Contacts of the strand formed by residues 108 - 115 (chain C) in PDB entry 5ODS
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 VAL 108 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83C LYS* 3.7 30.7 - - + +
86C LYS* 5.2 2.4 - - - +
88C LEU* 4.3 13.2 - - + -
104C MET* 4.0 35.6 - - + +
106C ASP 3.6 0.2 + - - -
107C ASP* 1.3 77.1 + - - +
109C THR* 1.3 60.9 + - - +
110C PHE 3.5 27.6 - - - +
111C TRP* 4.1 17.3 - - + -
121C LEU* 4.2 15.5 - - + -
122C VAL 3.6 7.6 - - - +
123C THR* 4.2 5.4 - - + -
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Residues in contact with THR 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C ASP* 3.4 3.7 + - - -
108C VAL* 1.3 73.4 - - - +
110C PHE* 1.3 61.8 + - + +
122C VAL* 2.7 29.8 + - + +
123C THR 4.3 2.5 - - - +
124C ASP* 4.7 15.6 + - - +
144C ARG* 4.1 20.2 - - - +
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Residues in contact with PHE 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C PHE* 4.9 23.1 - + - -
108C VAL* 3.5 5.4 + - - +
109C THR* 1.3 86.0 - - + +
111C TRP* 1.3 70.4 + - - +
112C LYS* 4.1 35.4 - - + -
120C ALA* 5.8 1.1 - - + -
122C VAL* 2.8 57.6 + - + +
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Residues in contact with TRP 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C GLU* 4.7 2.4 - - - +
70C SER* 2.9 28.2 + - - -
72C ILE* 3.8 27.4 - - + +
81C ALA* 3.5 34.1 - - + -
82C LEU 3.4 24.9 - - - -
83C LYS* 3.5 23.5 - - + +
88C LEU* 3.6 26.2 - - + -
89C GLN 5.4 0.2 - - - -
108C VAL* 4.1 11.0 - - + -
110C PHE* 1.3 90.1 - - - +
112C LYS* 1.3 63.5 + - - +
119C VAL* 4.3 7.6 - - + -
120C ALA 3.2 14.6 - - - +
121C LEU* 3.5 23.3 - - + -
130C TRP* 5.1 4.7 - + - -
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Residues in contact with LYS 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C MET 5.6 3.0 + - - -
33C GLU* 3.2 28.0 + - - +
72C ILE* 4.2 4.2 - - - +
110C PHE* 4.1 24.8 - - + -
111C TRP* 1.3 75.7 - - - +
113C TRP* 1.3 70.1 + - - +
114C ILE* 3.4 13.4 + - + -
119C VAL* 3.3 6.6 - - - +
120C ALA* 2.8 33.6 + - + +
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Residues in contact with TRP 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C GLU* 3.3 19.0 + - + +
72C ILE* 3.0 41.9 + - + +
73C MET 2.9 22.3 + - - +
74C ASN* 3.0 34.5 - - + -
75C PRO* 3.8 21.8 - - + +
79C VAL* 4.5 7.4 - - + -
81C ALA* 3.9 24.0 - - + -
90C ILE* 4.7 4.9 - - + -
112C LYS* 1.3 83.2 - - - +
114C ILE* 1.3 66.4 + - - +
115C SER* 3.5 10.9 + - - +
117C ASN 4.1 1.6 - - - -
118C THR 3.4 38.4 - - - -
119C VAL* 4.1 14.6 - - + +
132C MET* 4.1 19.5 - - + -
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Residues in contact with ILE 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C LYS* 3.4 16.0 + - + +
113C TRP* 1.3 76.6 - - - +
115C SER* 1.3 69.5 + - - +
118C THR* 2.9 19.9 + - + +
119C VAL 5.0 0.2 - - - -
120C ALA* 3.5 30.7 - - + +
129C HIS* 4.2 21.8 - - + +
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Residues in contact with SER 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C PRO* 3.5 14.4 - - - +
113C TRP* 3.4 11.5 - - - +
114C ILE* 1.3 85.6 - - - +
116C LEU* 1.3 69.0 + - - +
117C ASN 3.4 3.3 + - - -
118C THR* 2.7 37.7 + - - +
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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