Contacts of the strand formed by residues 122 - 127 (chain C) in PDB entry 1EFP
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 122 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C ILE 3.9 0.2 - - - -
118C LEU* 3.0 49.9 + - + -
119C ASP* 2.8 36.9 + - - +
121C ASP* 1.3 69.3 - - - +
123C PHE* 1.3 67.9 + - - +
135C VAL* 3.9 11.7 - - + -
136C VAL 3.3 11.9 - - - +
137C LYS* 3.5 28.6 + - + +
222D VAL* 5.3 4.3 - - + -
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Residues in contact with PHE 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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86C HIS* 4.3 2.7 - + - -
111C LEU* 4.3 17.0 - - + -
114C VAL* 4.1 22.7 - - + -
116C ALA 3.5 5.4 - - - +
117C ILE* 4.0 29.2 - - + -
118C LEU* 4.4 1.6 - - - +
119C ASP 4.3 0.7 - - - -
120C ALA 4.0 12.1 - - - -
121C ASP* 3.3 30.1 - - - -
122C THR* 1.3 76.6 - - - +
124C GLU* 1.3 62.4 + - - +
125C ARG* 6.1 0.2 - - + -
135C VAL* 3.4 6.7 - - - +
136C VAL* 2.8 44.3 + - + +
138C SER* 4.6 4.7 - - - -
143C LYS* 3.8 30.3 - - + -
145C PHE* 3.9 28.9 - + - -
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Residues in contact with GLU 124 (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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114C VAL* 3.5 5.0 - - - +
115C SER* 2.8 31.6 + - - +
116C ALA* 2.8 35.6 + - + +
118C LEU* 4.1 23.2 - - + +
123C PHE* 1.3 77.7 - - - +
125C ARG* 1.3 62.7 + - - +
133C ILE* 3.9 9.8 - - + +
134C GLN 3.3 4.5 - - - +
135C VAL* 4.2 16.8 - - + +
225D ARG* 3.3 36.1 + - - -
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Residues in contact with ARG 125 (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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111C LEU* 4.5 23.6 - - - +
112C SER* 2.9 27.6 + - - +
113C ASP* 3.7 10.4 - - - +
114C VAL* 4.5 2.9 - - + -
115C SER* 3.9 1.3 + - - -
124C GLU* 1.3 77.5 - - - +
126C PRO* 1.3 79.1 + - + +
127C ILE* 3.5 12.8 - - - +
133C ILE* 4.5 2.2 - - - +
134C GLN* 2.8 73.4 + - + +
136C VAL* 4.5 5.2 - - + -
126D ASN* 2.9 31.1 + - - +
127D ASP* 3.9 11.9 + - - +
128D MET* 3.8 28.2 - - - +
219D LEU* 5.5 1.1 - - - -
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Residues in contact with PRO 126 (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 SER 5.4 0.2 - - - +
113C ASP* 3.2 26.2 - - + +
115C SER* 3.8 15.0 - - - +
125C ARG* 1.3 95.8 + - + +
127C ILE* 1.3 62.9 + - - +
130C GLY* 4.2 15.9 - - - +
132C ALA 3.5 10.8 - - - +
133C ILE* 4.2 13.9 - - + -
148C ARG* 4.1 22.4 - - - +
269C LYS* 6.1 1.6 - - - +
127D ASP* 4.6 8.0 - - - +
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Residues in contact with ILE 127 (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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125C ARG* 3.5 28.7 - - - +
126C PRO* 1.3 75.6 - - - +
128C TYR* 1.3 89.9 + - + +
129C ALA 3.4 2.2 - - - -
130C GLY 2.9 9.8 + - - -
131C ASN 3.2 7.3 + - - -
132C ALA* 3.0 24.4 + - + +
134C GLN* 3.6 39.9 - - + +
26D VAL* 4.5 3.8 - - + -
125D ASP 3.8 9.2 - - - +
126D ASN* 4.4 8.3 - - + +
127D ASP* 4.1 3.6 - - - -
224D VAL* 3.9 16.4 - - + -
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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