Contacts of the strand formed by residues 124 - 131 (chain C) in PDB entry 3ESF
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 GLY 124 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C HIS* 3.5 7.0 - - - -
122C GLY 3.7 3.6 + - - -
123C SER* 1.3 75.9 - - - +
125C TRP* 1.3 70.1 + - - -
142C THR 3.3 12.3 - - - -
144C ASP 3.8 5.4 - - - -
162C VAL* 2.9 31.1 + - - +
163C TRP* 3.4 17.0 + - - +
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Residues in contact with TRP 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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72C GLN* 3.2 18.1 + - - -
75C ASN* 3.3 53.9 - - + +
76C HIS* 3.6 23.3 - + - -
79C TYR* 3.9 9.2 - - + -
120C HIS* 4.5 2.8 + - - -
124C GLY* 1.3 75.7 - - - -
126C ALA* 1.3 59.9 + - - +
127C TRP* 3.2 21.7 - + + +
141C GLN* 3.4 8.0 - - - +
142C THR* 2.8 43.5 + - - +
144C ASP 3.0 28.0 + - - -
146C GLY 4.2 0.4 - - - -
159C THR* 3.5 16.2 - - + +
160C CYS 3.7 3.8 - - - -
161C ASP* 3.3 49.6 - - + -
162C VAL* 4.0 4.2 - - - +
163C TRP* 3.6 4.0 - - - +
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Residues in contact with ALA 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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113C PHE* 3.6 22.2 - - + -
116C ALA* 4.4 11.2 - - + +
117C ALA* 3.9 35.4 - - + +
120C HIS* 6.4 0.2 - - + -
125C TRP* 1.3 72.7 - - - +
127C TRP* 1.3 62.4 + - - +
139C VAL* 5.6 0.4 - - + -
140C PHE 3.9 2.7 - - - -
141C GLN* 4.7 1.6 - - + +
159C THR* 3.0 4.3 + - - -
160C CYS 2.9 37.3 + - - +
162C VAL* 4.7 2.0 - - + +
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Residues in contact with TRP 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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74C PHE* 4.3 7.0 - + - -
75C ASN* 3.3 44.2 - - + -
78C PHE* 3.8 11.9 - + - -
113C PHE* 3.7 6.4 - - - -
125C TRP* 3.2 14.8 - + + +
126C ALA* 1.3 78.5 - - - +
128C LEU* 1.3 59.2 + - - +
129C VAL* 3.7 16.8 - - + -
139C VAL* 3.4 10.7 - - - +
140C PHE* 2.7 45.7 + + - +
142C THR* 2.9 32.4 + - + +
148C PRO* 3.4 25.1 - - + -
156C PRO* 3.8 30.1 - - + -
158C LEU 3.3 9.6 - - - +
159C THR* 3.4 35.7 - - + -
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Residues in contact with LEU 128 (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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95C LEU* 5.0 2.7 - - + -
99C ILE* 4.6 16.4 - - + -
103C PHE* 3.9 27.4 - - + -
109C PHE* 3.9 30.7 - - + -
113C PHE* 3.8 5.2 - - + -
127C TRP* 1.3 73.7 - - - +
129C VAL* 1.3 63.1 + - - +
137C LEU* 4.0 17.3 - - + -
138C LYS 3.5 16.4 - - - +
156C PRO* 4.0 0.3 - - - +
157C ILE* 2.9 47.4 + - + -
158C LEU* 3.0 32.7 + - + +
188C TRP* 5.1 0.9 - - + -
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Residues in contact with VAL 129 (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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127C TRP* 3.7 19.5 - - + -
128C LEU* 1.3 80.2 - - - +
130C GLN* 1.3 61.2 + - - +
137C LEU* 3.3 6.2 - - - +
138C LYS* 2.9 58.7 + - + +
140C PHE* 3.8 13.7 - - + -
148C PRO* 4.0 25.4 - - + -
154C LEU* 3.7 22.7 - - + -
155C LYS 3.3 10.3 - - - +
156C PRO* 4.2 7.2 - - + -
157C ILE* 4.0 4.9 - - - -
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Residues in contact with GLN 130 (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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129C VAL* 1.3 73.9 - - - +
131C ASP* 1.3 74.1 + - - +
132C THR* 3.4 4.8 + - - -
135C LYS* 3.3 49.5 + - - +
136C LYS 3.4 3.6 - - - +
137C LEU* 3.7 12.1 - - + -
153C ASP 3.4 1.6 - - - +
154C LEU* 3.5 4.5 - - - -
155C LYS* 2.8 69.9 + - - +
157C ILE* 4.0 6.5 - - + +
195C PHE* 3.7 27.9 + - - +
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Residues in contact with ASP 131 (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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129C VAL* 4.2 0.8 - - - +
130C GLN* 1.3 71.0 - - - +
132C THR* 1.3 54.7 + - - +
133C THR* 2.7 44.0 + - - -
134C THR* 3.0 26.5 + - - +
135C LYS* 2.7 36.0 + - - -
136C LYS* 2.8 14.8 + - + +
138C LYS* 5.2 12.1 + - + +
153C ASP* 3.3 15.5 - - - +
154C LEU* 4.3 11.7 - - + +
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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