Contacts of the helix formed by residues 33 - 54 (chain P) 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 P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29P SER 3.7 1.2 - - - +
30P ALA* 2.9 18.1 + - - +
32P TRP* 1.3 77.7 - - - +
34P PHE* 1.3 63.6 + - + +
35P GLY 3.2 2.9 - - - -
36P SER* 3.0 22.8 + - - -
37P LEU* 3.3 18.7 + - + +
228P LYS* 3.0 54.1 + - - +
229P ASP* 3.6 19.0 + - - +
232P GLY* 3.6 16.3 - - - -
3003Q CDL 3.8 16.0 - - + +
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Residues in contact with PHE 34 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30P ALA 3.7 14.1 - - - -
31P TRP* 3.5 42.4 + + - +
32P TRP 3.4 0.8 - - - -
33P ASN* 1.3 77.8 - - + +
35P GLY* 1.3 58.9 + - - +
37P LEU* 3.7 24.0 - - + -
38P LEU* 2.8 36.2 + - - +
94P CYS* 4.0 24.2 - - - +
97P LEU* 3.5 44.2 - - + -
98P HIS* 4.0 15.0 - - + +
236P MET* 4.7 14.6 - - + -
3003Q CDL 5.6 4.0 - - + -
3004T CDL 4.1 19.3 - - + -
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Residues in contact with GLY 35 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33P ASN 3.2 0.6 - - - -
34P PHE* 1.3 78.1 - - - +
36P SER* 1.3 64.2 + - - +
38P LEU* 3.1 3.5 + - - +
39P ALA* 3.0 20.8 + - - +
98P HIS* 3.7 4.7 + - - -
502P HEM 3.1 58.0 + - - +
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Residues in contact with SER 36 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32P TRP 5.0 0.5 + - - -
33P ASN 3.0 16.8 + - - -
35P GLY* 1.3 74.3 - - - +
37P LEU* 1.3 53.8 + - - +
39P ALA* 3.0 8.9 + - - +
40P VAL* 2.7 43.7 + - - +
229P ASP* 3.0 38.5 + - - +
502P HEM 3.9 5.1 - - - +
3002P UQ 3.7 28.1 + - - +
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Residues in contact with LEU 37 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33P ASN* 3.3 17.4 + - + +
34P PHE* 3.7 30.1 - - + +
35P GLY 3.2 0.2 - - - -
36P SER* 1.3 79.6 + - - +
38P LEU* 1.3 55.3 + - - +
40P VAL* 3.6 3.5 - - + +
41P CYS* 2.6 40.3 + - - +
90P PHE* 4.4 11.6 - - + -
94P CYS* 4.0 17.7 - - - -
229P ASP 5.1 2.0 - - - +
232P GLY 4.0 4.7 - - - +
233P LEU* 3.5 46.4 - - + +
236P MET* 3.6 27.8 - - + -
3003Q CDL 6.1 0.7 - - + -
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Residues in contact with LEU 38 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34P PHE 2.8 25.2 + - - +
35P GLY 3.1 4.9 + - - +
37P LEU* 1.3 75.1 - - - +
39P ALA* 1.3 62.6 + - - +
41P CYS* 3.2 5.6 - - - +
42P LEU* 3.0 22.9 + - - +
91P PHE* 3.7 32.1 - - + +
94P CYS* 3.6 12.3 - - + -
95P ILE* 3.6 30.3 - - + +
98P HIS* 3.4 43.1 - - + +
502P HEM 3.4 29.4 - - + -
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Residues in contact with ALA 39 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35P GLY 3.0 12.2 + - - +
36P SER 3.2 7.4 - - - +
38P LEU* 1.3 75.4 - - - +
40P VAL* 1.3 64.9 + - - +
42P LEU* 2.8 25.6 + - - +
43P MET* 3.1 14.3 + - + +
194P THR* 5.5 5.8 - - + -
502P HEM 3.6 14.9 - - + +
3002P UQ 3.8 30.5 - - + -
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Residues in contact with VAL 40 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36P SER* 2.7 30.6 + - - +
