Contacts of the helix formed by residues 113 - 132 (chain A) in PDB entry 4WLU
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 LEU 113 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A VAL* 3.5 27.4 - - + +
103A PRO 3.5 24.7 - - - +
104A ARG* 3.7 28.0 - - + +
108A MET* 4.1 15.5 - - + -
109A THR 4.3 0.7 - - - +
110A ARG* 3.3 16.2 - - - +
111A ASP 3.0 0.8 - - - -
112A ASP* 1.3 75.9 - - - +
114A PHE* 1.3 63.7 + - - +
115A ASN 3.2 2.9 + - - -
116A THR* 3.3 7.7 + - - -
117A ASN* 3.1 30.3 + - - +
142A ASN* 3.9 14.6 - - + +
143A PRO* 4.4 1.1 - - - -
402A NAD 3.6 17.9 - - - +
108C MET* 5.8 4.3 - - - -
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Residues in contact with PHE 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ASP* 3.0 18.4 + - - +
112A ASP 3.3 0.8 - - - -
113A LEU* 1.3 77.3 - - - +
115A ASN* 1.3 76.5 + - - +
117A ASN 4.7 0.7 - - - +
118A ALA* 2.9 48.9 + - + +
143A PRO* 3.9 18.2 - - + +
146A SER* 3.7 31.2 - - - -
147A THR* 5.6 0.7 - - + -
150A ILE* 3.9 15.3 - - + -
329A LYS* 3.6 51.6 - - + +
330A GLY* 4.1 2.2 - - - -
333A PHE* 3.7 25.6 - + + -
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Residues in contact with ASN 115 (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 ASP 4.7 1.4 + - - -
113A LEU 3.2 1.6 + - - -
114A PHE* 1.3 96.2 - - - +
116A THR* 1.3 58.7 + - - +
118A ALA* 4.8 1.8 - - - -
119A THR* 4.7 8.1 + - - -
329A LYS* 5.7 0.6 - - - -
333A PHE* 6.0 1.5 - - - -
107C GLY* 3.3 37.6 + - - +
108C MET* 4.0 2.7 - - + -
109C THR* 4.7 7.9 - - - +
112C ASP* 2.7 37.3 + - - +
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Residues in contact with THR 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A VAL* 4.0 21.3 - - + -
113A LEU* 3.3 7.6 + - - -
114A PHE 3.1 0.2 - - - -
115A ASN* 1.3 79.5 - - - +
117A ASN* 1.3 77.3 + - - +
118A ALA 3.3 1.7 + - - -
119A THR* 3.5 13.3 + - - -
120A ILE* 3.6 23.8 + - + +
105C LYS* 3.6 12.6 - - + +
106C PRO* 2.8 27.9 + - + +
108C MET* 3.5 21.2 - - - +
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Residues in contact with ASN 117 (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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101A GLY* 3.3 9.6 - - - -
102A VAL* 2.8 33.5 + - - +
113A LEU* 3.1 20.4 + - - +
114A PHE 4.6 0.2 - - - +
116A THR* 1.3 81.7 - - - +
118A ALA* 1.3 60.3 + - - +
119A THR 3.3 0.2 - - - -
120A ILE* 3.7 11.2 - - + +
121A VAL* 2.9 39.8 + - + +
141A ALA* 4.9 1.5 - - + +
142A ASN 2.8 29.6 + - - +
143A PRO* 4.9 1.6 - - + -
147A THR* 5.0 1.6 - - + -
402A NAD 3.1 22.8 + - - -
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Residues in contact with ALA 118 (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 PHE* 2.9 34.7 + - + +
115A ASN* 5.2 1.8 - - - -
117A ASN* 1.3 77.5 - - - +
119A THR* 1.3 57.5 + - - +
121A VAL* 3.9 1.6 - - - +
122A ALA* 2.9 30.1 + - - +
147A THR* 5.2 2.0 - - - +
150A ILE* 3.7 27.6 - - + +
333A PHE* 3.6 26.1 - - + -
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Residues in contact with THR 119 (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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115A ASN 4.7 6.9 + - - -
116A THR 3.5 9.5 + - - -
117A ASN 3.3 0.2 - - - -
118A ALA* 1.3 74.5 - - - +
120A ILE* 1.3 66.4 + - + +
122A ALA* 3.8 3.7 - - - +
123A THR* 2.8 39.5 + - - +
333A PHE* 3.6 20.0 - - + -
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Residues in contact with ILE 120 (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 ALA* 3.7 25.1 - - + +
101A GLY* 4.0 8.1 - - - -
102A VAL* 5.3 1.6 - - + -
116A THR* 3.6 22.6 + - + +
117A ASN* 3.3 27.9 + - - +
119A THR* 1.3 80.5 - - + +
121A VAL* 1.3 62.1 + - - +
123A THR* 3.8 3.8 - - - -
124A LEU* 3.1 42.2 + - + +
402A NAD 3.7 35.0 - - + +
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Residues in contact with VAL 121 (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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98A ILE* 5.3 4.9 - - + -
100A ALA 4.8 2.9 - - - +
117A ASN 2.9 20.4 + - - +
118A ALA 4.0 2.5 - - - +
120A ILE* 1.3 72.8 - - + +
122A ALA* 1.3 56.0 + - - +
124A LEU* 4.7 3.8 - - - +
125A THR* 2.7 45.3 + - + +
139A VAL* 4.6 6.5 - - + -
141A ALA* 3.7 30.1 - - + -
147A THR* 3.7 29.8 - - + +
150A ILE* 4.2 8.1 - - + -
151A THR* 3.4 25.6 - - - +
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Residues in contact with ALA 122 (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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118A ALA 2.9 19.8 + - - +
