Contacts of the helix formed by residues 61 - 72 (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 THR 61 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C ASP* 4.5 18.4 + - + +
60C THR* 5.6 2.7 - - - +
61C THR* 6.5 0.9 - - + -
56P THR* 3.0 19.5 + - - -
58P ASP* 2.9 20.9 + - + +
60P THR* 1.3 94.5 + - - +
62P ALA* 1.3 57.2 + - - -
63P PHE 3.5 1.6 - - - -
64P SER* 3.4 11.9 + - - -
65P SER* 2.9 30.0 + - - -
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Residues in contact with ALA 62 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55P TYR* 3.8 2.0 - - - +
56P THR 3.2 19.1 - - - +
58P ASP 2.7 19.4 + - - +
59P THR* 4.2 2.8 + - - +
60P THR 3.9 0.8 - - - -
61P THR* 1.3 72.1 - - - +
63P PHE* 1.3 64.0 + - - +
65P SER* 2.8 19.8 + - - -
66P VAL* 3.1 12.4 + - - +
133P LEU 3.7 13.9 - - - +
134P PRO 4.2 1.8 - - - -
135P TRP* 4.2 6.1 - - + -
175P LEU* 3.7 24.7 - - + -
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Residues in contact with PHE 63 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59P THR 5.3 2.3 + - - +
62P ALA* 1.3 78.1 - - - +
64P SER* 1.3 62.5 + - - +
66P VAL* 3.2 6.8 + - - +
67P THR* 3.1 35.9 + - + +
134P PRO* 3.2 25.6 + - + +
135P TRP* 4.0 11.1 - - + +
136P GLY* 4.2 1.8 - - - -
255P ASN 3.9 19.7 - - - -
256P TYR* 3.6 21.3 - - - -
257P THR 4.0 0.7 - - - -
258P PRO* 3.8 46.0 - - + -
3014P AZI 4.4 13.2 + - - -
45Q TYR* 3.5 28.7 - + - -
115Q TYR* 4.4 7.2 - + - -
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Residues in contact with SER 64 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60P THR 4.8 4.4 + - - -
61P THR* 3.4 19.2 + - - -
62P ALA 3.1 0.6 - - - -
63P PHE* 1.3 77.9 - - - +
65P SER* 1.3 61.1 + - - +
67P THR* 2.9 11.2 + - - -
68P HIS* 2.9 29.0 + - - +
45Q TYR* 3.6 25.7 + - - -
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Residues in contact with SER 65 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54P HIS 3.8 11.0 - - - -
55P TYR* 3.4 10.4 - - - -
56P THR* 3.3 34.8 + - - -
61P THR* 2.9 15.3 + - - -
62P ALA 2.8 15.1 + - - -
64P SER* 1.3 76.5 - - - +
66P VAL* 1.3 57.7 + - - +
68P HIS* 3.3 11.9 + - - +
69P ILE* 3.0 32.3 + - - +
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Residues in contact with VAL 66 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55P TYR* 4.0 19.3 - - + -
62P ALA 3.1 13.4 + - - +
63P PHE* 3.5 8.3 - - + +
64P SER 3.1 0.8 - - - -
65P SER* 1.3 75.8 + - - +
67P THR* 1.3 65.3 + - - +
69P ILE* 3.1 9.6 + - + +
70P CYS* 3.1 22.1 + - - -
80P ARG* 3.7 41.7 - - + +
134P PRO* 4.0 24.2 - - + -
501P HEM 4.2 14.4 - - + +
3014P AZI 3.9 9.2 - - - +
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Residues in contact with THR 67 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63P PHE* 3.1 30.7 + - + +
64P SER 2.9 12.7 + - - -
66P VAL* 1.3 76.2 - - - +
68P HIS* 1.3 57.5 + - - +
70P CYS* 3.3 3.0 + - - +
71P ARG* 2.8 40.6 + - - +
3014P AZI 4.4 5.8 - - - +
45Q TYR* 3.5 23.6 - - + +
115Q TYR* 2.9 45.3 - - + +
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Residues in contact with HIS 68 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54P HIS* 4.5 19.5 + - + +
64P SER 2.9 14.3 + - - +
65P SER* 3.5 15.1 + - - +
66P VAL 3.2 0.2 - - - -
67P THR* 1.3 77.1 + - - +
69P ILE* 1.3 58.2 + - - +
71P ARG* 4.9 1.6 - - - -
72P ASP* 2.8 38.9 + - + +
73P VAL* 3.2 26.7 + - + +
65R SER* 3.6 10.3 + - - -
67R ASP* 3.4 34.7 + - - -
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Residues in contact with ILE 69 (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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51P LEU* 3.7 47.6 - - + +
54P HIS* 3.7 29.2 - - + -
55P TYR* 4.3 7.6 - - + +
65P SER 3.0 19.7 + - - +
66P VAL* 3.1 15.5 + - + +
68P HIS* 1.3 79.7 - - - +
70P CYS* 1.3 63.4 + - - +
71P ARG 3.5 0.2 + - - -
73P VAL* 3.5 18.8 + - + +
76P GLY* 3.2 45.6 - - - +
80P ARG* 4.3 6.5 - - + -
501P HEM 5.0 6.3 - - + -
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Residues in contact with CYS 70 (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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66P VAL 3.1 15.0 + - - +
67P THR* 3.3 5.8 + - - +
69P ILE* 1.3 80.6 - - - +
71P ARG* 1.3 61.7 + - + +
73P VAL 5.4 0.4 - - - +
77P TRP* 3.6 33.7 - - + +
80P ARG* 3.5 54.3 - - - -
81P TYR* 4.1 13.7 - - + +
3014P AZI 5.4 0.9 - - - -
115Q TYR* 5.0 6.5 - - + +
118Q ARG* 6.2 0.4 - - - +
196Q PRO* 5.1 1.0 - - - +
197Q GLU* 4.3 11.8 - - - +
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Residues in contact with ARG 71 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67P THR* 2.8 24.8 + - - +
68P HIS* 4.9 0.9 - - - -
70P CYS* 1.3 79.4 - - + +
72P ASP* 1.3 74.4 + - - +
73P VAL 4.0 2.0 - - - +
45Q TYR* 3.4 39.7 + - - +
46Q VAL* 3.9 10.3 - - - +
50Q HIS* 4.6 14.4 + - + +
114Q SER* 3.4 19.0 + - - -
115Q TYR* 3.1 40.0 + - + +
192Q TRP* 6.3 0.6 - - - -
193Q ALA* 2.7 30.3 + - - +
194Q ALA* 4.0 1.2 + - - +
196Q PRO* 4.0 27.2 - - + +
66R ALA* 5.2 1.0 - - - +
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Residues in contact with ASP 72 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68P HIS* 2.8 27.2 + - + +
71P ARG* 1.3 80.2 - - - +
73P VAL* 1.3 63.2 + - - +
74P ASN* 3.4 3.6 + - - +
49Q ARG* 2.9 34.9 + - - -
50Q HIS* 2.9 26.9 + - - -
90Q TYR* 3.6 9.4 + - - -
65R SER* 3.4 1.9 - - - -
66R ALA* 2.9 33.4 + - + +
67R ASP* 3.6 21.5 - - - +
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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