Contacts of the helix formed by residues 33 - 42 (chain T) in PDB entry 1O7C
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 TYR 33 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32T THR* 1.3 74.5 - - - +
34T LYS* 1.3 77.3 + - + +
35T GLN 3.0 1.2 + - - -
36T LEU* 3.0 2.6 + - - -
37T GLU* 2.6 51.7 + - + +
40T ARG* 3.9 13.2 + - - -
52T MET* 4.6 14.3 - - + +
53T ALA* 5.4 1.0 - - - +
56T ARG* 4.3 25.1 - - - +
75T ILE* 3.3 56.8 + - + +
77T ASP* 4.8 7.4 - - + -
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Residues in contact with LYS 34 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32T THR* 3.8 4.1 + - - +
33T TYR* 1.3 95.0 - - + +
35T GLN* 1.3 57.8 + - + +
37T GLU* 3.1 22.9 - - - +
38T ALA* 3.0 27.9 + - - +
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Residues in contact with GLN 35 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2T VAL* 4.1 5.8 - - + +
30T LEU 3.9 3.0 + - - +
31T ALA* 3.7 3.1 - - - -
32T THR* 2.9 45.7 + - - +
33T TYR 3.0 0.6 - - - -
34T LYS* 1.3 74.9 - - + +
36T LEU* 1.3 63.2 + - - +
37T GLU 2.9 5.4 + - - -
38T ALA* 3.2 7.4 + - - +
39T ALA* 3.1 20.6 + - - +
93T TYR* 3.1 47.9 + - + -
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Residues in contact with LEU 36 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2T VAL* 3.6 9.1 - - + +
31T ALA* 4.5 2.5 - - + -
32T THR 2.9 24.2 + - - +
33T TYR 3.7 2.0 - - - +
35T GLN* 1.3 73.1 - - - +
37T GLU* 1.3 50.5 + - - +
39T ALA* 3.8 1.6 - - - -
40T ARG* 2.6 41.0 + - + +
44T PHE* 3.3 55.4 - - + +
52T MET* 5.0 2.7 - - - -
60T PRO* 3.3 38.6 - - + -
75T ILE* 3.6 7.4 - - + -
91T TYR* 3.6 21.1 - - + -
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Residues in contact with GLU 37 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33T TYR* 2.6 33.0 + - + +
34T LYS* 3.1 23.6 - - - +
35T GLN 2.9 1.2 - - - -
36T LEU* 1.3 74.4 - - - +
38T ALA* 1.3 53.6 + - - +
39T ALA 2.9 3.6 - - - -
40T ARG* 2.7 53.7 + - - +
41T LYS* 2.8 49.2 + - + +
75T ILE* 4.1 1.8 - - + -
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Residues in contact with ALA 38 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34T LYS 3.0 11.5 + - - +
35T GLN* 3.2 5.1 + - - +
37T GLU* 1.3 79.7 - - - +
39T ALA* 1.3 57.6 + - - +
41T LYS* 3.5 23.1 + - - +
42T ILE* 2.9 25.6 + - - +
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Residues in contact with ALA 39 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2T VAL* 3.7 18.6 - - + +
35T GLN 3.1 14.4 + - - +
36T LEU 3.8 1.8 - - - +
37T GLU 2.9 0.8 - - - -
38T ALA* 1.3 74.3 - - - +
40T ARG* 1.3 55.2 + - - +
41T LYS 3.2 1.3 - - - -
42T ILE* 2.5 35.9 - - + +
44T PHE* 2.8 45.9 + - + +
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Residues in contact with ARG 40 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33T TYR* 3.9 13.1 + - - -
36T LEU* 2.6 27.7 + - + +
37T GLU* 2.7 29.9 + - - +
39T ALA* 1.3 70.4 - - - +
41T LYS* 1.3 68.8 + - - +
42T ILE 3.0 4.9 - - - -
43T GLY* 3.1 10.4 + - - -
44T PHE* 3.2 20.1 + - - +
60T PRO* 5.0 2.0 - - + -
61T ILE 5.0 1.1 - - - -
62T VAL* 3.2 47.7 - - + +
74T GLY* 3.2 26.8 - - - -
75T ILE* 3.2 39.0 - - + +
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Residues in contact with LYS 41 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37T GLU* 2.8 49.4 + - + +
38T ALA* 3.5 23.7 + - - +
39T ALA 3.2 0.2 - - - -
40T ARG* 1.3 89.0 - - - +
42T ILE* 1.3 61.7 - - + +
43T GLY 3.4 0.2 - - - -
62T VAL* 4.7 4.5 - - - -
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Residues in contact with ILE 42 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38T ALA 2.9 21.3 - - - +
39T ALA* 2.5 30.7 - - + +
40T ARG 3.0 0.8 - - - -
41T LYS* 1.3 80.4 - - + +
43T GLY* 1.3 59.2 + - - +
44T PHE* 4.2 4.3 - - + +
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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