Contacts of the helix formed by residues 32 - 53 (chain C) in PDB entry 1L0N
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 32 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C ILE* 6.2 0.4 - - - +
28C SER 4.0 4.4 + - - -
29C SER* 2.9 20.6 + - - +
31C TRP* 1.3 83.2 + - - +
33C PHE* 1.3 61.3 + - + +
34C GLY 3.1 6.2 + - - -
35C SER* 2.9 25.6 + - - +
36C LEU* 3.1 22.6 + - + +
224C TYR* 5.8 1.2 - - - -
227C LYS* 3.5 48.9 - - - +
228C ASP* 4.1 13.1 + - - +
231C GLY* 4.1 10.9 - - - -
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Residues in contact with PHE 33 (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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29C SER* 3.8 15.7 - - - -
30C TRP* 3.8 31.2 - + - +
31C TRP 3.3 1.2 - - - -
32C ASN* 1.3 75.7 - - + +
34C GLY* 1.3 56.3 + - - +
36C LEU* 3.7 23.1 - - + +
37C LEU* 2.7 38.6 + - - +
92C ILE* 5.7 2.2 - - + -
93C CYS* 4.0 32.8 - - + +
96C MET* 3.4 46.9 - - + -
97C HIS* 3.9 19.5 - - + +
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Residues in contact with GLY 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C TRP 3.8 3.6 + - - -
32C ASN 3.1 1.8 - - - -
33C PHE* 1.3 79.5 - - - +
35C SER* 1.3 60.6 + - - +
37C LEU* 3.4 4.0 + - - +
38C GLY* 3.2 14.4 + - - -
97C HIS* 3.5 15.9 - - - -
381C HEM 3.3 49.8 - - - +
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Residues in contact with SER 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C TRP 4.9 0.2 + - - -
32C ASN* 2.9 16.4 + - - +
34C GLY* 1.3 71.2 - - - +
36C LEU* 1.3 58.9 + - - +
38C GLY* 2.9 5.3 + - - +
39C ILE* 2.6 43.7 + - - +
228C ASP* 3.5 40.4 + - - +
381C HEM 4.1 6.9 + - - +
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Residues in contact with LEU 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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32C ASN* 3.1 31.8 + - + +
33C PHE* 3.7 27.4 - - + +
34C GLY 3.3 0.2 - - - -
35C SER* 1.3 80.9 + - - +
37C LEU* 1.3 57.1 + - - +
39C ILE* 3.1 6.4 + - + +
40C CYS* 2.7 34.3 + - - +
93C CYS* 4.2 13.5 - - - -
228C ASP 5.1 0.4 - - - +
231C GLY* 3.5 29.2 - - - +
232C ALA* 3.6 18.6 - - + +
235C LEU* 3.8 23.5 - - + +
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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 PHE 2.7 22.7 + - - +
34C GLY 3.8 1.3 - - - +
36C LEU* 1.3 68.3 - - - +
38C GLY* 1.3 56.8 + - - +
40C CYS* 2.9 5.4 + - - +
41C LEU* 2.6 37.2 + - - +
90C PHE* 3.7 22.2 - - + +
93C CYS* 3.6 10.8 - - + -
94C LEU* 3.5 37.5 - - + +
97C HIS* 3.5 40.6 - - + -
381C HEM 3.6 37.5 - - + +
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Residues in contact with GLY 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 3.2 8.9 + - - -
35C SER* 2.9 8.4 + - - -
37C LEU* 1.3 78.2 - - - +
39C ILE* 1.3 61.7 + - - +
41C LEU* 3.1 7.4 + - - +
42C ILE* 3.0 24.4 + - - +
381C HEM 4.0 11.0 - - - +
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Residues in contact with ILE 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* 2.6 26.3 + - - +
36C LEU* 3.4 11.9 - - + +
38C GLY* 1.3 71.5 - - - +
40C CYS* 1.3 59.0 + - - +
42C ILE* 3.0 12.9 + - + +
43C LEU* 2.9 35.4 + - + +
232C ALA* 3.9 29.4 - - + -
235C LEU* 3.8 19.7 - - + -
236C ILE* 5.5 7.0 - - + -
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Residues in contact with CYS 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 LEU 2.7 22.4 + - - +
37C LEU* 3.4 4.5 - - - +
39C ILE* 1.3 73.4 - - - +
41C LEU* 1.3 58.4 + - - +
43C LEU* 3.8 8.9 - - + +
44C GLN* 2.8 34.8 + - - +
86C GLY* 4.6 4.0 - - - +
89C MET* 4.0 11.2 - - - -
90C PHE* 3.4 47.1 - - + -
93C CYS* 4.4 3.8 - - - -
235C LEU* 3.6 26.5 - - - -
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Residues in contact with LEU 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 21.7 + - - +
38C GLY* 3.4 7.9 - - - +
40C CYS* 1.3 74.9 - - - +
42C ILE* 1.3 60.9 + - - +
44C GLN* 3.4 1.8 + - - -
45C ILE* 3.2 25.2 + - + +
90C PHE* 3.6 16.8 - - + -
186C PRO* 4.2 26.0 - - + +
189C ILE* 3.7 31.4 - - + -
190C MET* 4.0 30.5 - - + +
193C ALA* 5.0 5.8 - - + -
381C HEM 4.8 9.4 - - + -
382C HEM 4.4 8.3 - - + -
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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 GLY 3.0 18.5 + - - +
39C ILE* 3.4 15.0 - - + +
41C LEU* 1.3 71.8 - - - +
43C LEU* 1.3 61.3 + - - +
44C GLN 3.1 1.6 - - - -
45C ILE* 2.9 8.6 + - - +
46C LEU* 2.8 47.0 + - + +
190C MET* 6.1 4.7 - - - -
