Contacts of the strand formed by residues 134 - 141 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132B ARG* 3.5 12.2 + - - -
134B HIS* 3.4 30.5 + + - -
99D ARG* 4.0 4.7 - - - +
100D ASP* 3.4 20.1 + - - +
128D PHE* 3.6 10.9 - - - -
129D ASN* 2.9 32.4 + - + -
132D ARG* 3.4 51.7 + - + +
133D GLY* 1.3 78.9 - - - +
135D LEU* 1.3 82.5 - - - +
136D GLN* 4.5 6.5 + - - -
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Residues in contact with LEU 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B ARG* 2.7 33.8 + - - -
93D LEU* 4.4 4.7 - - + -
96D ALA* 3.7 40.4 - - + +
97D ILE* 3.7 21.3 - - + +
99D ARG* 5.0 0.4 - - - +
100D ASP* 2.9 15.3 + - - +
101D PHE* 3.8 20.0 - - + -
126D LEU* 4.1 7.0 - - + -
127D GLY 3.4 6.7 - - - +
128D PHE* 4.0 12.8 - - + -
134D HIS* 1.3 77.6 - - - +
136D GLN* 1.3 54.9 + - - +
155D LEU* 3.4 32.8 - - + -
193D TYR* 4.1 9.2 - - + -
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Residues in contact with GLN 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B ARG* 3.9 10.5 - - - +
136B GLN* 4.5 18.4 - - - +
101D PHE* 4.5 0.4 - - - -
126D LEU* 3.7 1.3 - - - -
127D GLY* 2.8 37.6 + - - +
129D ASN* 2.8 35.0 + - + +
134D HIS* 4.5 5.8 + - - -
135D LEU* 1.3 77.8 - - - +
137D ILE* 1.3 75.4 + - - +
138D ALA* 4.0 1.9 + - - +
152D LEU* 4.0 32.8 - - + +
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Residues in contact with ILE 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B ARG* 4.9 1.0 - - - +
101D PHE* 3.7 28.3 - - + -
107D PHE* 4.1 13.2 - - + -
110D LYS* 3.6 32.8 - - + +
111D LEU* 3.7 18.6 - - + +
114D ALA* 3.7 28.7 - - + -
125D TRP 3.2 13.7 - - - +
126D LEU* 4.3 9.6 - - + -
136D GLN* 1.3 86.2 + - - +
138D ALA* 1.3 64.6 + - - +
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Residues in contact with ALA 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D ALA* 4.8 2.1 - - - +
124D GLY* 3.9 0.5 - - - -
125D TRP* 2.8 34.3 + - - +
136D GLN* 4.0 2.2 + - - +
137D ILE* 1.3 80.0 - - - +
139D ALA* 1.3 62.8 + - - +
146D LEU* 4.0 24.2 - - + -
150D THR* 5.2 5.6 - - + -
152D LEU* 4.0 15.5 - - + -
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Residues in contact with ALA 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D ALA* 3.9 26.9 - - + +
117D GLY 6.2 0.2 - - - -
118D VAL* 3.9 11.2 - - + -
123D TRP 3.4 10.5 - - - +
124D GLY* 4.5 0.2 - - - -
138D ALA* 1.3 78.0 - - - +
140D CYS* 1.3 65.2 + - - +
141D PRO* 4.6 2.1 - - - +
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Residues in contact with CYS 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D VAL* 4.7 3.8 - - - +
122D GLY* 3.2 3.3 - - - -
123D TRP* 2.9 37.8 + - + +
125D TRP* 3.7 26.0 - - - +
139D ALA* 1.3 80.3 - - - +
141D PRO* 1.3 67.7 - - + +
142D ASN 4.5 0.2 - - - +
144D ASP* 3.3 26.5 - - + +
145D PRO 4.5 0.7 - - - -
146D LEU* 3.8 26.2 - - - -
149D THR* 4.5 7.4 - - - -
150D THR* 4.7 5.4 - - - -
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Residues in contact with PRO 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D VAL* 5.5 2.2 - - + -
121D SER 3.7 7.4 - - - +
122D GLY* 4.2 0.2 - - - -
139D ALA 4.6 2.5 - - - +
140D CYS* 1.3 87.1 - - + +
142D ASN* 1.3 80.3 + - - +
144D ASP* 2.9 40.2 + - + +
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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