Contacts of the helix formed by residues 33 - 54 (chain C) in PDB entry 3L73
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 ASN 33 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C SER 3.7 1.6 - - - +
30C ALA* 2.7 18.4 + - - +
32C TRP* 1.3 77.4 - - - +
34C PHE* 1.3 64.9 + - + +
35C GLY 3.2 3.1 - - - -
36C SER* 2.9 23.9 + - - -
37C LEU* 3.3 18.1 + - + +
228C LYS* 3.1 54.2 + - - +
229C ASP* 3.5 18.9 + - - +
232C GLY* 3.6 14.7 - - - -
2003D CDL 3.7 16.9 + - + +
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Residues in contact with PHE 34 (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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30C ALA 3.8 13.7 - - - -
31C TRP* 3.4 41.3 - + - +
32C TRP 3.4 1.0 - - - -
33C ASN* 1.3 78.4 - - + +
35C GLY* 1.3 55.4 + - - +
37C LEU* 3.6 24.6 - - + +
38C LEU* 2.8 39.7 + - - +
94C CYS* 4.1 18.2 - - - +
97C LEU* 3.5 45.5 - - + -
98C HIS* 4.0 25.4 - - + +
236C MET* 4.8 10.5 - - + -
2003D CDL 5.6 5.2 - - + -
2004G CDL 4.2 18.8 - - + -
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Residues in contact with GLY 35 (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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32C TRP 4.3 0.2 + - - -
33C ASN 3.2 0.8 - - - -
34C PHE* 1.3 76.3 - - - +
36C SER* 1.3 62.7 + - - +
38C LEU* 3.1 6.3 + - - +
39C ALA* 2.9 20.6 + - - +
98C HIS* 3.7 8.7 + - - -
502C HEM 3.1 52.8 + - - +
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Residues in contact with SER 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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33C ASN 2.9 17.5 + - - -
35C GLY* 1.3 73.1 - - - +
37C LEU* 1.3 51.8 + - - +
39C ALA* 3.0 5.7 + - - +
40C VAL* 2.7 43.1 + - - +
229C ASP* 3.2 38.4 + - - +
502C HEM 3.9 3.6 - - - +
2002C UQ 3.6 34.7 + - - +
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Residues in contact with LEU 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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33C ASN* 3.3 16.3 + - + +
34C PHE* 3.6 30.1 - - + +
35C GLY 3.2 0.2 - - - -
36C SER* 1.3 79.6 + - - +
38C LEU* 1.3 54.1 + - - +
40C VAL* 3.6 3.1 - - + +
41C CYS* 2.6 39.5 + - - +
90C PHE* 4.4 12.1 - - + -
94C CYS* 4.0 15.7 - - - -
229C ASP 5.1 1.6 - - - +
232C GLY 4.2 4.5 - - - +
233C LEU* 3.6 46.7 - - + +
236C MET* 3.6 27.8 - - + -
2003D CDL 6.1 1.1 - - + -
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Residues in contact with LEU 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 PHE 2.8 21.1 + - - +
35C GLY 3.3 4.9 - - - +
37C LEU* 1.3 71.3 - - - +
39C ALA* 1.3 64.4 + - - +
41C CYS* 3.2 4.5 - - - +
42C LEU* 2.9 22.9 + - - +
91C PHE* 3.6 30.1 - - + +
94C CYS* 3.5 26.0 - - + -
95C ILE* 3.5 15.3 - - + +
98C HIS* 3.4 46.2 - - + +
502C HEM 3.4 29.8 - - + -
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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 GLY 2.9 12.7 + - - +
36C SER* 3.0 8.0 + - - +
38C LEU* 1.3 75.6 - - - +
40C VAL* 1.3 65.0 + - - +
42C LEU* 2.9 19.8 + - - +
43C MET* 3.1 16.6 + - - +
194C THR* 5.5 5.6 - - + -
198C LEU* 6.3 0.7 - - + -
502C HEM 3.6 14.1 - - + +
