Contacts of the helix formed by residues 32 - 53 (chain P) in PDB entry 1PP9
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 P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28P SER 3.9 2.8 - - - +
29P SER* 2.9 29.8 + - - +
31P TRP* 1.3 76.2 - - - +
33P PHE* 1.3 63.0 + - - +
34P GLY 3.2 1.1 + - - -
35P SER* 3.0 23.8 + - - -
36P LEU* 3.1 14.2 + - + +
227P LYS* 3.2 35.8 + - - +
228P ASP* 3.7 20.6 + - - +
231P GLY* 4.0 9.3 - - - -
3003Q CDL 3.6 31.0 + - + +
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Residues in contact with PHE 33 (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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29P SER 4.0 11.2 - - - -
30P TRP* 3.6 40.8 - + - +
31P TRP 3.3 1.4 - - - -
32P ASN* 1.3 73.9 - - - +
34P GLY* 1.3 59.2 + - - +
36P LEU* 3.6 14.4 - - + +
37P LEU* 2.9 35.2 + - - +
93P CYS* 3.9 30.3 - - - +
96P MET* 3.7 37.2 - - + -
97P HIS* 3.8 18.2 - - + +
3003Q CDL 3.9 38.6 - - + -
3004T CDL 4.1 14.4 - - + -
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Residues in contact with GLY 34 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32P ASN 3.2 0.4 - - - -
33P PHE* 1.3 76.5 - - - +
35P SER* 1.3 61.6 + - - +
37P LEU* 3.2 5.8 + - - +
38P GLY* 3.2 16.5 + - - -
97P HIS* 3.5 14.7 + - - -
502P HEM 3.0 54.4 + - - +
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Residues in contact with SER 35 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31P TRP 4.9 0.6 + - - -
32P ASN* 3.0 14.2 + - - -
34P GLY* 1.3 73.0 - - - +
36P LEU* 1.3 69.0 + - - +
38P GLY* 3.2 3.5 + - - +
39P ILE* 3.0 31.0 + - - +
228P ASP* 3.4 31.4 + - - +
502P HEM 4.0 5.9 - - - +
3002P UQ 3.4 29.9 + - - -
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Residues in contact with LEU 36 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32P ASN* 3.1 23.7 + - + +
33P PHE* 3.8 22.0 - - + +
34P GLY 3.2 0.2 - - - -
35P SER* 1.3 81.0 - - - +
37P LEU* 1.3 58.7 + - - +
39P ILE* 3.3 7.7 + - + +
40P CYS* 2.9 32.9 + - - -
93P CYS* 4.0 12.1 - - - -
228P ASP 5.0 0.2 - - - +
231P GLY* 3.6 28.3 - - - +
232P ALA* 3.7 12.1 - - + +
235P LEU* 3.7 19.3 - - + +
3003Q CDL 3.5 40.2 - - + -
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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 PHE 2.9 24.9 + - - +
34P GLY 3.5 4.7 - - - +
35P SER 3.2 0.2 - - - -
36P LEU* 1.3 75.8 - - - +
38P GLY* 1.3 59.9 + - - +
40P CYS* 3.3 4.6 + - - +
41P LEU* 2.9 30.0 + - - +
90P PHE* 3.7 24.1 - - + +
93P CYS* 3.7 8.3 - - + -
94P LEU* 3.6 40.2 - - + +
97P HIS* 3.4 41.3 - - + +
502P HEM 3.6 30.6 - - + +
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Residues in contact with GLY 38 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34P GLY 3.2 9.4 + - - -
35P SER* 3.2 8.7 + - - -
37P LEU* 1.3 76.7 - - - +
39P ILE* 1.3 58.5 + - - +
41P LEU* 3.4 7.9 + - - +
42P ILE* 3.0 38.9 + - - +
502P HEM 4.2 9.4 - - - +
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Residues in contact with ILE 39 (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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35P SER* 3.0 21.3 + - - +
36P LEU* 3.6 12.8 - - + +
38P GLY* 1.3 75.8 - - - +
40P CYS* 1.3 59.6 + - - +
