Contacts of the helix formed by residues 35 - 47 (chain C) in PDB entry 1BDF
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 PHE 35 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8C PHE 6.0 0.9 - - - -
31C LEU* 3.9 12.1 - - + +
32C GLU* 2.9 41.7 + - + +
33C ARG 3.2 7.1 - - - -
34C GLY* 1.3 77.3 - - - +
36C GLY* 1.3 67.5 + - - +
37C HIS 3.4 0.2 - - - -
38C THR* 3.7 10.3 - - + -
39C LEU* 3.1 29.7 + - + +
46D ILE* 3.5 26.5 - - + -
50D SER* 3.7 22.9 - - - -
223D ILE* 3.3 28.5 - - + -
224D LEU* 5.5 1.1 - - + -
227D GLN* 3.3 37.2 - - + +
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Residues in contact with GLY 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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31C LEU* 3.4 24.7 - - - +
32C GLU 4.4 1.4 + - - -
34C GLY* 3.3 2.4 - - - +
35C PHE* 1.3 77.4 - - - +
37C HIS* 1.3 52.3 + - - +
40C GLY* 2.7 34.8 + - - -
187C VAL* 3.8 27.8 - - - +
199C ASP* 5.6 1.4 + - - +
201C LEU* 3.6 7.6 - - - +
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Residues in contact with HIS 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C GLY* 3.9 12.2 + - - +
36C GLY* 1.3 73.9 - - - +
38C THR* 1.3 61.2 + - - +
40C GLY 3.8 0.2 - - - -
41C ASN* 2.5 42.1 + - - +
185C TYR* 3.3 30.5 - + - -
187C VAL* 3.5 27.0 - - + +
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Residues in contact with THR 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 3.1 18.8 + - - -
35C PHE* 3.5 12.9 + - + -
36C GLY 3.3 0.8 - - - -
37C HIS* 1.3 79.2 - - - +
39C LEU* 1.3 62.0 + - + +
41C ASN* 4.3 1.8 - - - +
42C ALA* 3.2 22.2 + - - +
41D ASN 5.6 1.1 - - - -
42D ALA* 3.7 34.4 - - - +
45D ALA* 3.1 23.1 - - + +
46D ILE* 4.3 10.7 - - + +
224D LEU* 4.2 16.2 - - + -
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Residues in contact with LEU 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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11C PRO* 3.9 21.3 - - + -
28C LEU* 5.1 8.1 - - + -
31C LEU* 4.1 12.1 - - + -
35C PHE* 3.1 18.9 + - + +
38C THR* 1.3 74.0 - - + +
40C GLY* 1.3 59.0 + - - +
42C ALA* 3.0 3.3 + - - -
43C LEU* 2.7 45.9 + - + +
201C LEU* 4.2 9.9 - - + -
224C LEU* 4.8 3.6 - - + -
224D LEU* 3.7 24.9 - - + -
227D GLN* 3.9 28.9 - - + +
228D LEU* 3.7 28.3 - - + -
231D PHE* 5.2 0.2 - - + -
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Residues in contact with GLY 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 GLY 2.7 23.9 + - - -
37C HIS 3.9 0.7 - - - -
38C THR 3.4 0.2 - - - -
39C LEU* 1.3 73.8 - - - +
41C ASN* 1.3 55.9 + - - +
43C LEU* 4.3 2.4 - - - +
44C ARG* 3.0 30.1 + - - +
185C TYR* 3.5 18.5 - - - +
201C LEU* 3.7 20.3 - - - +
203C ILE* 5.5 2.1 - - - +
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Residues in contact with ASN 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 HIS* 2.5 31.4 + - - +
38C THR* 4.3 2.0 - - - +
40C GLY* 1.3 74.0 - - - +
42C ALA* 1.3 66.3 + - - +
44C ARG* 2.7 38.1 + - - +
45C ALA* 3.3 21.7 + - - +
185C TYR* 2.6 21.3 + - - -
38D THR* 5.8 0.7 - - - -
41D ASN* 5.6 10.3 - - + -
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Residues in contact with ALA 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 THR 3.2 17.9 + - - +
39C LEU* 3.0 6.2 + - + +
41C ASN* 1.3 79.4 - - - +
43C LEU* 1.3 62.7 + - - +
45C ALA* 3.2 10.9 + - - +
46C ILE* 3.1 21.7 + - - +
224C LEU* 3.6 32.1 - - + -
38D THR* 3.8 20.6 - - + +
42D ALA* 4.7 5.8 - - + -
224D LEU* 5.4 0.4 - - + -
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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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28C LEU* 4.1 17.3 - - + -
39C LEU* 2.7 32.3 + - + +
40C GLY 4.3 1.3 - - - +
42C ALA* 1.3 70.8 - - + +
44C ARG* 1.3 65.5 + - - +
45C ALA 2.9 2.0 - - - -
46C ILE* 2.8 16.3 + - - +
47C LEU* 2.8 21.5 + - + +
203C ILE* 3.9 29.6 - - + -
217C ILE* 4.7 9.9 - - + +
220C ALA* 3.7 28.7 - - + +
221C ALA* 3.7 22.4 - - + +
224C LEU* 4.4 11.2 - - + -
228D LEU* 4.8 5.8 - - + -
231D PHE* 5.6 2.0 - - + -
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Residues in contact with ARG 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 GLY 3.0 21.5 + - - +
41C ASN* 2.7 32.5 + - - +
42C ALA 3.5 0.2 - - - -
43C LEU* 1.3 74.5 - - - +
45C ALA* 1.3 56.5 + - - +
47C LEU* 4.1 1.3 - - - +
48C LEU* 3.1 41.6 + - + +
183C ILE* 3.6 42.8 - - + -
184C ALA* 5.0 1.2 - - - +
185C TYR* 3.5 30.6 - - + +
203C ILE* 6.2 0.4 - - - +
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Residues in contact with ALA 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 ASN 3.3 16.9 + - - +
42C ALA 3.2 3.9 + - - +
43C LEU 2.9 1.2 - - - -
44C ARG* 1.3 76.3 - - - +
46C ILE* 1.3 63.5 + - - +
48C LEU* 3.8 3.3 + - - +
49C SER* 2.8 28.2 + - - -
50C SER* 4.6 0.2 + - - -
38D THR* 3.3 25.1 - - - +
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Residues in contact with ILE 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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42C ALA 3.1 19.5 - - - +
43C LEU* 2.8 7.2 + - - +
45C ALA* 1.3 75.6 - - - +
47C LEU* 1.3 60.1 + - - +
50C SER* 2.7 34.1 + - - +
51C MET* 3.6 4.5 + - - -
220C ALA* 3.5 30.3 - - + +
223C ILE* 3.4 38.8 - - + -
224C LEU* 4.6 10.1 - - + -
35D PHE* 3.7 31.6 - - + -
38D THR* 4.1 14.8 - - + +
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Residues in contact with LEU 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C LEU* 2.8 21.6 + - + +
44C ARG 4.3 0.7 - - - +
46C ILE* 1.3 76.9 - - - +
48C LEU* 1.3 57.1 + - - +
49C SER 3.1 5.2 + - - -
51C MET* 3.3 29.3 - - + +
178C SER* 4.3 2.3 + - - -
180C VAL* 3.3 18.4 - - + +
183C ILE* 3.6 39.9 - - + -
203C ILE* 4.4 4.7 - - + -
205C MET* 5.0 2.9 - - + -
216C ALA* 2.9 40.8 - - + +
217C ILE* 3.6 25.6 - - + -
220C ALA* 3.6 11.9 - - + -
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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