2002C UQ 3.9 31.0 - - + -
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Residues in contact with VAL 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 SER* 2.7 30.4 + - - +
37C LEU* 3.6 3.4 - - + +
39C ALA* 1.3 71.8 - - + +
41C CYS* 1.3 57.4 + - - +
43C MET* 3.0 15.5 + - + +
44C THR* 2.7 38.1 + - - +
233C LEU* 3.7 38.4 - - + -
2002C UQ 5.3 9.6 - - + -
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Residues in contact with CYS 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 LEU 2.6 23.5 + - - +
38C LEU* 3.2 9.9 - - - +
40C VAL* 1.3 74.3 - - - +
42C LEU* 1.3 56.2 + - - +
44C THR* 3.2 9.6 + - - -
45C GLN* 3.0 31.3 + - - +
87C GLY* 4.0 6.5 - - - -
90C PHE* 3.3 35.4 - - + -
91C PHE* 3.3 38.8 - - + -
94C CYS* 5.4 0.4 - - - -
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Residues in contact with LEU 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 LEU 2.9 12.4 + - - +
39C ALA* 2.9 14.5 + - - +
41C CYS* 1.3 73.6 - - - +
43C MET* 1.3 67.9 + - + +
45C GLN* 3.4 1.3 + - - +
46C ILE* 3.2 35.4 + - + +
91C PHE* 3.5 26.4 - - + -
187C PRO 4.3 4.9 - - - +
190C ILE* 4.0 17.5 - - + -
191C ALA* 3.7 36.3 - - + +
194C THR* 4.4 8.7 - - + +
501C HEM 4.1 14.6 - - + -
502C HEM 5.4 2.9 - - + -
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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* 3.1 11.5 + - - +
40C VAL* 3.0 16.6 + - + +
42C LEU* 1.3 78.4 - - + +
44C THR* 1.3 58.5 + - - +
46C ILE* 3.3 9.1 + - + +
47C LEU* 2.9 30.5 + - - +
2002C UQ 5.0 15.5 - - - -
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Residues in contact with THR 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 VAL* 2.7 24.6 + - - +
41C CYS* 3.3 10.2 - - - -
43C MET* 1.3 77.7 - - - +
45C GLN* 1.3 63.6 + - - +
47C LEU* 3.7 6.6 - - + +
48C THR* 2.9 48.3 + - + +
83C LEU* 6.0 4.9 - - + +
87C GLY* 6.4 0.2 - - - -
240C PHE* 5.4 13.5 - - + -
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Residues in contact with GLN 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 CYS* 3.0 17.5 + - - +
42C LEU 3.8 6.5 - - - +
43C MET 3.3 0.2 - - - -
44C THR* 1.3 80.1 - - - +
46C ILE* 1.3 54.9 + - - +
48C THR* 3.0 7.7 + - - -
49C GLY* 2.6 32.9 + - - -
83C LEU 4.1 1.0 - - - +
84C HIS* 3.0 38.2 + - - +
87C GLY* 3.6 22.2 - - - +
88C ALA* 3.4 9.9 - - - +
91C PHE* 3.9 16.2 - - + -
501C HEM 3.4 52.8 - - + -
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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 LEU* 3.2 35.3 + - + +
43C MET* 3.6 10.1 - - + +
45C GLN* 1.3 76.6 - - + +
47C LEU* 1.3 66.2 + - - +
49C GLY 3.8 0.2 - - - -
50C LEU* 2.9 40.0 + - + +
187C PRO* 4.0 20.4 - - + +
188C PHE* 4.3 25.4 - - + -
191C ALA* 5.0 5.8 - - + -
501C HEM 3.7 21.9 - - + +
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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
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43C MET 2.9 18.9 + - - +
44C THR* 3.7 7.4 - - + +
45C GLN 3.3 0.2 - - - -
46C ILE* 1.3 81.4 - - + +
48C THR* 1.3 64.4 + - + +
50C LEU* 3.3 10.4 + - + +
51C LEU* 3.2 26.9 + - + +
58E PHE* 4.4 23.8 - - + -
2005E PEE 4.4 23.1 - - + -
