Contacts of the helix formed by residues 38 - 50 (chain C) in PDB entry 1ORR
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 GLY 38 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36C ARG* 3.1 0.6 + - - -
37C LYS* 1.4 73.3 - - - +
39C ALA* 1.3 59.7 + - - +
40C THR 3.2 3.2 - - - +
41C ASP* 3.1 25.4 + - - +
42C ASN* 2.8 32.8 + - - +
201C PHE* 3.6 25.1 - - - -
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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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10C CYS* 3.4 37.3 - - + +
34C LEU* 3.9 25.1 - - - -
36C ARG* 2.9 22.0 + - + +
37C LYS 3.4 0.6 + - - -
38C GLY* 1.3 76.9 - - - +
40C THR* 1.3 57.9 + - - +
42C ASN 3.2 0.5 + - - -
43C LEU* 2.8 26.9 + - - +
1400C NAD 4.0 11.2 - - - +
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Residues in contact with THR 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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34C LEU* 4.3 19.3 + - + +
36C ARG 4.7 0.2 + - - -
38C GLY* 3.2 1.6 - - - +
39C ALA* 1.3 79.2 - - - +
41C ASP* 1.3 64.0 + - - +
43C LEU* 3.2 8.8 + - + +
44C HIS* 3.0 49.2 + - + +
34D LEU* 4.7 4.9 - - - +
40D THR* 3.7 37.3 - - + +
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Residues in contact with ASP 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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38C GLY* 3.1 27.9 + - - +
40C THR* 1.3 74.3 + - - +
42C ASN* 1.3 62.0 + - - +
44C HIS* 3.1 13.6 + - - +
45C TRP* 2.8 30.1 + - - +
199C ARG* 3.9 5.7 + - - +
201C PHE* 4.2 18.3 - - + -
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Residues in contact with ASN 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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10C CYS 3.0 31.7 + - - +
11C GLY* 3.5 11.9 + - - -
15C SER* 3.5 14.3 + - - -
38C GLY 2.8 14.4 + - - +
39C ALA 3.5 0.9 - - - +
41C ASP* 1.3 78.4 - - - +
43C LEU* 1.3 63.0 + - - +
45C TRP* 3.2 3.5 + - - +
46C LEU* 2.9 29.5 + - - +
199C ARG* 2.8 56.1 + - - +
201C PHE* 3.4 12.1 - - - -
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Residues in contact with LEU 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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10C CYS* 3.8 14.5 - - - +
34C LEU* 4.3 13.7 - - + -
39C ALA 2.8 14.7 + - - +
40C THR* 3.5 12.1 - - + +
42C ASN* 1.3 78.5 - - - +
44C HIS* 1.3 65.2 + - + +
46C LEU* 3.3 5.2 + - + +
47C SER* 2.9 37.6 + - - +
52C PHE* 3.8 24.7 - - + -
54C PHE* 4.0 48.9 - - + -
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Residues in contact with HIS 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 THR* 3.0 41.6 + - + +
41C ASP* 3.1 12.9 + - - +
43C LEU* 1.3 85.4 - - + +
45C TRP* 1.3 63.9 + - - +
47C SER* 3.4 9.1 + - - -
48C SER* 3.3 18.9 + - - -
40D THR* 4.5 8.1 + - - -
41D ASP* 5.1 8.5 + - - -
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Residues in contact with TRP 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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15C SER* 3.7 24.0 - - - -
16C ASN* 5.0 3.8 - - - -
19C SER* 3.8 21.1 - - - -
41C ASP 2.8 16.3 + - - +
42C ASN 3.5 5.6 - - - +
44C HIS* 1.3 74.7 - - - +
46C LEU* 1.3 82.6 + - + +
48C SER* 2.7 32.0 + - - -
49C LEU* 3.4 29.4 + - + +
199C ARG* 3.4 63.0 - - + +
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Residues in contact with LEU 46 (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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9C GLY 3.8 23.1 - - - +
10C CYS* 4.9 3.6 - - - -
15C SER* 3.6 27.4 - - - +
18C ALA* 3.9 13.2 - - + -
19C SER* 3.9 17.3 - - - +
22C LEU* 3.7 6.8 - - + +
30C VAL* 4.8 4.9 - - + -
42C ASN 2.9 23.1 + - - +
43C LEU* 3.7 7.9 - - - +
45C TRP* 1.3 91.1 - - + +
47C SER* 1.3 59.4 + - - +
49C LEU* 2.7 27.5 + - + +
50C GLY 3.2 10.7 + - - +
52C PHE* 3.7 24.0 - - + -
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Residues in contact with SER 47 (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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43C LEU* 2.9 23.6 + - - +
44C HIS* 3.7 9.7 - - - -
45C TRP 3.2 0.4 - - - -
46C LEU* 1.3 76.8 - - - +
48C SER* 1.3 60.9 + - - +
50C GLY 3.3 20.2 + - - +
51C ASN* 5.3 1.6 - - - +
52C PHE* 4.0 12.5 - - - -
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Residues in contact with SER 48 (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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44C HIS 3.3 8.6 + - - -
45C TRP* 2.7 29.9 + - - -
46C LEU 3.0 1.2 - - - -
47C SER* 1.3 79.3 - - - +
49C LEU* 1.3 64.7 + - - +
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Residues in contact with LEU 49 (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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19C SER* 3.7 33.4 - - - +
22C LEU* 3.9 18.1 - - + +
45C TRP* 3.5 40.8 - - + +
46C LEU* 2.7 15.5 + - + +
48C SER* 1.3 89.6 - - - +
50C GLY* 1.3 55.4 + - - +
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Residues in contact with GLY 50 (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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22C LEU* 4.0 10.7 - - - +
46C LEU 3.2 8.7 + - - +
47C SER* 3.3 18.0 + - - +
48C SER 3.6 1.6 - - - -
49C LEU* 1.3 80.8 - - - +
51C ASN* 1.3 70.5 + - - +
52C PHE* 3.7 10.3 - - - -
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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