Contacts of the strand formed by residues 153 - 160 (chain A) in PDB entry 2L28
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 153 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A ASP* 3.9 18.1 + - - -
26A ASP* 5.4 0.7 - - - -
116A THR* 4.2 15.5 - - + -
117A ARG 3.0 13.7 - - - +
118A LEU* 3.7 22.7 - - + -
143A THR* 3.8 1.1 - - - -
144A VAL* 2.5 49.4 + - + +
146A ASP* 3.3 28.4 + - - -
151A LEU 3.1 20.6 + - - -
152A THR* 1.3 79.1 - - - +
154A THR* 1.3 58.8 + - - +
155A TYR* 4.1 23.7 + - + -
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Residues in contact with THR 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A VAL 2.9 17.5 - - - +
116A THR* 3.1 3.6 - - - -
117A ARG* 2.9 41.5 + - - +
141A SER* 4.3 3.1 - - - -
142A ARG* 3.4 26.7 - - - +
143A THR* 2.5 40.3 + - - +
153A HIS* 1.3 72.7 - - - +
155A TYR* 1.3 61.0 + - - +
156A GLU* 3.4 20.0 + - + +
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Residues in contact with TYR 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A TYR* 3.3 50.4 - + - +
115A VAL 3.8 2.2 - - - -
116A THR* 3.7 12.3 - - + +
140A SER* 3.5 3.8 - - - +
141A SER* 3.2 20.0 + - - -
142A ARG* 3.1 14.7 + - + +
144A VAL* 3.5 32.1 - - + -
153A HIS* 4.1 23.8 + + - -
154A THR* 1.3 70.1 - - - +
156A GLU* 1.3 61.1 + - - +
157A VAL* 4.0 8.4 + - + +
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Residues in contact with GLU 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A LEU 3.4 1.0 - - - +
114A LEU* 3.3 7.4 - - - +
115A VAL* 2.9 57.4 + - + +
117A ARG* 4.5 14.1 - - - +
133A TRP* 5.0 1.7 - - - -
138A LYS* 4.8 4.8 - - - -
140A SER 3.2 6.3 - - - +
141A SER* 4.1 10.4 - - - -
154A THR* 4.1 21.9 - - + +
155A TYR* 1.3 75.3 - - - +
157A VAL* 1.3 61.5 + - - +
158A TRP* 3.3 35.0 + - + +
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Residues in contact with VAL 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A THR* 4.3 10.8 - - + -
113A LEU 3.3 2.5 - - - +
114A LEU* 3.6 25.4 - - + -
138A LYS* 3.7 0.7 - - - -
139A VAL* 2.7 57.9 + - + +
140A SER* 2.7 26.1 + - - +
155A TYR* 4.7 8.1 - - + +
156A GLU* 1.3 78.1 - - - +
158A TRP* 1.3 54.6 + - - +
159A GLN* 5.3 1.6 - - + +
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Residues in contact with TRP 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A THR* 3.1 12.4 - - - +
113A LEU* 2.8 61.7 + - + -
115A VAL* 4.5 1.8 - - + +
133A TRP* 3.2 59.5 - + + -
136A PHE* 4.2 5.4 - - + -
137A THR* 2.9 12.6 - - - +
138A LYS* 3.3 61.7 - - + -
156A GLU* 3.3 37.7 + - - +
157A VAL* 1.3 79.1 - - - +
159A GLN* 1.3 61.4 + - - +
160A LYS 4.2 0.2 - - - -
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Residues in contact with GLN 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A ASP* 3.5 4.5 - - - +
112A THR* 4.1 15.0 - - + +
136A PHE* 3.9 0.4 - - - -
137A THR* 2.6 27.8 + - - -
139A VAL* 3.0 39.1 - - + +
157A VAL* 5.3 1.1 - - + +
158A TRP* 1.3 75.9 - - - +
160A LYS* 1.3 67.2 + - - +
161A LYS* 3.2 24.3 - - - +
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Residues in contact with LYS 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A ASP 4.6 13.2 + - - +
109A ASP* 5.1 4.5 - - - +
110A VAL 3.6 10.5 - - - +
111A ASP* 2.7 42.1 + - - +
135A ASP* 3.4 26.5 + - - +
136A PHE* 3.2 41.3 - - + -
159A GLN* 1.3 71.5 - - - +
161A LYS* 1.3 86.9 + - - +
162A ALA* 5.4 0.4 - - - +
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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