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Residues in contact with THR 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 THR* 2.9 33.5 + - + +
45C GLN* 3.0 6.5 + - - +
47C LEU* 1.3 72.9 - - + +
49C GLY* 1.3 63.0 + - - +
51C LEU* 3.2 8.4 + - - +
52C LEU* 2.9 25.8 + - - +
80C ILE* 3.7 13.7 - - + +
83C LEU* 4.3 22.0 - - + -
84C HIS* 2.7 40.9 + - - +
58E PHE* 4.6 20.6 - - + -
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Residues in contact with GLY 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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45C GLN 2.6 23.2 + - - -
48C THR* 1.3 75.6 + - - +
50C LEU* 1.3 55.2 + - - +
52C LEU* 3.1 2.1 + - - +
53C ALA 2.9 24.1 + - - -
84C HIS* 3.3 19.7 - - - -
501C HEM 3.1 28.4 - - - +
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Residues in contact with LEU 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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46C ILE* 2.9 35.7 + - + +
47C LEU* 3.7 12.1 - - + +
49C GLY* 1.3 71.7 - - - +
51C LEU* 1.3 68.0 + - + +
53C ALA* 3.0 12.9 + - - +
54C MET* 3.1 30.2 + - + +
184C PHE* 3.6 34.3 - - + -
188C PHE* 5.0 1.3 - - + -
501C HEM 3.3 11.4 - - + +
181P ALA* 5.1 6.7 - - + +
185P LEU* 3.8 34.5 - - + -
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Residues in contact with LEU 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 LEU* 3.2 20.4 + - + +
48C THR* 3.2 10.9 + - - +
50C LEU* 1.3 80.2 - - + +
52C LEU* 1.3 62.5 + - - +
54C MET* 3.6 10.8 + - - +
55C HIS* 3.4 23.4 + - - -
70C THR* 5.8 0.2 - - - +
80C ILE* 4.1 21.3 - - + +
58E PHE* 3.6 49.1 - - + +
61E SER* 3.1 24.6 + - - +
62E LEU* 4.3 21.8 - - + -
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Residues in contact with LEU 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 THR 2.9 16.7 + - - +
49C GLY 3.5 7.2 - - - +
50C LEU 3.0 0.4 - - - -
51C LEU* 1.3 74.4 - - - +
53C ALA* 1.3 60.4 + - - +
54C MET 3.1 5.6 - - - -
55C HIS* 3.1 16.0 + - - +
56C TYR* 3.3 12.8 + - - +
70C THR* 4.3 20.4 + - + +
80C ILE* 3.4 26.0 - - + -
81C ARG* 3.8 20.6 - - + +
84C HIS* 3.9 28.5 - - + -
501C HEM 3.3 44.0 - - + +
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Residues in contact with ALA 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 GLY 2.9 16.6 + - - +
50C LEU* 3.0 6.5 + - - +
52C LEU* 1.3 72.3 - - - +
54C MET* 1.3 58.6 + - - +
55C HIS 3.0 8.9 + - - -
56C TYR* 3.7 14.8 + - - +
180C PHE* 4.0 20.6 - - + -
184C PHE* 4.4 11.4 - - + -
501C HEM 3.5 28.7 - - + +
177P THR* 4.3 7.4 - - - +
180P PHE* 6.0 1.0 - - - -
181P ALA* 4.5 6.2 - - + +
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Residues in contact with MET 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C LEU* 3.1 29.8 - - + +
51C LEU* 3.8 14.8 - - - +
52C LEU 3.1 2.0 - - - -
53C ALA* 1.3 76.8 - - - +
55C HIS* 1.3 74.0 + - + +
62E LEU* 3.5 32.3 - - + -
174P PRO 4.6 1.6 - - - +
177P THR* 3.2 28.6 + - - -
178P ARG* 4.1 25.0 + - + +
181P ALA* 3.9 23.1 - - + -
182P LEU* 4.8 15.0 - - + +
185P LEU* 6.1 3.4 - - + -
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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