Contacts of the helix formed by residues 35 - 45 (chain C) in PDB entry 2OOR
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 SER 35 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34C GLY* 1.3 74.1 - - - -
36C ALA* 1.3 60.7 + - - +
37C GLU* 3.8 12.1 + - - +
38C ASP* 3.3 28.9 + - - +
39C ALA* 2.9 32.1 + - - +
187C LEU* 4.8 0.9 - - - -
194C MET* 4.6 8.3 - - - -
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Residues in contact with ALA 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C SER* 1.3 73.2 - - - +
37C GLU* 1.3 70.2 + - - +
40C ALA* 3.2 25.3 + - - +
194C MET* 4.1 14.0 - - + +
197C GLN* 3.6 41.9 - - + +
198C ILE* 3.7 26.2 - - + +
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Residues in contact with GLU 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C SER* 3.2 11.0 + - - +
36C ALA* 1.3 84.9 + - - +
38C ASP* 1.3 70.9 + - - +
40C ALA* 3.3 13.5 + - - +
41C PHE* 3.2 23.2 - - + -
197C GLN 6.1 0.7 - - - -
201C ALA* 4.9 11.5 - - + +
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Residues in contact with ASP 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C GLY* 4.8 2.4 - - - -
35C SER* 3.3 23.6 + - - +
37C GLU* 1.3 81.8 - - - +
39C ALA* 1.3 61.7 + - - +
40C ALA 3.5 0.7 + - - -
41C PHE* 3.8 26.1 - - + -
42C ILE* 3.2 22.7 + - - +
185C MET* 3.4 21.2 - - + +
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Residues in contact with ALA 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C SER 2.9 18.6 + - - +
36C ALA 4.2 3.1 - - - +
38C ASP* 1.3 76.7 - - - +
40C ALA* 1.3 62.3 + - - +
42C ILE* 3.8 6.9 - - - +
43C MET* 3.8 8.7 - - - +
161C LEU* 3.6 21.8 - - + +
185C MET* 3.8 11.6 - - - +
187C LEU* 3.6 37.0 - - + -
198C ILE* 4.4 8.5 - - + -
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Residues in contact with ALA 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C ALA 3.2 19.0 + - - +
37C GLU 3.6 6.7 - - - +
38C ASP 3.3 1.0 - - - -
39C ALA* 1.3 78.7 - - - +
41C PHE* 1.3 59.9 + - - +
43C MET* 3.1 21.1 + - - +
44C LYS* 3.4 13.8 + - + +
198C ILE* 3.8 24.5 - - - +
201C ALA* 3.6 26.2 - - + -
202C MET* 4.1 8.1 - - + +
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Residues in contact with PHE 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C GLU* 3.2 29.2 - - + -
38C ASP* 3.8 29.8 - - + -
40C ALA* 1.3 75.8 - - + +
42C ILE* 1.3 74.3 + - + +
43C MET 3.2 1.6 - - - -
44C LYS* 3.3 26.6 + - + +
45C ASN* 3.8 11.8 + - - +
201C ALA* 6.2 1.8 - - + -
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Residues in contact with ILE 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C ASP 3.2 20.4 - - - +
39C ALA* 3.8 8.7 + - - +
40C ALA 3.3 0.4 - - - -
41C PHE* 1.3 89.2 - - + +
43C MET* 1.3 55.6 + - - +
45C ASN 4.3 1.9 + - - +
46C ALA* 3.3 19.4 + - - +
124C VAL* 3.8 12.5 - - + +
159C THR* 3.8 29.4 - - + +
161C LEU* 4.3 10.8 - - + -
185C MET* 3.6 31.9 - - + -
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Residues in contact with MET 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C ALA 3.8 6.1 - - - +
40C ALA 3.1 8.3 + - - +
42C ILE* 1.3 74.8 - - - +
44C LYS* 1.3 65.0 + - - +
45C ASN 3.4 1.1 - - - -
46C ALA* 3.1 14.7 - - - +
49C VAL* 3.5 34.5 - - + +
69C MET* 3.6 30.7 - - + +
73C LEU* 3.2 27.5 - - + +
78C VAL* 4.3 1.6 - - - +
124C VAL* 4.2 13.7 - - + -
126C PHE* 3.5 37.2 - - + -
161C LEU* 3.7 22.4 - - + -
198C ILE* 5.0 2.9 - - - -
202C MET* 4.6 5.2 - - + -
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Residues in contact with LYS 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C ALA* 3.7 13.9 - - + +
41C PHE* 3.3 20.5 + - + +
43C MET* 1.3 78.2 - - - +
45C ASN* 1.3 73.0 + - - +
46C ALA 3.9 4.3 - - - +
72C VAL* 5.4 2.1 - - + +
73C LEU* 4.5 5.1 - - + +
76C GLU* 4.6 29.1 + - + +
78C VAL* 3.9 10.4 - - - +
201C ALA 4.7 5.1 + - - +
202C MET* 3.7 54.9 + - + +
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Residues in contact with ASN 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C PHE 3.8 9.5 + - - +
42C ILE 4.4 3.6 - - - +
43C MET 3.4 0.8 - - - -
44C LYS* 1.3 91.3 - - - +
46C ALA* 1.3 58.7 + - - +
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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