Contacts of the strand formed by residues 125 - 131 (chain C) in PDB entry 2Q5E
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 PHE 125 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C VAL* 5.1 0.2 - - + -
123C ALA* 4.2 3.4 - - - +
124C ASP* 1.3 90.3 - - + +
126C ILE* 1.3 68.7 + - - +
127C VAL* 4.4 1.3 - - + -
139C TYR* 3.7 0.3 - - - -
140C VAL* 2.9 60.6 + - + +
142C LYS* 3.3 46.2 - - + -
173C VAL* 5.1 4.5 - - + -
176C LEU* 3.8 58.8 - - + -
177C LEU* 4.2 14.8 - - + -
179C ARG* 6.3 0.4 - - - -
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Residues in contact with ILE 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A ARG* 4.5 30.7 - - + +
120C ILE 5.7 1.6 - - - +
123C ALA* 5.1 13.9 - - + +
125C PHE* 1.3 80.0 - - - +
127C VAL* 1.3 72.4 + - - +
128C PRO* 4.4 3.0 - - + +
137C GLN* 3.7 39.3 - - + +
138C VAL 3.1 4.5 - - - +
139C TYR* 3.7 28.7 - - + -
176C LEU* 4.9 3.1 - - - +
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Residues in contact with VAL 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C PHE* 4.4 5.2 - - + -
126C ILE* 1.3 84.8 - - - +
128C PRO* 1.3 69.0 - - + +
129C ILE* 3.4 26.3 + - + +
136C HIS 3.5 0.2 - - - +
137C GLN* 3.2 4.9 - - - -
138C VAL* 2.7 48.7 + - + +
140C VAL* 4.4 8.3 - - + -
172C PRO* 4.1 22.9 - - + +
173C VAL* 4.4 15.5 - - + -
176C LEU* 3.9 25.1 - - + -
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Residues in contact with PRO 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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126C ILE* 4.4 3.4 - - + +
127C VAL* 1.3 87.4 - - + +
129C ILE* 1.3 66.9 + - - +
135C THR* 3.3 21.8 - - + -
136C HIS 3.1 7.4 - - - +
137C GLN* 3.3 13.4 - - - +
172C PRO* 5.5 2.0 - - + +
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Residues in contact with ILE 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C PHE* 4.7 7.9 - - + -
127C VAL* 3.4 22.9 - - + +
128C PRO* 1.3 83.3 - - - +
130C GLU* 1.3 73.7 + - - +
131C ILE* 3.7 12.6 + - + +
134C THR 3.5 0.7 - - - +
135C THR* 3.7 4.2 - - - +
136C HIS* 2.7 33.9 + - - +
138C VAL* 3.3 30.5 - - + -
168C LYS* 3.5 44.6 - - + +
169C TYR* 4.2 13.2 - - + -
172C PRO* 4.1 5.4 - - + -
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Residues in contact with GLU 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 ILE* 1.3 74.9 - - - +
131C ILE* 1.3 59.9 + - - +
132C GLU* 3.1 12.6 + - - -
133C GLY* 2.9 42.5 + - - -
134C THR 3.6 10.1 - - - +
135C THR* 4.2 6.9 - - - +
168C LYS* 3.0 27.7 + - + +
130F GLU* 5.3 15.9 - - + -
168F LYS* 4.7 13.4 - - - +
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Residues in contact with ILE 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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117C PHE* 3.6 25.8 - - + -
129C ILE* 4.0 11.7 - - + +
130C GLU* 1.3 80.8 - - - +
132C GLU* 1.3 85.8 + - + +
134C THR* 3.0 22.4 + - - +
136C HIS* 3.9 14.4 - - + +
168C LYS* 4.3 12.1 - - - +
194H PHE* 3.4 38.8 - - + -
199H TYR* 5.4 7.2 - - - +
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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