Contacts of the helix formed by residues 40 - 55 (chain C) in PDB entry 2BHT
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 VAL 40 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C GLU* 3.2 17.2 + - + +
35C ASN* 3.7 9.6 - - - +
39C SER* 1.3 68.7 + - - +
41C LYS* 1.3 70.3 + - + +
42C ASP 3.0 6.1 - - - -
43C ARG* 3.0 20.8 + - - +
44C ALA 4.1 0.9 + - - -
150C HIS* 3.8 15.3 + - + +
178C THR* 3.7 26.2 - - + +
278C ILE* 4.7 5.8 - - + -
280C CYS* 3.1 43.3 + - + +
320C PLP 4.8 12.6 - - + +
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Residues in contact with LYS 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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39C SER* 2.8 14.9 + - - +
40C VAL* 1.3 80.0 - - + +
42C ASP* 1.3 63.2 + - - +
43C ARG 2.9 0.5 + - - -
44C ALA* 3.1 10.6 + - + +
45C ALA* 2.9 26.3 + - - +
71C ASN* 3.8 6.2 - - + +
72C THR* 3.0 50.1 + - + +
75C ALA* 3.9 4.0 - - + -
140C GLN* 3.7 11.4 - - - +
146C ASN* 6.2 0.2 - - - +
150C HIS* 6.3 0.4 - - - +
175C THR* 4.5 6.0 - - - +
208C GLY* 4.9 2.4 + - - -
320C PLP 1.5 94.4 + - + +
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Residues in contact with ASP 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ILE* 3.4 21.9 - - + +
35C ASN* 3.5 19.7 - - + +
36C PRO* 2.8 21.3 - - + +
37C ALA* 2.7 49.5 + - - +
39C SER* 3.4 15.6 + - - +
40C VAL 3.0 0.4 - - - -
41C LYS* 1.3 78.2 - - - +
43C ARG* 1.3 59.8 + - - +
45C ALA* 4.3 0.2 - - - +
46C LEU* 3.4 15.3 + - - +
75C ALA* 3.6 12.2 - - - +
78C MET* 3.9 8.6 - - - +
79C ILE* 4.8 0.5 - - - +
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Residues in contact with ARG 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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8C ILE* 4.3 15.5 - - + -
9C GLY* 3.4 18.4 - - - -
10C ASN 3.7 1.0 - - - +
11C THR* 3.8 0.6 - - - +
30C LYS* 3.9 3.0 - - - +
32C GLU* 2.5 44.1 + - - +
35C ASN* 4.5 2.5 - - - +
40C VAL 3.0 10.2 + - - +
41C LYS 3.0 0.4 - - - -
42C ASP* 1.3 79.8 - - - +
44C ALA* 1.3 59.0 + - - +
46C LEU* 4.2 2.9 - - - +
47C SER* 3.2 18.0 + - - -
149C ALA* 3.3 18.2 - - + +
150C HIS* 3.5 18.4 - - + -
153C THR* 2.5 43.6 + - - +
154C THR* 2.8 31.1 + - - +
157C GLU* 2.7 29.3 + - - -
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Residues in contact with ALA 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C VAL 4.1 0.6 + - - -
41C LYS* 3.1 15.2 + - + +
43C ARG* 1.3 75.2 - - - +
45C ALA* 1.3 61.2 + - - +
46C LEU 3.2 1.6 - - - -
47C SER* 4.1 2.0 - - - -
48C MET* 2.7 44.7 + - + +
72C THR* 6.0 1.1 - - + -
140C GLN* 6.0 1.8 - - - +
145C ASP 4.5 0.4 - - - -
146C ASN* 3.7 39.9 - - + +
149C ALA* 4.1 6.7 - - + -
150C HIS* 4.8 5.2 - - - +
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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 LYS 2.9 17.0 + - - +
42C ASP 4.3 1.8 - - - +
44C ALA* 1.3 79.0 - - - +
46C LEU* 1.3 60.2 + - - +
48C MET* 3.9 11.5 - - - +
49C ILE* 3.4 28.8 + - - +
72C THR* 4.6 5.0 - - + +
75C ALA* 3.5 29.4 - - + +
76C LEU* 3.8 21.4 - - + +
79C ILE* 4.2 4.3 - - + -
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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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5C GLU* 3.9 30.7 - - + +
8C ILE* 3.6 27.4 - - + -
42C ASP 3.4 15.9 + - - +
43C ARG 4.2 2.7 - - - +
44C ALA 3.2 0.6 - - - -
45C ALA* 1.3 75.7 - - - +
47C SER* 1.3 66.5 + - - +
49C ILE* 3.5 1.3 + - - +
50C VAL* 3.1 42.7 + - + +
79C ILE* 3.3 30.0 - - + +
83C LYS* 4.5 4.3 - - - -
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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 ARG 3.2 17.4 + - - -
44C ALA 3.1 2.5 + - - -
46C LEU* 1.3 77.5 - - - +
