Contacts of the strand formed by residues 125 - 132 (chain A) in PDB entry 2X30
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 ILE 125 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A LEU* 4.1 15.7 - - + -
94A LEU* 4.9 1.6 - - + -
100A ARG* 5.2 0.2 - - - -
101A VAL* 3.7 18.4 - - + -
103A LEU* 3.6 29.6 - - + -
117A VAL* 3.7 28.3 - - + +
118A ILE* 3.9 22.8 - - + +
121A HIS* 3.8 20.2 - - + -
122A GLY 3.0 16.5 + - - +
123A ASP* 4.2 4.0 - - - -
124A LYS* 1.3 88.2 - - + +
126A ALA* 1.3 66.6 + - - +
127A VAL* 4.7 3.1 - - + -
160A CYS* 4.9 0.9 - - - -
161A ALA* 4.0 20.8 + - - +
162A ARG* 4.8 1.3 + - - +
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Residues in contact with ALA 126 (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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100A ARG* 4.3 6.7 - - - +
101A VAL 3.0 7.8 + - - +
102A ASN* 3.2 24.7 - - - +
103A LEU* 2.9 23.9 + - - -
125A ILE* 1.3 76.8 - - - +
127A VAL* 1.3 64.6 + - - +
160A CYS* 5.0 0.4 - - - -
162A ARG* 3.4 38.1 - - + +
164A VAL* 4.5 7.0 - - + -
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Residues in contact with VAL 127 (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 LEU* 3.2 14.6 - - + +
107A ALA* 3.7 17.0 - - + -
114A VAL* 4.1 25.1 - - + -
118A ILE* 4.6 2.9 - - + -
125A ILE* 4.7 2.9 - - + -
126A ALA* 1.3 78.3 - - - +
128A GLY* 1.3 70.3 + - - +
129A LEU* 3.8 4.7 + - + -
155A LEU* 3.6 28.9 - - + -
160A CYS* 3.7 21.5 - - - -
162A ARG 3.1 6.5 + - - -
163A TYR* 3.2 11.3 - - + +
164A VAL* 2.9 22.4 + - - -
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Residues in contact with GLY 128 (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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102A ASN* 4.8 6.2 - - - +
103A LEU 2.8 15.9 + - - +
104A GLY* 3.8 18.9 - - - +
107A ALA* 5.4 0.2 - - - +
126A ALA 4.2 0.4 + - - -
127A VAL* 1.3 81.2 - - - +
129A LEU* 1.3 63.7 + - - +
130A ASP* 4.1 7.1 + - - +
164A VAL* 3.2 17.5 - - - -
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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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107A ALA* 6.1 0.4 - - + -
108A LEU* 6.0 0.7 - - + -
127A VAL* 4.4 2.9 - - + -
128A GLY* 1.3 78.8 - - - +
130A ASP* 1.3 64.2 + - - +
131A VAL* 3.8 7.6 + - + +
136A LEU* 3.8 34.3 - - + -
148A LEU* 4.2 10.3 - - + -
151A THR* 4.2 14.4 - - + -
152A LEU* 3.9 32.1 - - + -
155A LEU* 4.3 13.2 - - + -
163A TYR* 4.1 20.9 - - + -
164A VAL 2.7 11.7 + - - +
165A VAL* 3.6 12.9 - - + -
166A THR 2.8 28.9 + - - +
185A VAL* 4.7 0.7 - - + -
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Residues in contact with ASP 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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23A GLY* 5.8 0.3 - - - -
128A GLY* 4.1 5.5 + - - +
129A LEU* 1.3 77.4 + - - +
131A VAL* 1.3 59.9 + - - +
135A THR 3.7 0.2 - - - +
136A LEU* 3.4 7.4 - - - +
137A ARG* 2.9 49.3 + - + +
139A ASN* 5.9 1.2 + - - -
166A THR* 3.7 18.8 + - - +
168A ILE* 3.4 31.0 - - + +
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Residues in contact with VAL 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* 3.9 12.1 - - + +
130A ASP* 1.3 73.9 - - - +
132A ARG* 1.3 59.3 + - - +
133A GLY 3.1 29.8 + - - +
134A THR* 4.5 1.3 - - - -
135A THR 3.5 7.6 - - - +
136A LEU* 3.7 16.6 - - + -
148A LEU* 4.0 23.6 - - + -
165A VAL* 4.6 4.7 - - + -
166A THR 2.9 16.5 + - - +
167A ASP* 3.7 5.7 - - - +
168A ILE* 2.7 28.9 + - - +
169A ALA 3.7 1.6 + - - -
181A LEU* 3.8 29.1 - - + +
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Residues in contact with ARG 132 (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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130A ASP 3.9 0.4 + - - -
131A VAL* 1.3 72.5 - - - +
133A GLY* 1.3 59.3 + - - +
134A THR 3.2 0.5 + - - -
135A THR* 2.7 37.3 + - - +
137A ARG* 4.4 31.4 - - + +
143A ARG* 5.7 3.4 - - - +
168A ILE* 4.2 20.3 + - + -
169A ALA* 4.3 23.2 + - + +
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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