Contacts of the strand formed by residues 204 - 209 (chain O) 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 204 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32O GLY 4.4 1.7 - - - +
33O LEU* 3.4 18.7 - - + +
34O VAL* 3.3 20.6 + - - +
49O LEU* 4.0 24.2 - - + -
50O PHE 3.1 7.6 - - - +
51O ILE* 4.1 16.8 - - + -
127O THR* 6.0 0.7 - - - -
128O THR* 5.6 1.8 - - + -
199O PHE* 3.9 18.8 - - - +
200O THR 3.1 16.1 + - - +
201O SER* 3.3 17.9 + - - +
202O ALA 3.5 1.1 - - - -
203O ARG* 1.3 83.4 - - - +
205O ALA* 1.3 62.2 + - - +
224O LEU* 3.8 41.1 - - + +
226O ILE* 4.3 8.5 - - + -
387O LEU* 3.7 5.1 - - - +
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Residues in contact with ALA 205 (chain O).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34O VAL* 3.1 13.5 - - + +
48O GLY 3.5 3.1 - - - +
49O LEU* 3.6 3.6 - - - -
50O PHE* 2.8 41.2 + - + +
204O MET* 1.3 76.4 - - - +
206O LEU* 1.3 60.5 + - - +
207O ILE* 3.8 6.4 + - + -
386O ALA* 3.6 31.2 - - + -
387O LEU* 3.8 15.5 - - + -
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Residues in contact with LEU 206 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33O LEU* 4.5 3.2 - - + +
34O VAL 2.8 11.9 + - - +
35O ILE* 3.4 10.7 - - + +
36O ALA 3.0 25.6 + - - +
47O ILE* 3.6 27.8 - - + -
48O GLY 3.6 8.5 - - - +
49O LEU* 4.3 18.8 - - + +
120O MET* 4.7 8.1 - - - -
123O LEU* 4.8 2.7 - - + -
205O ALA* 1.3 70.3 - - - +
207O ILE* 1.3 59.7 + - - +
216O LEU* 3.7 42.6 - - + +
219O VAL* 4.6 6.7 - - + -
220O ALA* 4.0 17.9 - - + +
224O LEU* 4.0 15.3 - - + -
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Residues in contact with ILE 207 (chain O).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24O LEU* 5.8 0.7 - - + -
34O VAL 5.1 0.4 - - - +
36O ALA* 3.1 19.1 - - + +
37O SER* 5.3 0.4 - - - -
47O ILE* 3.3 7.1 - - - +
48O GLY 2.8 32.6 + - - +
50O PHE* 3.7 15.3 - - + -
205O ALA* 4.1 15.7 - - + +
206O LEU* 1.3 82.2 - - - +
208O GLY* 1.3 64.1 + - - +
209O LEU* 5.5 2.9 - - + -
216O LEU* 4.2 3.1 - - - -
378O PHE* 6.2 0.2 - - + -
379O LEU* 3.6 24.6 - - + +
382O VAL* 3.7 37.5 - - + -
383O GLY* 3.7 24.7 - - - -
386O ALA* 4.1 4.5 - - + -
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Residues in contact with GLY 208 (chain O).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36O ALA 2.9 9.7 + - - -
37O SER* 3.0 4.3 - - - -
38O LEU 2.9 25.3 + - - -
46O ARG 3.3 6.3 - - - -
47O ILE* 3.8 4.9 - - - -
207O ILE* 1.3 78.1 - - - +
209O LEU* 1.3 68.1 + - - +
211O VAL* 3.5 20.4 - - - -
216O LEU* 3.8 4.6 - - - +
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Residues in contact with LEU 209 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24O LEU* 5.6 0.4 - - + -
38O LEU* 3.5 16.2 - - + +
40O ASN* 4.3 14.1 - - - +
44O ALA 5.0 0.7 - - - +
45O SER* 3.3 6.3 - - - -
46O ARG* 2.8 38.9 + - + +
47O ILE* 4.5 0.2 - - - +
207O ILE* 5.5 2.0 - - + -
208O GLY* 1.3 82.0 - - - +
210O GLY* 1.3 65.1 + - - +
211O VAL* 3.2 3.6 + - - +
375O SER* 3.4 46.9 - - - +
378O PHE* 3.5 36.3 - - + -
379O LEU* 3.8 18.2 - - + -
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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