Contacts of the strand formed by residues 95 - 100 (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 LYS 95 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46O ARG* 4.8 3.0 - - - +
89O ILE* 3.9 4.9 - - - +
94O GLY* 1.3 71.3 - - - -
96O LEU* 1.3 64.1 + - - +
97O SER* 4.5 11.0 - - - -
108O THR 4.5 0.4 - - - -
109O VAL* 3.2 8.5 - - - +
110O GLU* 2.9 70.5 + - + +
119O LEU* 4.0 2.8 - - - +
376O GLU* 5.0 5.3 + - - -
32V ALA* 3.0 46.0 - - + +
34V VAL* 4.2 17.6 - - - +
69V SER* 3.7 17.3 - - - +
71V ASN* 4.8 2.7 - - + +
72V VAL* 4.0 13.1 - - + +
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Residues in contact with LEU 96 (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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73O SER* 4.1 37.6 + - - +
74O SER* 5.6 1.1 - - - -
85O ILE* 4.2 10.5 - - + -
89O ILE* 3.8 29.8 - - + -
95O LYS* 1.3 75.5 - - - +
97O SER* 1.3 71.6 + - - +
107O TYR* 4.9 5.8 - - + -
108O THR 3.5 10.1 - - - +
109O VAL* 3.8 15.5 - - + -
122O PHE* 5.5 2.9 - - + +
123O LEU* 4.8 12.1 - - + -
126O VAL* 4.3 11.7 - - + -
69V SER* 3.2 3.2 + - - -
70V LEU* 3.1 40.2 + - + +
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Residues in contact with SER 97 (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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73O SER* 5.7 0.4 - - - -
95O LYS* 4.5 12.8 - - - -
96O LEU* 1.3 78.1 - - - +
98O VAL* 1.3 68.9 + - - +
99O THR* 4.0 12.7 + - - -
106O ALA 4.3 0.2 - - - -
107O TYR* 3.4 4.2 - - - -
108O THR* 2.9 45.0 + - - -
110O GLU* 5.5 0.2 - - - -
67V SER* 4.6 4.5 - - - -
68V VAL 3.3 15.5 + - - -
69V SER* 3.9 10.8 - - - -
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Residues in contact with VAL 98 (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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70O ARG* 3.7 29.4 - - + +
73O SER* 3.6 32.8 - - - +
96O LEU* 5.3 0.7 - - + -
97O SER* 1.3 81.2 + - - +
99O THR* 1.3 66.1 + - - +
100O SER* 4.7 1.6 - - - +
105O MET* 3.8 27.8 - - + -
106O ALA 3.3 8.1 - - - +
107O TYR* 3.7 24.2 - - + -
66V ALA 3.8 1.4 - - - +
67V SER* 3.3 1.9 - - - -
68V VAL* 2.8 36.2 + - + +
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Residues in contact with THR 99 (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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97O SER* 4.0 7.1 + - - -
98O VAL* 1.3 77.0 - - - +
100O SER* 1.3 61.3 + - - +
101O THR* 5.3 2.1 - - + +
104O ASN 3.9 0.7 - - - +
105O MET* 3.2 2.8 - - - -
106O ALA* 2.7 46.3 + - + +
108O THR* 5.5 4.3 + - - +
65V VAL* 3.1 34.3 - - + -
66V ALA 3.3 2.9 - - - +
67V SER* 3.0 22.4 + - - +
77V ARG* 4.5 6.1 + - - +
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Residues in contact with SER 100 (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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54O GLY* 5.5 1.3 - - - -
55O SER 5.9 0.7 - - - -
66O SER* 4.7 2.2 + - - -
70O ARG* 3.3 38.3 + - - +
99O THR* 1.3 75.0 - - - +
101O THR* 1.3 66.7 + - - +
104O ASN 3.3 7.2 - - - -
105O MET* 3.4 27.7 - - - +
176O LEU* 3.9 7.2 - - - +
65V VAL* 3.4 6.3 - - - +
66V ALA 2.8 34.6 + - - -
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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
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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