Contacts of the strand formed by residues 134 - 141 (chain C) in PDB entry 2P4K
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 HIS 134 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A ARG* 3.4 11.9 + - - -
134A HIS* 3.3 31.6 + + - -
100C ASP* 3.5 18.7 + - - +
128C PHE* 3.7 11.4 - - - -
129C ASN* 2.9 31.9 + - + -
132C ARG* 3.3 49.8 + - + +
133C GLY* 1.3 80.5 - - - +
135C LEU* 1.3 73.6 + - - +
136C GLN* 4.5 8.1 + - - -
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Residues in contact with LEU 135 (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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132A ARG* 2.7 34.9 + - - -
93C LEU* 4.3 4.7 - - + -
96C ALA* 3.8 17.7 - - + +
97C ILE* 3.7 44.2 - - + +
100C ASP* 2.9 14.9 + - - +
101C PHE* 3.7 18.8 - - + -
126C LEU* 4.0 6.7 - - + -
127C GLY 3.4 6.5 - - - +
128C PHE* 4.1 4.9 - - + -
134C HIS* 1.3 73.6 - - - +
136C GLN* 1.3 57.9 + - - +
155C LEU* 3.4 33.7 - - + -
193C TYR* 4.1 16.4 - - + -
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Residues in contact with GLN 136 (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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132A ARG* 3.8 11.0 - - - +
136A GLN* 4.5 18.2 - - - +
101C PHE* 4.4 1.6 - - - -
126C LEU* 4.5 0.4 - - - -
127C GLY* 2.8 36.3 + - - +
129C ASN* 2.9 33.3 + - + +
134C HIS* 4.5 6.5 + - - -
135C LEU* 1.3 79.5 - - - +
137C ILE* 1.3 72.3 + - - +
138C ALA* 4.1 1.8 + - - +
152C LEU* 3.9 34.3 - - + +
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Residues in contact with ILE 137 (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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132A ARG* 4.9 1.0 - - - +
101C PHE* 3.6 32.8 - - + -
107C PHE* 4.2 9.0 - - + +
110C LYS* 3.6 32.3 - - + +
111C LEU* 3.6 21.8 - - + +
114C ALA* 3.8 27.8 - - + -
125C TRP 3.2 12.3 - - - +
126C LEU* 4.3 9.6 - - + -
136C GLN* 1.3 82.1 + - - +
138C ALA* 1.3 66.5 + - - +
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Residues in contact with ALA 138 (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 ALA* 4.9 2.1 - - - +
124C GLY* 3.6 0.7 - - - -
125C TRP* 2.7 38.6 + - + +
136C GLN* 4.1 1.5 + - + +
137C ILE* 1.3 82.7 - - - +
139C ALA* 1.3 61.3 + - - +
146C LEU* 4.0 14.8 - - + -
150C THR* 5.2 5.8 - - + -
152C LEU* 3.9 24.5 - - + -
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Residues in contact with ALA 139 (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 ALA* 4.1 26.2 - - + +
118C VAL* 4.1 10.5 - - + -
123C TRP 3.3 10.3 - - - +
124C GLY* 4.8 0.2 - - - -
138C ALA* 1.3 77.3 - - - +
140C CYS* 1.3 66.1 + - - +
141C PRO* 4.4 2.8 - - - +
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Residues in contact with CYS 140 (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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118C VAL* 4.8 3.0 - - - +
122C GLY* 3.1 2.9 - - - -
123C TRP* 2.8 38.4 + - + +
125C TRP* 3.8 24.0 - - + +
139C ALA* 1.3 80.0 - - - +
141C PRO* 1.3 68.3 - - + +
142C ASN 4.4 0.3 - - - +
144C ASP* 3.2 27.4 - - + +
146C LEU* 3.8 26.9 - - - -
149C THR* 4.5 8.5 - - - -
150C THR* 4.6 5.4 - - - -
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Residues in contact with PRO 141 (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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118C VAL* 5.4 2.2 - - + -
121C SER 3.7 7.4 - - - +
122C GLY* 4.2 0.2 - - - -
139C ALA 4.4 2.7 - - - +
140C CYS* 1.3 88.4 - - + +
142C ASN* 1.3 80.1 + - - +
144C ASP* 2.9 38.7 + - + +
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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