Contacts of the helix formed by residues 32 - 37 (chain S) 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 MET 32 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26S PHE* 4.1 1.8 - - - -
30S GLY 5.0 0.2 - - - +
31S LEU* 1.3 77.6 - - - +
33S ARG* 1.3 68.0 + - - +
34S ASP 4.5 3.8 - - - +
35S ASP* 2.7 30.0 + - - +
36S THR* 3.7 4.9 + - - +
61S ARG* 3.6 39.5 - - - +
81S THR* 4.3 12.1 - - + +
85S GLU 4.7 3.1 - - - +
86S ASP* 3.6 13.0 - - - +
87S LYS* 3.2 45.8 - - + +
89S TYR* 4.2 12.6 - - + -
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Residues in contact with ARG 33 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377P LEU* 3.0 28.2 + - + +
378P LYS* 2.8 33.3 + - - +
379P TRP* 3.2 47.9 - - + +
21S TYR* 5.0 2.0 - - + -
26S PHE* 3.5 27.4 - - + -
32S MET* 1.3 70.2 - - - +
34S ASP* 1.3 93.8 + - - +
36S THR* 2.8 30.0 + - - +
86S ASP* 2.9 24.2 + - - +
88S SER* 3.5 23.9 + - - +
91S GLU* 5.6 0.6 - - - +
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Residues in contact with ASP 34 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379P TRP* 3.7 9.4 - - - -
32S MET* 3.2 2.0 + - - +
33S ARG* 1.3 107.6 + - - +
35S ASP* 1.3 59.3 + - - +
36S THR 3.1 0.8 + - - -
37S ILE* 3.5 12.2 + - - +
58S ARG* 2.8 19.1 + - - -
86S ASP* 5.0 1.0 + - - -
87S LYS 4.8 1.7 + - - +
88S SER* 2.7 36.8 + - - -
89S TYR* 3.2 24.8 + - + -
90S LEU* 3.1 27.2 + - + +
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Residues in contact with ASP 35 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211P ILE* 3.6 23.8 - - - +
31S LEU* 3.6 23.7 - - + -
32S MET* 2.7 34.0 + - - +
34S ASP* 1.3 77.8 - - - +
36S THR* 1.3 58.1 + - - +
37S ILE 3.5 2.0 + - - +
58S ARG* 3.8 15.7 + - - +
61S ARG* 2.8 39.3 + - - +
62S ILE* 4.2 10.1 - - + +
89S TYR* 2.6 28.7 + - - -
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Residues in contact with THR 36 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209P THR 5.5 1.4 - - - +
210P GLY 5.3 2.1 - - - +
211P ILE* 3.9 13.4 - - + +
312P GLN* 2.9 41.8 + - - +
313P ARG 4.7 1.4 + - - -
317P PHE* 4.0 16.8 - - + -
379P TRP* 3.8 1.7 - - - -
26S PHE* 3.8 33.8 - - + -
31S LEU* 4.1 10.1 - - + -
32S MET 3.9 6.3 - - - +
33S ARG* 2.8 19.3 + - - +
35S ASP* 1.3 80.6 - - - +
37S ILE* 1.3 66.2 + - - +
38S HIS* 3.6 0.5 + - - -
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Residues in contact with ILE 37 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210P GLY 5.1 3.5 - - - +
211P ILE* 5.4 3.6 - - - +
311P LYS* 3.7 26.5 - - + +
379P TRP* 3.8 32.3 - - + -
33S ARG 3.8 1.8 + - - -
34S ASP* 3.5 15.1 + - - +
35S ASP 3.5 2.8 - - - +
36S THR* 1.3 81.6 + - - +
38S HIS* 1.3 69.3 + - - +
39S GLU* 3.4 7.7 + - + +
43S VAL* 3.7 42.4 - - + -
58S ARG* 4.0 8.5 + - - +
90S LEU* 4.2 7.6 - - + -
94S LEU* 3.8 19.3 - - + -
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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
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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