42P ILE* 3.3 10.6 + - + +
43P LEU* 2.9 42.9 + - + +
228P ASP 5.2 1.1 - - - +
232P ALA* 3.4 34.8 - - + -
235P LEU* 3.9 16.2 - - + -
236P ILE* 5.6 4.0 - - + -
3006Q PEE 4.3 30.5 - - + -
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Residues in contact with CYS 40 (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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36P LEU 2.9 22.9 + - - +
37P LEU* 3.7 6.3 - - - +
39P ILE* 1.3 76.9 - - - +
41P LEU* 1.3 59.1 + - - +
43P LEU* 3.3 6.8 + - - +
44P GLN* 2.9 33.8 + - - +
86P GLY* 4.6 3.8 - - - +
89P MET* 4.0 14.6 - - - -
90P PHE* 3.8 46.4 - - + -
93P CYS* 4.2 7.0 - - - -
235P LEU* 4.0 16.2 - - - -
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Residues in contact with LEU 41 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37P LEU 2.9 16.5 + - - +
38P GLY* 3.6 8.1 - - - +
40P CYS* 1.3 78.3 - - - +
42P ILE* 1.3 60.0 + - + +
44P GLN* 3.4 1.5 + - - +
45P ILE* 2.9 52.2 + - + +
90P PHE* 3.9 11.8 - - + -
186P PRO* 3.9 10.5 - - + +
189P ILE* 4.1 15.9 - - + +
190P MET* 3.8 34.8 - - + +
193P ALA* 4.9 8.3 - - + -
501P HEM 4.1 24.2 - - + -
502P HEM 5.2 6.5 - - + -
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Residues in contact with ILE 42 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38P GLY* 3.0 23.5 + - - +
39P ILE* 3.8 10.5 - - + +
41P LEU* 1.3 76.7 - - + +
43P LEU* 1.3 63.0 + - + +
45P ILE* 3.3 8.6 + - + +
46P LEU* 2.8 50.8 + - + +
190P MET* 6.3 2.9 - - - -
3006Q PEE 4.4 20.6 - - + -
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Residues in contact with LEU 43 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39P ILE* 2.9 29.5 + - + +
40P CYS* 3.6 7.4 - - - +
42P ILE* 1.3 78.6 - - + +
44P GLN* 1.3 63.6 + - - +
46P LEU* 3.2 7.1 + - + +
47P THR* 2.8 40.3 + - + +
82P MET* 4.7 7.2 - - + -
86P GLY* 6.1 2.0 - - - -
235P LEU* 6.0 2.7 - - + -
236P ILE* 5.4 4.0 - - + -
239P LEU* 3.9 27.6 - - + -
3006Q PEE 3.1 55.2 - - + -
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Residues in contact with GLN 44 (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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40P CYS 2.9 19.9 + - - +
41P LEU 3.7 2.5 - - - +
43P LEU* 1.3 79.9 - - - +
45P ILE* 1.3 54.1 + - - +
47P THR* 3.7 2.5 + - - -
48P GLY* 2.7 34.3 + - - -
82P MET 3.9 4.5 - - - +
83P HIS* 3.0 45.6 + - - +
86P GLY* 3.3 22.3 - - - -
87P ALA 3.6 12.5 - - - +
90P PHE* 4.0 13.9 - - + -
501P HEM 3.4 48.4 - - + +
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Residues in contact with ILE 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 LEU* 2.9 42.1 + - + +
42P ILE* 3.7 9.0 - - + +
44P GLN* 1.3 75.9 - - + +
46P LEU* 1.3 62.5 + - + +
49P LEU* 2.9 40.1 + - + +
186P PRO* 4.0 19.3 - - + +
187P PHE* 3.8 27.8 - - + -
190P MET* 4.1 23.8 - - + -
501P HEM 3.9 18.6 - - + +
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Residues in contact with LEU 46 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42P ILE* 2.8 33.7 + - + +
43P LEU* 3.9 10.8 - - + +
45P ILE* 1.3 78.5 - - + +
47P THR* 1.3 62.8 + - + +
49P LEU* 3.4 11.9 + - + +
50P PHE* 3.2 39.5 + - + -
3006Q PEE 3.8 40.4 - - + -
58R PHE* 4.4 11.2 - - + -