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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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39C ILE* 2.9 23.3 + - + +
40C CYS* 3.9 9.4 - - - +
42C ILE* 1.3 79.0 - - - +
44C GLN* 1.3 71.0 + - + +
46C LEU* 4.1 5.3 - - - +
47C THR* 3.0 42.3 + - + +
82C MET* 4.1 23.1 - - + +
86C GLY* 4.3 7.0 - - - -
235C LEU* 5.8 3.4 - - + -
236C ILE* 4.4 16.8 - - + -
239C LEU* 3.6 32.5 - - + -
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Residues in contact with GLN 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 CYS 2.8 21.5 + - - +
41C LEU* 3.8 5.4 - - - +
43C LEU* 1.3 85.4 - - + +
45C ILE* 1.3 59.6 - - - +
47C THR* 4.2 2.0 - - - -
48C GLY 3.5 1.6 + - - -
83C HIS* 2.9 65.5 + - - +
86C GLY* 3.0 11.6 - - - +
87C ALA* 2.7 35.2 + - - +
90C PHE* 4.7 2.5 - - + -
382C HEM 3.2 49.5 + - + +
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Residues in contact with ILE 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 LEU* 3.2 17.4 + - + +
42C ILE* 2.9 10.1 + - - +
44C GLN* 1.3 77.6 - - - +
46C LEU* 1.3 59.8 + - + +
48C GLY* 3.5 0.2 - - - -
49C LEU* 2.8 37.1 + - + +
186C PRO* 3.9 33.2 - - + +
187C PHE* 3.6 38.4 - - + -
190C MET* 4.3 18.2 - - + -
382C HEM 3.8 12.1 - - + +
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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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42C ILE* 2.8 32.8 + - + +
43C LEU* 4.1 4.9 - - - +
45C ILE* 1.3 77.2 - - + +
47C THR* 1.3 65.9 + - + +
49C LEU* 3.4 4.9 + - - +
50C PHE* 3.1 37.8 + - + -
54E VAL* 6.4 0.4 - - + -
58E PHE* 3.5 40.4 - - + -
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Residues in contact with THR 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* 3.0 26.7 + - + +
44C GLN* 4.2 0.5 - - - -
46C LEU* 1.3 78.1 - - + +
48C GLY* 1.3 64.2 + - - +
50C PHE 3.6 0.7 + - - +
51C LEU* 3.2 22.7 + - - +
79C ILE* 3.6 24.3 - - - +
82C MET* 4.2 24.4 - - + -
83C HIS* 3.1 23.1 + - - +
58E PHE* 3.7 29.2 - - + -
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Residues in contact with GLY 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 GLN 3.5 4.4 + - - -
45C ILE 3.3 5.4 + - - -
46C LEU 3.1 0.8 - - - -
47C THR* 1.3 80.3 + - - +
49C LEU* 1.3 64.2 + - - +
51C LEU* 3.3 3.5 + - - +
52C ALA 3.1 16.1 + - - -
83C HIS* 3.4 25.4 - - - -
382C HEM 3.3 29.6 - - - +
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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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45C ILE* 2.8 22.4 + - + +
46C LEU* 3.4 6.7 + - - +
47C THR 3.4 0.2 - - - -
48C GLY* 1.3 71.8 - - - +
50C PHE* 1.3 69.6 + - + +
52C ALA* 2.9 21.8 + - + +
53C MET* 3.3 22.3 + - + +
183C PHE* 3.7 29.4 - - + -
187C PHE* 6.2 0.7 - - + -
382C HEM 3.7 6.2 - - + +
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Residues in contact with PHE 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 LEU* 3.1 32.5 + - + +
47C THR 4.0 4.3 - - - +
48C GLY 3.4 0.4 - - - -
49C LEU* 1.3 91.1 - - + +
51C LEU* 1.3 61.5 + - - +
53C MET* 3.4 14.9 + - - +
54C HIS* 3.2 25.5 - - - -
79C ILE* 4.1 18.2 - - + -
58E PHE* 3.3 53.2 - + + -
59E VAL* 5.2 1.3 - - + -
61E SER* 3.7 17.9 - - - +
62E MET* 3.5 28.9 - - + -
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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 THR 3.2 7.3 + - - +
48C GLY 3.3 9.0 - - - +
49C LEU 3.1 0.2 - - - -
50C PHE* 1.3 77.9 - - - +
52C ALA* 1.3 56.2 + - - +
53C MET 3.0 3.7 + - - -
54C HIS* 3.1 5.2 + - - +
55C TYR* 3.0 27.0 + - - +
69C ILE* 4.0 19.0 - - + +
79C ILE* 3.6 26.7 - - + -
80C ARG* 3.9 21.1 - - + +
83C HIS* 3.8 26.7 - - + +
382C HEM 3.2 56.3 - - + +
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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 GLY 3.1 8.4 + - - +
49C LEU* 2.9 13.2 + - + +
51C LEU* 1.3 78.5 - - - +
53C MET* 1.3 58.5 + - - +
54C HIS 3.2 2.3 + - - -
55C TYR* 4.0 13.6 - - - +
179C PHE* 4.1 17.2 - - + -
183C PHE* 3.8 29.2 - - + -
382C HEM 3.9 10.3 - - + +
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Residues in contact with MET 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 LEU* 3.3 23.8 - - + +
50C PHE* 3.5 26.7 - - - +
51C LEU 3.0 1.0 + - - -
52C ALA* 1.3 77.2 - - - +
54C HIS* 1.3 77.4 + - + +
55C TYR 5.1 0.2 - - - -
62E MET* 3.6 50.3 - - + -
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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
------------------------------------------------------------
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