Contacts of the strand formed by residues 127 - 131 (chain A) in PDB entry 2XJZ
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 ARG 127 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122A PHE* 4.4 4.2 - - - -
125A GLY 4.2 7.0 - - - +
126A ASP* 1.3 78.0 - - - +
128A TYR* 1.3 58.5 + - - +
137A CYS* 4.0 3.1 - - - +
138A GLU* 3.2 55.5 + - + +
93B ARG* 3.5 28.0 - - - +
337I VAL* 4.3 25.8 + - + +
338I MET 3.1 9.6 - - - +
339I VAL* 4.0 18.7 - - + +
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Residues in contact with TYR 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A VAL* 3.3 38.8 - - + +
113A PHE* 3.8 17.8 - + - -
122A PHE* 3.9 21.1 - - + -
127A ARG* 1.3 72.4 - - - +
129A LEU* 1.3 65.4 + - - +
130A LEU* 4.6 7.0 - - + -
135A ILE* 3.7 22.4 - - + -
136A VAL 3.4 12.6 - - - +
137A CYS* 4.1 0.7 - - - +
138A GLU 4.2 2.2 - - - +
141A ILE* 5.0 1.1 - - - -
337I VAL* 3.7 5.3 - - - +
338I MET* 2.7 61.8 + - + +
339I VAL 3.7 19.8 + - - -
340I VAL* 3.5 30.6 - - + -
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Residues in contact with LEU 129 (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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128A TYR* 1.3 77.9 - - - +
130A LEU* 1.3 63.2 + - - +
131A ILE* 3.5 32.5 + - + +
134A ASP 3.4 4.0 - - - +
135A ILE* 3.7 2.6 - - - -
136A VAL* 2.8 31.4 + - - +
141A ILE* 3.7 43.0 - - + +
145A THR* 5.7 0.7 - - - +
336I ASP* 3.3 53.4 - - + +
337I VAL* 4.0 10.3 - - + +
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Residues in contact with LEU 130 (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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103A VAL* 3.7 38.6 - - + +
104A LYS* 4.1 24.0 - - + +
106A LYS* 4.5 9.2 - - + -
108A TYR* 3.4 26.7 - - + +
128A TYR* 4.4 6.2 + - + -
129A LEU* 1.3 76.2 - - - +
131A ILE* 1.4 58.8 + - - +
132A ASN 3.5 21.5 + - - +
133A SER 4.3 0.4 - - - -
134A ASP 3.4 9.6 - - - +
135A ILE* 4.4 7.9 - - + -
336I ASP* 3.1 32.4 + - - +
338I MET* 4.8 3.4 - - - -
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Residues in contact with ILE 131 (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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129A LEU* 3.5 39.5 - - + +
130A LEU* 1.4 69.7 - - - +
132A ASN* 1.3 82.6 - - - +
134A ASP* 2.8 35.1 + - - +
136A VAL* 3.8 20.6 - - + -
141A ILE* 5.8 0.4 - - + -
144A TRP* 3.5 36.6 - - + -
145A THR* 5.4 2.5 - - - +
149A GLY 5.5 7.4 - - - +
336I ASP* 5.9 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