Contacts of the strand formed by residues 118 - 123 (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 THR 118 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C TRP* 3.4 7.5 - - - -
114C ILE* 2.9 32.2 + - + -
115C SER* 2.7 33.5 + - - +
116C LEU 3.5 2.9 + - - -
117C ASN* 1.3 82.4 + - - +
119C VAL* 1.3 62.9 + - - +
129C HIS* 4.7 21.3 - - + +
130C TRP 3.6 12.8 - - - +
131C SER* 4.3 9.2 - - - +
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Residues in contact with VAL 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C ILE* 4.1 18.2 - - + -
81C ALA* 5.3 2.9 - - + -
90C ILE* 4.6 11.4 - - + -
111C TRP* 4.3 5.6 - - + -
112C LYS 3.3 19.3 - - - +
113C TRP* 4.1 20.6 - - + -
114C ILE* 5.0 0.7 - - - -
118C THR* 1.3 73.7 - - - +
120C ALA* 1.3 69.9 + - - +
121C LEU* 3.9 11.3 + - + +
129C HIS* 4.8 1.1 - - - -
130C TRP* 2.9 65.3 + - + +
132C MET 5.6 0.2 - - - +
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Residues in contact with ALA 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C PHE* 6.5 0.9 - - + -
111C TRP* 3.2 10.2 - - - +
112C LYS* 2.8 36.3 + - + +
114C ILE* 3.5 32.2 - - + +
119C VAL* 1.3 72.3 - - - +
121C LEU* 1.3 61.3 + - - +
122C VAL* 5.2 3.9 - - + +
127C VAL* 5.1 7.2 - - + -
128C TYR 3.2 11.2 - - - +
129C HIS* 4.0 9.6 - - + +
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Residues in contact with LEU 121 (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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88C LEU* 3.6 22.7 - - + -
104C MET* 4.2 12.1 - - - -
108C VAL* 4.2 12.1 - - + -
110C PHE 3.8 2.7 - - - -
111C TRP* 3.5 33.7 - - + -
119C VAL* 4.1 15.0 - - + +
120C ALA* 1.3 79.2 - - - +
122C VAL* 1.3 63.3 + - - +
123C THR 4.1 0.4 - - - -
127C VAL* 3.4 4.7 - - - +
128C TYR* 2.7 50.7 + - + +
130C TRP* 4.1 9.6 - - + -
138C PRO* 3.9 33.0 - - + -
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Residues in contact with VAL 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C VAL* 3.5 2.6 - - - +
109C THR* 2.7 40.3 + - + +
110C PHE* 2.8 46.1 + - + +
120C ALA* 5.2 3.4 - - + +
121C LEU* 1.3 78.6 - - - +
123C THR* 1.3 67.7 + - - +
126C ALA 3.8 4.3 - - - +
127C VAL* 4.2 19.3 - - + -
144C ARG* 4.1 20.4 - - - +
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Residues in contact with THR 123 (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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104C MET* 4.6 2.7 - - - -
106C ASP* 3.3 42.4 + - - +
107C ASP 3.4 14.4 - - - +
108C VAL* 4.2 10.5 - - + -
109C THR* 4.3 2.7 - - - +
122C VAL* 1.3 77.2 - - - +
124C ASP* 1.3 65.0 + - - +
125C ASN 3.1 2.0 + - - -
126C ALA 3.0 27.6 + - - +
128C TYR* 3.5 24.7 + - + -
144C ARG* 3.1 23.9 + - - -
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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