37P LEU* 3.6 3.8 - - + +
39P ALA* 1.3 72.0 - - + +
41P CYS* 1.3 59.4 + - - +
43P MET* 3.1 25.5 + - + +
44P THR* 2.7 38.1 + - - +
233P LEU* 3.7 38.4 - - + -
3002P UQ 5.0 4.5 - - + -
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Residues in contact with CYS 41 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37P LEU 2.6 23.8 + - - +
38P LEU* 3.2 10.3 - - - +
40P VAL* 1.3 75.2 - - - +
42P LEU* 1.3 55.6 + - - +
44P THR* 3.2 8.4 + - - -
45P GLN* 3.0 32.0 + - - +
87P GLY* 4.0 6.7 - - - -
90P PHE* 3.5 25.5 - - + -
91P PHE* 3.3 52.3 - - + -
94P CYS* 5.5 0.7 - - - -
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Residues in contact with LEU 42 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38P LEU 3.0 12.2 + - - +
39P ALA* 2.8 18.1 + - - +
41P CYS* 1.3 73.3 - - - +
43P MET* 1.3 63.1 - - + +
45P GLN* 3.3 2.4 + - - +
46P ILE* 3.1 39.4 + - + +
91P PHE* 3.6 22.9 - - + -
187P PRO* 4.4 5.2 - - + +
190P ILE* 3.9 21.8 - - + -
191P ALA* 3.7 36.6 - - + +
194P THR* 4.5 8.1 - - + +
501P HEM 4.2 14.4 - - + -
502P HEM 5.4 2.2 - - + -
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Residues in contact with MET 43 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39P ALA* 3.1 6.3 + - + +
40P VAL* 3.1 37.3 + - + +
42P LEU* 1.3 80.1 - - + +
44P THR* 1.3 57.7 + - - +
46P ILE* 3.7 9.4 + - + +
47P LEU* 3.0 28.4 + - - +
3002P UQ 3.6 30.3 - - + -
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Residues in contact with THR 44 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40P VAL* 2.7 23.8 + - - +
41P CYS* 3.3 10.7 - - - -
43P MET* 1.3 75.1 - - - +
45P GLN* 1.3 63.9 + - - +
47P LEU* 3.3 6.3 + - + +
48P THR* 2.9 48.1 + - + +
83P LEU* 6.1 4.0 - - + +
87P GLY* 6.5 0.7 - - - -
240P PHE* 5.5 11.7 - - + -
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Residues in contact with GLN 45 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41P CYS* 3.0 17.4 + - - +
42P LEU 3.3 6.9 + - - +
44P THR* 1.3 80.7 - - - +
46P ILE* 1.3 54.1 + - - +
48P THR* 3.0 4.0 + - - +
49P GLY* 2.6 32.9 + - - -
83P LEU 4.1 1.0 - - - +
84P HIS* 3.0 46.1 + - - +
87P GLY* 3.7 18.2 - - - +
88P ALA* 3.3 16.0 - - - +
91P PHE* 3.9 15.7 - - + -
501P HEM 3.5 47.0 - - + -
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Residues in contact with ILE 46 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42P LEU* 3.1 36.9 + - + +
43P MET* 3.8 7.9 - - - +
45P GLN* 1.3 78.5 - - + +
47P LEU* 1.3 58.5 + - - +
49P GLY* 3.7 0.2 - - - -
50P LEU* 2.9 47.7 + - + +
187P PRO* 3.9 31.2 - - + +
188P PHE* 4.4 25.6 - - + -
191P ALA* 4.9 5.8 - - + -
501P HEM 3.7 11.7 - - + +
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Residues in contact with LEU 47 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43P MET 3.0 19.7 + - - +
44P THR* 3.6 6.7 - - + +
45P GLN 3.2 0.2 - - - -
46P ILE* 1.3 80.8 - - - +
48P THR* 1.3 63.2 + - + +
50P LEU* 3.8 11.8 - - + +
51P LEU* 3.3 27.7 + - + +
58R PHE* 4.6 22.2 - - + -
3005R PEE 4.3 23.3 - - + -
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Residues in contact with THR 48 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44P THR* 2.9 33.6 + - + +
