Contacts of the strand formed by residues 153 - 161 (chain A) in PDB entry 2ZZA
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 TYR 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 LEU* 3.9 16.6 - - + -
27A ALA* 3.4 28.1 + - - +
28A GLU* 3.6 21.7 + - + -
31A LEU* 4.4 7.1 - - + +
115A THR* 3.6 24.7 - - + -
116A HIS 3.0 13.9 - - - +
117A ILE* 4.0 9.6 - - + -
118A GLU 4.6 0.2 - - - +
142A SER* 3.7 1.2 - - - -
143A TYR* 2.7 81.8 + + + +
144A ALA 5.6 1.8 - - - -
149A ASN* 4.6 13.4 - - + -
151A HIS 3.3 17.7 - - - -
152A ASN* 1.3 75.1 - - - +
154A ARG* 1.3 59.8 + - - +
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Residues in contact with ARG 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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114A LEU 3.6 0.7 - - - +
115A THR* 3.3 4.2 - - - -
116A HIS* 2.8 76.0 + - + +
137A GLU* 4.1 16.8 + - - -
140A HIS* 5.2 8.0 - - + +
141A GLU 3.4 9.9 - - - +
142A SER* 3.9 18.4 - - - +
153A TYR* 1.3 76.2 - - - +
155A PHE* 1.3 69.6 + - - +
156A SER* 3.9 3.9 + - - -
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Residues in contact with PHE 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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6A ILE* 5.6 0.2 - - + -
31A LEU* 3.9 28.9 - - + -
113A TYR* 3.9 39.7 - + + -
114A LEU 3.4 8.7 - - - -
115A THR* 3.9 14.3 - - + +
139A GLU* 4.2 9.4 - - + -
140A HIS* 3.0 32.7 - - - +
141A GLU* 2.8 19.0 + - + +
143A TYR* 4.2 8.0 - - + -
154A ARG* 1.3 75.2 - - - +
156A SER* 1.3 63.5 + - - +
157A LEU* 3.9 26.5 - - + -
165A 1PE 3.3 50.3 - - - -
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Residues in contact with SER 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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112A LEU 3.4 2.8 - - - +
113A TYR* 3.9 0.2 - - - -
114A LEU* 2.6 43.7 + - - +
116A HIS* 4.2 19.8 - - - -
137A GLU* 2.6 24.6 + - - -
139A GLU 3.5 5.4 - - - -
154A ARG* 4.3 6.7 + - - -
155A PHE* 1.3 79.5 - - - +
157A LEU* 1.3 58.9 + - - +
158A LEU* 3.2 23.2 + - - +
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Residues in contact with LEU 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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111A ARG* 4.6 13.5 - - + +
112A LEU 3.7 13.0 - - - +
113A TYR* 3.7 45.5 - - + +
137A GLU* 3.4 2.4 - - - -
138A ILE* 2.6 45.5 + - + +
139A GLU* 3.0 50.5 + - + +
155A PHE* 3.9 9.1 - - + -
156A SER* 1.3 70.3 - - - +
158A LEU* 1.3 63.0 + - - +
34B ARG* 5.1 4.0 - - - +
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Residues in contact with LEU 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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111A ARG* 3.1 9.5 - - - +
112A LEU* 2.9 39.9 + - + +
114A LEU* 3.8 25.4 - - + -
116A HIS* 5.9 1.1 - - + -
130A TYR* 3.8 22.0 - - + -
135A TRP* 4.0 29.2 - - + -
136A GLN 3.6 2.7 - - - -
137A GLU* 3.7 25.8 - - + +
156A SER* 3.2 25.1 - - - +
157A LEU* 1.3 76.3 - - - +
159A GLU* 1.3 59.3 + - - +
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Residues in contact with GLU 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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110A ASP 3.5 8.7 - - - +
111A ARG* 4.5 18.4 + - + +
135A TRP* 3.4 3.9 - - - -
136A GLN* 3.0 55.4 + - + +
138A ILE* 3.7 27.7 - - + +
158A LEU* 1.3 75.0 - - - +
160A ARG* 1.3 73.3 + - - +
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Residues in contact with ARG 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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106A LEU 3.4 10.9 + - - -
107A ALA* 3.2 27.8 + - - +
108A ALA 4.6 0.2 - - - -
109A ALA 3.1 32.0 + - - +
110A ASP* 2.8 22.4 + - - +
133A TYR* 3.7 43.7 - - - +
134A ASN 3.5 15.2 - - - +
135A TRP* 3.4 24.1 - - + -
159A GLU* 1.3 81.3 - - - +
161A VAL* 1.3 71.2 + - - +
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Residues in contact with VAL 161 (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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134A ASN* 2.8 42.4 + - + +
135A TRP 4.3 1.1 - - - -
136A GLN* 3.6 41.5 - - + +
159A GLU 3.7 2.5 - - - +
160A ARG* 1.3 92.0 + - - +
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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