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Residues in contact with THR 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 LEU* 2.8 31.6 + - + +
44P GLN* 3.7 2.1 + - - -
46P LEU* 1.3 73.3 - - + +
48P GLY* 1.3 62.3 + - - +
50P PHE 3.4 1.0 + - - -
51P LEU* 2.9 27.5 + - - +
79P ILE* 3.6 31.1 - - + +
82P MET* 4.1 23.6 - - + +
83P HIS* 2.9 30.2 + - - +
58R PHE* 3.9 24.7 - - + -
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Residues in contact with GLY 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 GLN 2.7 24.6 + - - -
45P ILE 3.7 0.2 - - - -
47P THR* 1.3 74.2 + - - +
49P LEU* 1.3 56.3 + - - +
51P LEU* 3.2 2.7 + - - +
52P ALA* 2.9 24.8 + - - +
83P HIS* 3.6 7.0 - - - -
501P HEM 3.3 38.9 - - - +
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Residues in contact with LEU 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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180C ALA* 4.9 5.1 - - + +
184C ILE* 4.6 15.7 - - + -
45P ILE* 2.9 38.4 + - + +
46P LEU* 3.9 13.2 - - + +
48P GLY* 1.3 74.4 - - - +
50P PHE* 1.3 70.3 + - + +
52P ALA* 3.1 13.2 + - + +
53P MET* 3.2 23.3 + - + +
183P PHE* 3.9 18.4 - - + -
187P PHE* 4.3 11.0 - - + -
501P HEM 3.4 23.1 - - + -
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Residues in contact with PHE 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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46P LEU* 3.2 35.6 + - + +
47P THR 3.9 3.6 - - - +
48P GLY 3.3 0.2 - - - -
49P LEU* 1.3 84.8 - - + +
51P LEU* 1.3 60.7 + - - +
53P MET* 3.3 38.2 + - + +
54P HIS* 3.3 20.2 - - - -
79P ILE* 4.3 17.9 - - + -
58R PHE* 3.4 47.8 - + + -
59R VAL* 5.1 1.6 - - + -
61R SER* 3.4 18.6 + - - +
62R MET* 3.9 15.9 - - + -
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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
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47P THR 2.9 17.1 + - - +
48P GLY 3.6 3.1 - - - +
50P PHE* 1.3 70.8 - - - +
52P ALA* 1.3 58.9 + - - +
53P MET 3.0 4.7 - - - -
54P HIS* 2.9 20.4 + - - -
55P TYR* 3.0 13.3 + - - +
69P ILE* 3.7 38.8 - - + +
79P ILE* 3.8 13.7 - - + +
80P ARG* 3.8 20.0 - - + +
83P HIS* 3.5 37.9 - - + +
501P HEM 3.5 39.3 - - + +
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Residues in contact with ALA 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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176C THR* 3.7 16.1 - - - +
179C PHE* 6.0 1.4 - - - -
180C ALA* 4.0 7.2 - - + +
48P GLY 2.9 16.3 + - - +
49P LEU* 3.1 8.0 + - - +
51P LEU* 1.3 77.1 - - - +
53P MET* 1.3 58.1 + - - +
54P HIS 3.1 1.6 + - - -
55P TYR* 3.9 9.4 + - - +
179P PHE* 4.0 15.7 - - + -
183P PHE* 4.0 27.1 - - + -
501P HEM 3.7 17.0 - - + +
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Residues in contact with MET 53 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173C ALA* 4.2 4.3 - - - +
176C THR* 3.0 19.7 - - - +
177C ARG* 3.5 31.9 + - + +
180C ALA* 4.5 5.2 - - + -
181C PHE* 4.1 26.9 - - + -
49P LEU* 3.2 13.2 + - + +
50P PHE* 3.4 58.6 - - + +
51P LEU 3.0 1.0 - - - -
52P ALA* 1.3 77.9 - - - +
54P HIS* 1.3 70.8 + - + +
62R MET* 3.8 29.8 - - - +
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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