Contacts of the helix formed by residues 122 - 134 (chain A) in PDB entry 3W7F
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 THR 122 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120A PHE* 3.4 1.8 - - - +
121A GLU* 1.3 85.2 - - + +
123A ASP* 1.3 66.4 + - - +
124A ALA* 4.1 9.0 + - - +
125A GLU* 3.2 35.4 + - - +
126A LEU 3.3 7.8 + - - -
185A SER* 3.4 15.1 - - - -
187A GLN* 4.4 13.7 - - + -
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Residues in contact with ASP 123 (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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122A THR* 1.3 71.7 - - - +
124A ALA* 1.3 55.5 + - - +
126A LEU* 2.8 9.0 + - - +
127A PHE* 2.7 60.3 + - + -
185A SER* 2.7 27.5 + - - -
187A GLN* 5.4 1.2 - - - +
188A ARG* 2.9 37.8 + - - +
214A TYR* 3.8 4.5 + - - -
215A TYR* 2.7 31.1 + - - -
218A ILE* 4.8 0.2 - - - +
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Residues in contact with ALA 124 (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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122A THR* 3.2 9.1 - - - +
123A ASP* 1.3 78.8 - - - +
125A GLU* 1.3 63.2 + - + +
127A PHE* 4.0 9.8 - - - +
128A GLY* 3.1 19.2 + - - -
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Residues in contact with GLU 125 (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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119A MET 5.3 0.9 - - - +
120A PHE* 4.0 20.7 - - + -
121A GLU* 2.7 42.7 + - - +
122A THR* 3.2 19.1 + - - +
123A ASP 3.1 0.8 - - - -
124A ALA* 1.3 77.4 - - + +
126A LEU* 1.3 65.7 + - - +
128A GLY* 3.3 1.9 + - - -
129A TYR* 3.1 21.1 + - - +
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Residues in contact with LEU 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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120A PHE* 3.4 29.7 - - + -
122A THR 3.3 6.6 + - - +
123A ASP* 2.8 13.6 + - - +
125A GLU* 1.3 78.0 - - - +
127A PHE* 1.3 70.8 + - + +
129A TYR* 3.0 15.9 + - + +
130A CYS* 3.1 16.5 + - - -
166A LEU* 4.8 4.9 - - + -
169A ILE* 3.5 29.2 - - + -
183A TYR 3.2 26.2 - - - +
184A PHE* 4.4 2.0 - - + -
185A SER* 4.6 1.6 - - - +
215A TYR* 4.0 35.7 - - + +
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Residues in contact with PHE 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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123A ASP* 2.7 48.1 + - + +
124A ALA* 4.1 7.9 - - - +
126A LEU* 1.3 87.5 - - + +
128A GLY* 1.3 62.2 + - - +
130A CYS* 3.2 14.7 + - + +
131A TYR* 3.2 18.0 + - - +
162A GLU* 4.0 11.6 - - - +
166A LEU* 4.3 24.5 - - + -
215A TYR* 4.7 2.2 - + - -
218A ILE* 4.1 29.4 - - + -
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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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124A ALA 3.1 16.5 + - - -
125A GLU* 3.3 2.2 + - - -
126A LEU 3.3 0.4 - - - -
127A PHE* 1.3 76.7 - - - +
129A TYR* 1.3 61.7 + - - +
131A TYR* 3.5 13.1 - - - +
132A GLY* 3.3 16.1 + - - -
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Residues in contact with TYR 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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110A THR* 3.8 20.6 - - + -
114A ASP* 3.5 23.4 + - + -
117A PHE* 6.3 0.4 - + - -
120A PHE* 3.4 35.9 - + + -
125A GLU 3.1 6.3 + - - +
126A LEU* 3.0 15.5 + - + +
128A GLY* 1.3 78.0 - - - +
130A CYS* 1.3 68.4 + - - +
132A GLY* 3.2 1.7 + - - +
133A VAL* 3.1 56.4 + - + +
165A GLN* 4.7 11.0 + - - -
169A ILE* 5.0 1.1 - - + -
183A TYR* 3.7 32.2 + + - -
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Residues in contact with CYS 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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126A LEU* 3.1 33.0 + - - -
127A PHE* 3.5 17.0 - - + +
129A TYR* 1.3 75.4 - - - +
131A TYR* 1.3 66.3 + - - +
134A ALA* 3.0 22.5 + - - +
135A GLY 3.0 6.4 + - - -
162A GLU* 3.9 29.3 - - + +
165A GLN* 3.7 29.2 - - + -
166A LEU* 4.4 11.0 - - - -
169A ILE* 4.4 5.4 - - - -
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Residues in contact with TYR 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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106A ASN* 2.9 32.3 + - + -
127A PHE 3.2 11.1 + - - +
128A GLY* 3.5 13.9 - - - +
130A CYS* 1.3 77.8 - - - +
132A GLY* 1.3 66.4 + - - +
135A GLY* 2.9 25.3 + - - +
136A THR* 3.0 28.4 + - + +
139A GLU* 2.9 42.5 + - - -
158A ARG* 4.1 9.0 - - + -
162A GLU* 3.5 27.3 - - - +
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Residues in contact with GLY 132 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A ASN* 4.7 1.6 - - - -
107A LEU* 3.3 18.9 - - - -
110A THR* 3.4 20.4 - - - -
128A GLY 3.3 6.6 + - - -
129A TYR 3.2 7.1 + - - -
131A TYR* 1.3 89.7 - - - +
133A VAL* 1.3 59.1 + - - +
136A THR* 2.9 20.0 + - - +
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Residues in contact with VAL 133 (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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48A ASP* 6.0 0.9 - - - +
107A LEU* 3.7 16.2 - - + +
110A THR* 3.3 30.3 - - + -
111A VAL* 4.9 6.5 - - + -
129A TYR* 3.1 37.4 + - + +
132A GLY* 1.3 76.1 - - - +
134A ALA* 1.3 61.6 + - - +
136A THR* 4.0 2.9 - - - -
137A VAL* 3.6 13.7 - - - +
165A GLN* 3.2 37.0 - - + +
301A FPS 3.8 19.5 - - + +
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Residues in contact with ALA 134 (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 CYS 3.0 4.7 + - - +
131A TYR 3.4 0.4 + - - -
133A VAL* 1.3 80.6 - - - +
135A GLY* 1.3 66.1 + - - +
136A THR 3.1 1.8 - - - -
137A VAL* 3.2 11.5 + - - +
138A GLY 3.2 15.6 + - - -
161A GLY* 3.3 33.8 - - - +
165A GLN* 3.7 22.2 - - + +
302A FPS 3.9 19.6 - - + +
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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