48C MET* 1.3 65.9 + - - +
49C ILE 3.1 1.0 + - - -
50C VAL* 3.1 9.6 + - - +
51C GLU* 3.1 31.3 + - - +
145C ASP* 2.9 29.1 + - - +
148C LYS* 4.1 7.1 + - - +
149C ALA* 3.7 15.5 + - - -
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Residues in contact with MET 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 ALA* 2.7 35.8 + - + +
45C ALA* 3.9 10.1 - - - +
47C SER* 1.3 72.9 - - - +
49C ILE* 1.3 61.1 + - - +
52C ALA* 3.4 22.5 + - - +
66C GLU* 4.5 1.8 - - - +
72C THR* 4.6 10.1 - - + -
76C LEU* 4.7 1.3 - - + -
138C LEU* 3.9 31.8 - - + +
140C GLN* 3.8 36.6 - - + -
143C ASN* 3.3 37.2 + - - +
145C ASP* 3.7 12.3 - - - +
146C ASN* 3.9 15.5 - - - +
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Residues in contact with ILE 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C ALA 3.4 9.6 + - - +
46C LEU 3.9 1.3 - - - +
47C SER 3.1 0.8 - - - -
48C MET* 1.3 79.1 - - - +
50C VAL* 1.3 69.6 + - + +
52C ALA* 3.4 2.4 + - - +
53C GLU* 3.1 22.8 + - - +
58C ILE* 3.7 11.5 - - + +
64C LEU* 4.0 26.0 - - + -
76C LEU* 3.6 27.1 - - + +
79C ILE* 3.3 35.0 - - + -
80C ALA* 4.8 2.7 - - + +
83C LYS* 3.7 30.3 - - + -
85C TYR* 4.5 14.1 - - + -
87C MET* 5.7 0.2 - - - -
138C LEU* 4.3 6.5 - - + -
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Residues in contact with VAL 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C LEU* 3.1 37.9 + - + +
47C SER* 3.1 2.7 + - - +
49C ILE* 1.3 80.9 - - - +
51C GLU* 1.3 67.2 + - - +
53C GLU* 3.3 11.1 + - - +
54C LYS* 2.8 49.4 + - + +
83C LYS* 4.0 20.6 - - - +
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Residues in contact with GLU 51 (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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47C SER* 3.1 25.1 + - - +
50C VAL* 1.3 87.0 - - - +
52C ALA* 1.3 57.0 + - - +
54C LYS* 3.2 28.8 + - - +
55C ARG* 2.9 43.5 + - - +
145C ASP* 2.8 36.6 - - + +
148C LYS* 4.0 16.4 + - - +
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Residues in contact with ALA 52 (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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48C MET 3.4 18.4 + - - +
49C ILE 3.4 1.7 + - - +
50C VAL 3.2 0.6 - - - -
51C GLU* 1.3 75.1 - - - +
53C GLU* 1.3 64.8 + - - +
55C ARG* 3.5 9.3 + - - +
56C GLY 3.2 2.3 + - - -
57C ARG* 2.9 48.6 + - + +
58C ILE* 3.3 24.3 + - + -
138C LEU* 5.1 5.6 - - + -
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Residues in contact with GLU 53 (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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49C ILE* 3.1 16.4 + - - +
50C VAL* 3.4 13.8 - - - +
52C ALA* 1.3 76.9 - - - +
54C LYS* 1.3 63.9 + - + +
56C GLY* 3.0 14.7 + - - -
58C ILE* 3.6 16.0 - - - +
59C LYS* 6.0 0.2 - - + -
60C PRO* 3.9 16.9 - - + +
83C LYS* 4.2 21.9 + - - +
85C TYR* 2.5 42.7 + - - +
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Residues in contact with LYS 54 (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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50C VAL* 2.8 38.6 + - + +
51C GLU* 3.2 32.4 + - - +
53C GLU* 1.3 79.0 - - + +
55C ARG* 1.3 62.2 + - + +
56C GLY 3.7 0.2 + - - -
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Residues in contact with ARG 55 (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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51C GLU* 2.9 40.7 + - - +
52C ALA* 3.9 11.0 - - - +
53C GLU 3.1 0.4 - - - -
54C LYS* 1.3 79.5 - - + +
56C GLY* 1.3 57.8 + - - +
57C ARG* 3.4 7.6 - - + +
144C PRO* 6.0 2.6 - - - +
145C ASP* 2.9 41.2 + - - -
148C LYS* 4.3 5.1 - - - +
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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