Contacts of the strand formed by residues 125 - 131 (chain A) in PDB entry 4J2X
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 PRO 125 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A LEU* 4.0 23.1 - - + -
106A TRP* 3.9 28.7 - - + +
123A SER 3.5 6.3 - - - +
124A GLN* 1.4 122.2 + - - +
126A CYS* 1.3 60.2 + - - +
143A LEU* 4.1 6.4 + - - +
171A MET* 4.0 11.2 - - + -
172A PHE 3.8 5.6 - - - +
173A TYR* 4.0 15.3 - - + -
179A ILE* 4.4 1.3 - - + -
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Residues in contact with CYS 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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121A GLN 5.8 0.2 - - - -
124A GLN* 3.5 19.7 - - - -
125A PRO* 1.3 73.8 - - - +
127A ALA* 1.3 61.0 + - - +
128A PHE* 4.8 5.4 - - + -
140A GLN* 5.1 9.6 - - - +
141A LEU 5.5 1.8 - - - -
143A LEU* 4.5 2.9 - - - -
170A LYS 4.3 0.2 - - - -
171A MET* 3.3 11.4 - - - +
172A PHE* 2.7 62.5 + - + +
173A TYR 3.9 2.0 - - - -
174A GLY* 3.9 15.5 - - - -
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Residues in contact with ALA 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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99A VAL* 4.9 2.7 - - + -
126A CYS* 1.3 74.9 - - - +
128A PHE* 1.3 73.8 + - - +
140A GLN* 3.8 0.7 - - - +
141A LEU* 3.1 48.5 + - + +
143A LEU* 3.8 22.8 - - + +
169A VAL* 4.2 6.1 - - + -
170A LYS 3.3 5.4 - - - +
171A MET* 4.0 14.6 - - + -
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Residues in contact with PHE 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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126A CYS* 4.8 1.8 - - + -
127A ALA* 1.3 89.9 - - - +
129A ILE* 1.3 60.9 + - - +
138A MET* 3.9 31.1 - - + +
139A GLN 3.3 7.6 - - - -
140A GLN* 3.4 53.2 - - + -
141A LEU* 4.5 2.2 - - - +
168A SER 3.6 0.5 - - - +
169A VAL* 3.4 7.5 - - - +
170A LYS* 2.9 38.1 + - + +
172A PHE* 3.5 37.5 - + - -
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Residues in contact with ILE 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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76A ILE* 5.2 1.6 - - + -
97A PRO* 4.8 4.3 - - + -
99A VAL* 4.2 13.5 - - + -
128A PHE* 1.3 75.3 - - - +
130A GLY* 1.3 65.0 + - - +
137A GLU 4.2 0.7 - - - +
138A MET* 3.2 8.9 - - - -
139A GLN* 2.8 53.1 + - + +
141A LEU* 3.8 22.9 - - + +
151A ALA* 3.8 22.7 - - + -
154A LEU* 3.8 23.6 - - + +
167A LEU* 4.4 16.6 - - + -
168A SER 3.5 4.5 - - - +
169A VAL* 3.6 26.0 - - + -
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Residues in contact with GLY 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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129A ILE* 1.3 77.7 - - - +
131A ILE* 1.3 63.3 + - - +
137A GLU 4.3 8.1 - - - -
138A MET* 4.2 14.6 - - - +
154A LEU* 4.5 8.3 - - - -
167A LEU* 3.2 11.4 - - - +
168A SER* 2.8 34.2 + - - -
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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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93A PHE* 4.2 10.8 - - + -
130A GLY* 1.3 78.6 - - - +
132A GLY* 1.3 58.7 + - - +
133A ASN* 2.8 29.2 - - - +
134A SER* 3.5 19.1 - - - +
137A GLU 5.2 1.4 + - - -
138A MET* 5.4 0.2 - - - +
154A LEU* 4.9 7.9 - - + -
155A TYR 4.0 14.6 - - - +
156A ILE* 3.6 26.5 - - + -
157A SER 5.6 0.2 - - - +
160A ASP* 4.2 0.7 - - + +
162A ARG* 3.5 21.5 - - - +
165A PHE* 3.6 28.0 - - + -
166A MET 3.8 4.5 - - - -
167A LEU* 4.1 8.1 - - + -
168A SER* 5.2 2.8 - - - -
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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