9 - - - +
26H PRO* 1.4 75.7 - - - +
27H GLU* 3.5 18.2 + - - +
28H GLU* 3.0 40.3 + - - +
29H ALA* 2.8 22.2 + - - +
92H VAL* 5.8 0.9 - - - -
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Residues in contact with PRO 26 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417G PHE* 4.2 20.9 - - + -
420G LYS* 6.3 3.8 - - + -
24H LEU 4.5 2.0 - - - +
25H THR* 1.4 87.9 - - - +
27H GLU* 1.3 74.8 + - - +
29H ALA* 3.2 2.1 + - - +
30H ALA* 2.9 30.7 + - - +
48H PHE* 4.0 12.0 - - + -
87H LEU* 4.3 1.4 - - - +
92H VAL* 4.0 32.1 - - + +
93H ILE* 4.1 16.4 - - + -
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Residues in contact with GLU 27 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420G LYS* 3.9 26.1 - - - +
25H THR* 3.1 16.6 + - - +
26H PRO* 1.3 96.8 - - - +
28H GLU* 1.3 59.8 + - + +
30H ALA* 3.5 6.0 + - - +
31H GLU* 3.1 28.4 + - - +
34H TYR* 5.3 1.7 + - - -
48H PHE* 4.6 12.3 - - + -
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Residues in contact with GLU 28 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23H ALA 4.7 0.7 - - - +
24H LEU* 3.8 21.2 - - + +
25H THR* 3.0 44.1 + - - +
27H GLU* 1.3 81.0 - - + +
29H ALA* 1.3 61.4 + - - +
31H GLU* 3.4 21.1 + - - +
32H GLU* 3.6 12.3 + - - +
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Residues in contact with ALA 29 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22H LYS* 6.5 0.2 - - + -
24H LEU* 3.8 22.4 - - + +
25H THR 2.8 16.2 + - - +
26H PRO 3.8 3.1 - - - +
28H GLU* 1.3 73.8 - - - +
30H ALA* 1.3 62.6 + - - +
32H GLU* 3.8 11.0 + - - +
33H LEU* 3.3 24.1 + - - +
87H LEU* 3.8 18.8 - - + -
90H GLU* 5.8 0.7 - - - +
92H VAL* 4.7 11.4 - - + -
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Residues in contact with ALA 30 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26H PRO 2.9 16.8 + - - +
27H GLU* 3.7 5.4 - - - +
29H ALA* 1.3 75.2 - - - +
31H GLU* 1.3 63.8 + - - +
33H LEU* 3.2 3.3 + - - +
34H TYR* 3.1 53.1 + - + +
48H PHE* 3.8 14.8 - - + -
83H VAL* 4.2 4.4 - - + +
87H LEU* 3.8 20.6 - - + +
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Residues in contact with GLU 31 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27H GLU 3.1 14.0 + - - +
28H GLU* 3.4 14.1 - - - +
30H ALA* 1.3 77.6 - - - +
32H GLU* 1.3 62.6 + - + +
33H LEU 3.3 1.2 + - - -
34H TYR* 3.3 27.4 + - - +
41H TYR* 2.6 38.9 + - - -
45H LYS* 4.9 5.5 + - - -
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Residues in contact with GLU 32 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24H LEU* 3.4 28.4 - - + +
28H GLU 3.6 11.2 + - - +
29H ALA* 3.9 9.5 - - - +
30H ALA 3.3 0.6 - - - -
31H GLU* 1.3 76.6 - - + +
33H LEU* 1.3 68.8 + - + +
34H TYR 4.6 0.7 - - - +
36H LYS* 4.6 8.5 + - - -
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Residues in contact with LEU 33 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29H ALA 3.3 11.7 - - - +
30H ALA 3.2 4.8 + - - +
31H GLU 3.2 0.6 - - - -
32H GLU* 1.3 85.0 - - + +
34H TYR* 1.3 68.1 + - - +
35H PRO* 3.7 2.9 - - - +
36H LYS* 4.2 6.4 + - - +
79H VAL* 5.8 0.9 - - - +
83H VAL* 4.1 22.0 - - + +
86H ARG* 3.5 55.0 - - + +
87H LEU* 3.7 34.5 - - + -
90H GLU* 5.2 2.0 - - - +
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Residues in contact with TYR 34 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27H GLU* 5.3 1.4 + - - -
30H ALA* 3.1 35.6 + - + +
31H GLU* 3.3 34.2 + - - +
32H GLU 4.6 0.7 - - - +
33H LEU* 1.3 76.9 - - - +
35H PRO* 1.4 73.7 - - + +
36H LYS* 3.0 22.1 + - - +
41H TYR* 3.5 35.0 - + + -
44H ALA* 3.8 22.7 - - + -
45H LYS* 3.3 39.7 - - + +
48H PHE* 3.6 22.8 - - + -
83H VAL* 4.3 18.8 - - + -
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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