45P GLN* 3.0 5.2 + - - +
47P LEU* 1.3 71.2 - - + +
49P GLY* 1.3 65.8 + - - +
51P LEU* 3.3 10.2 + - - +
52P LEU* 3.0 26.2 + - - +
80P ILE* 3.8 10.2 - - + +
83P LEU* 4.4 20.0 - - + -
84P HIS* 2.6 43.4 + - - +
58R PHE* 4.7 19.5 - - + -
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Residues in contact with GLY 49 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45P GLN 2.6 23.8 + - - -
48P THR* 1.3 75.5 + - - +
50P LEU* 1.3 55.7 + - - +
52P LEU* 3.2 2.4 + - - +
53P ALA 2.8 22.9 + - - -
84P HIS* 3.4 13.2 - - - -
501P HEM 3.1 36.8 - - - +
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Residues in contact with LEU 50 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181C ALA* 5.2 6.5 - - + -
185C LEU* 3.9 32.8 - - + -
46P ILE* 2.9 36.6 + - + +
47P LEU* 3.8 13.5 - - + +
48P THR 3.3 0.2 - - - -
49P GLY* 1.3 70.8 - - - +
51P LEU* 1.3 68.0 + - + +
53P ALA* 2.9 13.9 + - - +
54P MET* 3.0 30.5 + - + +
184P PHE* 3.6 34.1 - - + -
188P PHE* 5.1 1.6 - - + -
501P HEM 3.3 11.4 - - + +
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Residues in contact with LEU 51 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47P LEU* 3.3 20.2 + - + +
48P THR* 3.3 11.0 + - - +
50P LEU* 1.3 79.9 - - + +
52P LEU* 1.3 60.7 + - - +
54P MET* 3.7 11.3 + - - +
55P HIS* 3.4 23.7 + - - -
70P THR* 5.7 0.2 - - - +
80P ILE* 4.0 20.9 - - + +
58R PHE* 3.7 47.3 - - + +
61R SER* 3.2 25.0 + - - +
62R LEU* 4.4 20.2 - - + -
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Residues in contact with LEU 52 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48P THR 3.0 15.2 + - - +
49P GLY 3.5 7.2 - - - +
50P LEU 3.0 0.2 - - - -
51P LEU* 1.3 72.8 - - - +
53P ALA* 1.3 66.5 + - - +
54P MET 3.1 2.2 - - - -
55P HIS* 3.1 16.1 + - - +
56P TYR* 3.3 12.6 + - - +
70P THR* 4.2 23.5 + - + -
77P GLY* 5.5 0.2 - - - -
80P ILE* 3.4 24.5 - - + +
81P ARG* 3.8 19.1 - - + +
84P HIS* 3.9 28.5 - - + -
501P HEM 3.3 45.2 - - + +
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Residues in contact with ALA 53 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177C THR* 4.2 7.4 - - - +
180C PHE* 6.1 0.9 - - - -
181C ALA* 4.6 6.3 - - + +
49P GLY 2.8 16.8 + - - +
50P LEU* 2.9 6.4 + - - +
52P LEU* 1.3 72.3 - - - +
54P MET* 1.3 58.2 + - - +
55P HIS 3.0 9.0 + - - -
56P TYR* 3.6 15.0 + - - +
180P PHE* 4.1 21.8 - - + -
184P PHE* 4.3 12.8 - - + -
501P HEM 3.4 27.5 - - + +
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Residues in contact with MET 54 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C PRO 4.6 2.3 - - - +
177C THR* 3.1 29.6 + - - -
178C ARG* 4.1 25.2 + - + +
181C ALA* 4.0 22.4 - - + -
182C LEU* 4.8 15.5 - - + +
185C LEU* 6.2 2.2 - - + -
50P LEU* 3.0 28.2 + - + +
51P LEU* 3.9 15.5 - - - +
52P LEU 3.1 0.8 - - - -
53P ALA* 1.3 77.5 - - - +
55P HIS* 1.3 72.2 + - + +
62R LEU* 3.6 31.6 - - + -
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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
------------------------------------------------------------
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