Contacts of the strand formed by residues 106 - 110 (chain C) in PDB entry 3ELP
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 GLN 106 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C LEU* 4.0 4.5 - - - +
105C ASP* 1.3 74.7 - - - +
107C ILE* 1.3 68.1 + - - +
108C ILE* 2.9 34.9 - - + +
131C LYS* 3.0 33.8 + - + +
133C SER* 4.5 6.7 - - - -
146C ALA 3.8 6.1 + - - -
148C THR* 3.1 27.7 + - - +
150C GLU* 2.7 24.7 + - + +
151C THR* 2.6 22.9 + - - -
152C LYS* 3.0 24.3 + - - -
153C LEU 3.5 3.5 + - - -
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Residues in contact with ILE 107 (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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98C THR* 4.9 9.9 - - + -
101C LEU* 4.7 2.7 - - + -
106C GLN* 1.3 76.6 - - - +
108C ILE* 1.3 73.6 + - - +
109C CYS* 4.0 18.6 - - - -
121C PHE* 4.4 14.4 - - + -
125C ALA* 5.3 2.0 - - + -
130C LEU* 4.9 17.0 - - + -
131C LYS 2.8 15.8 + - - +
132C ILE* 3.4 18.5 - - + +
133C SER 2.9 26.2 + - - +
151C THR* 5.3 0.2 - - - -
153C LEU* 3.1 41.3 - - + +
155C TRP* 4.5 6.5 - - + +
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Residues in contact with ILE 108 (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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106C GLN* 2.9 31.6 - - - +
107C ILE* 1.3 72.0 - - - +
109C CYS* 1.3 61.6 + - - +
133C SER* 3.3 25.4 - - - +
135C VAL* 3.5 26.2 - - + -
137C CYS* 4.3 4.5 - - - -
143C LEU* 3.7 20.6 - - + -
146C ALA* 4.1 20.9 - - + +
147C ILE* 5.3 0.7 - - + +
151C THR* 4.0 13.7 - - + -
153C LEU 2.8 9.7 + - - +
154C VAL* 3.3 14.9 - - + +
155C TRP* 2.7 32.9 + - - +
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Residues in contact with CYS 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 ILE* 4.0 10.8 - - - -
108C ILE* 1.3 79.2 - - - +
110C MET* 1.3 68.3 + - - +
111C ASP 2.9 0.3 + - - -
118C ASN* 5.3 0.4 - - - +
121C PHE* 3.7 37.5 - - + -
132C ILE* 4.3 9.6 - - - -
133C SER 2.9 7.4 + - - +
134C PHE* 3.5 24.0 - - + -
135C VAL* 2.9 24.7 + - - +
137C CYS* 4.5 1.1 - - - -
155C TRP* 3.4 21.5 - - + +
157C GLU* 5.0 2.9 - - - +
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Residues in contact with MET 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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109C CYS* 1.3 74.4 - - - +
111C ASP* 1.3 74.9 + - - +
112C ASP 3.0 9.2 + - - -
118C ASN* 4.3 3.5 + - - -
135C VAL 3.3 4.0 - - - +
136C ASP* 3.9 10.5 - - - +
137C CYS* 3.6 22.5 - - + -
138C SER* 4.4 1.6 - - - +
155C TRP 3.0 11.2 + - - +
156C ILE* 3.9 15.9 - - + -
157C GLU* 3.4 36.4 + - - +
160C THR* 3.2 32.3 - - + -
165C LYS* 3.7 19.7 - - - +
167C ILE* 3.2 35.7 - - + -
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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