Contacts of the helix formed by residues 42 - 52 (chain L) in PDB entry 1O1F
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 42 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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788J THR* 1.7 65.5 - - + +
791J GLN* 5.6 0.7 - - + -
792J ALA* 5.4 1.1 - - - +
35L ARG* 4.1 5.2 - - - +
40L ASN 4.9 0.2 - - - +
41L PRO* 1.3 75.5 - - - +
43L ASN* 1.3 59.1 + - - +
44L ALA* 3.9 3.3 + - - +
45L GLU* 3.0 39.6 + - - +
46L ILE* 3.1 11.5 + - - +
81L GLN* 4.5 2.2 - - - +
116L GLU* 3.7 15.7 + - - +
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Residues in contact with ASN 43 (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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795J ARG* 1.5 66.0 + - - +
31L GLY* 5.5 2.6 - - - -
32L ASP* 5.5 3.0 + - - -
35L ARG* 3.6 10.9 - - - +
42L THR* 1.3 72.9 - - - +
44L ALA* 1.3 57.0 + - - +
46L ILE* 3.3 17.2 + - - +
47L ASN* 2.9 29.3 + - - +
116L GLU* 3.2 5.3 + - + +
118L MET* 5.2 0.2 - - - +
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Residues in contact with ALA 44 (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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42L THR* 3.2 4.0 - - - +
43L ASN* 1.3 77.4 - - - +
45L GLU* 1.3 56.3 + - - +
47L ASN* 3.5 7.6 - - - +
48L LYS* 2.8 36.1 + - + +
116L GLU* 3.0 16.4 + - + +
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Residues in contact with GLU 45 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788J THR* 4.9 1.2 - - - +
41L PRO* 3.5 22.1 - - + +
42L THR* 3.0 35.7 + - - +
44L ALA* 1.3 78.0 - - - +
46L ILE* 1.3 59.5 + - - +
47L ASN 3.2 0.2 - - - -
48L LYS* 3.9 4.2 - - - +
49L ILE* 2.8 50.4 + - + +
75L ALA* 5.0 0.7 - - - -
78L ASN* 2.9 36.8 + - - +
81L GLN* 5.2 5.7 + - - +
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Residues in contact with ILE 46 (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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30L VAL* 5.0 6.1 - - + -
31L GLY* 3.7 40.2 - - - +
34L ALA* 5.7 0.2 - - + -
35L ARG* 4.7 1.3 - - - +
41L PRO* 3.4 42.6 - - + +
42L THR 3.1 10.5 + - - +
43L ASN* 3.6 22.7 - - - +
45L GLU* 1.3 77.1 - - - +
47L ASN* 1.3 52.7 - - - +
49L ILE* 4.2 6.0 - - + +
50L LEU* 2.5 54.1 + - + +
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Residues in contact with ASN 47 (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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43L ASN 2.9 17.1 + - - +
44L ALA* 3.5 9.8 - - - +
46L ILE* 1.3 76.4 - - - +
48L LYS* 1.3 76.3 + - - +
50L LEU* 3.4 8.9 - - - +
51L GLY* 3.1 19.1 + - - -
57L GLU* 3.6 18.5 - - - +
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Residues in contact with LYS 48 (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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44L ALA* 2.8 21.4 + - + +
45L GLU* 3.9 6.3 - - - +
46L ILE 3.5 0.2 - - - -
47L ASN* 1.3 87.1 - - - +
49L ILE* 1.3 54.8 + - + +
51L GLY* 3.1 3.0 + - - -
52L ASN* 1.9 61.2 + - - +
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Residues in contact with ILE 49 (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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41L PRO* 6.1 0.9 - - + -
45L GLU* 2.8 42.6 + - + +
46L ILE* 4.2 7.0 - - + +
48L LYS* 1.3 77.4 - - + +
50L LEU* 1.3 54.1 - - + +
52L ASN* 2.3 15.1 - - - +
53L PRO* 1.6 48.8 - - + +
71L MET* 5.5 15.3 - - + +
74L ALA* 5.6 13.0 - - + -
75L ALA* 5.6 9.0 - - + -
78L ASN* 5.4 4.7 - - - +
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Residues in contact with LEU 50 (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 ALA* 4.9 15.7 - - + +
30L VAL* 5.5 5.8 - - + -
46L ILE* 2.5 43.3 - - + +
47L ASN* 3.4 6.1 - - - +
49L ILE* 1.3 80.8 - - + +
51L GLY* 1.3 55.9 + - - +
53L PRO* 2.6 24.1 - - - +
55L LYS* 2.9 37.5 + - + +
57L GLU* 0.9 52.0 - - + +
63L ILE* 6.4 0.9 - - + -
71L MET* 4.7 22.2 - - + -
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Residues in contact with GLY 51 (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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47L ASN 3.1 7.3 + - - -
48L LYS* 3.1 6.1 + - - -
50L LEU* 1.3 76.7 - - - +
52L ASN* 1.3 59.3 + - - +
54L SER* 2.7 24.8 + - - -
55L LYS 3.6 11.2 + - - -
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Residues in contact with ASN 52 (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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48L LYS* 1.9 68.6 + - - +
49L ILE* 2.3 14.2 - - + +
51L GLY* 1.3 72.5 - - - +
53L PRO* 1.3 64.9 - - + +
54L SER* 3.3 3.1 + - - -
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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