119A THR* 3.8 4.9 - - - +
120A ILE 3.4 0.2 - - - -
121A VAL* 1.3 76.8 - - - +
123A THR* 1.3 57.1 + - - +
125A THR* 3.4 5.6 + - - -
126A ALA* 3.0 30.3 + - - +
150A ILE* 4.0 12.7 - - + +
154A VAL* 4.0 12.7 - - + +
333A PHE* 4.0 17.0 - - + -
334A VAL* 5.8 0.2 - - + -
337A LEU* 4.8 9.6 - - + -
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Residues in contact with THR 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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86A LEU* 5.3 4.4 - - + +
119A THR* 2.8 31.7 + - - +
120A ILE* 3.8 5.1 - - - -
122A ALA* 1.3 76.1 - - - +
124A LEU* 1.3 70.5 + - + +
126A ALA* 3.3 8.3 + - - +
127A ALA* 3.2 20.1 + - - +
402A NAD 6.1 3.1 - - - +
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Residues in contact with LEU 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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30A LEU* 4.1 22.6 - - + +
56A TYR* 4.2 9.9 - - + -
86A LEU* 4.0 21.5 - - + -
98A ILE* 4.0 17.3 - - + -
100A ALA* 3.3 33.4 - - + -
120A ILE* 3.1 27.3 + - + +
121A VAL 4.3 1.1 - - - +
123A THR* 1.3 85.7 - - + +
125A THR* 1.3 59.3 + - - +
127A ALA* 3.3 7.9 + - - +
128A CYS* 3.1 29.4 + - - -
402A NAD 3.9 22.4 - - + +
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Residues in contact with THR 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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98A ILE* 3.8 23.1 - - + -
121A VAL* 2.7 33.7 + - + +
122A ALA* 3.4 5.4 + - - -
124A LEU* 1.3 73.2 - - - +
126A ALA* 1.3 61.7 + - - +
128A CYS* 3.4 6.7 + - - -
129A ALA* 2.9 24.3 + - - +
137A ILE* 4.6 2.7 - - + -
139A VAL* 4.8 0.9 - - + -
151A THR* 3.5 41.6 - - + +
154A VAL* 3.7 15.8 - - - +
155A PHE* 3.3 14.2 - - - -
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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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122A ALA 3.0 20.1 + - - +
123A THR* 3.5 8.3 - - - +
124A LEU 3.3 0.2 - - - -
125A THR* 1.3 77.8 + - - +
127A ALA* 1.3 61.4 + - - +
129A ALA* 3.3 3.9 + - - +
130A GLN* 3.1 27.6 + - - +
154A VAL* 3.5 16.8 - - + +
158A HIS* 3.8 15.8 + - + +
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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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86A LEU* 3.5 31.9 - - + -
87A PRO* 6.3 0.2 - - + -
90A LEU* 3.6 10.9 - - + +
123A THR 3.2 8.3 + - - +
124A LEU 3.5 9.0 - - - +
125A THR 3.3 0.2 - - - -
126A ALA* 1.3 78.3 - - - +
128A CYS* 1.3 57.0 + - - +
130A GLN* 3.3 2.3 + - - -
131A HIS* 2.9 46.5 + - + +
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Residues in contact with CYS 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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30A LEU* 4.0 9.0 - - - -
90A LEU* 3.7 13.0 - - - +
96A VAL* 3.8 30.1 - - - -
98A ILE* 4.3 6.1 - - - -
124A LEU 3.1 19.4 + - - -
125A THR* 3.5 12.8 - - - +
127A ALA* 1.3 73.7 - - - +
129A ALA* 1.3 62.5 + - - +
132A CYS* 2.8 40.2 + - - -
137A ILE* 3.9 24.0 - - + -
155A PHE* 4.0 5.2 - - + -
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Residues in contact with ALA 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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125A THR 2.9 18.4 + - - +
126A ALA* 3.3 6.3 + - - +
128A CYS* 1.3 74.7 - - - +
130A GLN* 1.3 64.8 + - - +
133A PRO* 3.5 20.2 - - - +
154A VAL 4.7 0.2 - - - +
155A PHE* 3.6 25.7 - - + -
158A HIS* 3.9 21.7 - - + +
160A VAL* 3.8 23.3 - - + +
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Residues in contact with GLN 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 ALA 3.1 19.5 + - - +
127A ALA* 3.7 4.9 - - - +
128A CYS 3.2 0.2 - - - -
129A ALA* 1.3 81.4 + - - +
131A HIS* 1.3 81.0 + - + +
132A CYS 3.8 0.2 - - - -
133A PRO* 4.1 6.5 - - - +
158A HIS* 3.2 36.2 + - + +
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Residues in contact with HIS 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A PRO* 3.5 44.9 - - + +
90A LEU* 4.0 16.8 - - + -
91A LYS* 3.6 41.7 + - + +
92A GLY 4.4 2.3 + - - -
127A ALA* 2.9 33.2 + - + +
130A GLN* 1.3 94.9 + - + +
132A CYS* 1.3 63.9 + - - +
133A PRO* 3.6 4.6 - - - +
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Residues in contact with CYS 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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90A LEU* 3.4 34.8 - - - +
92A GLY 4.8 1.1 - - - +
93A CYS* 4.3 9.4 - - - +
96A VAL* 3.6 31.6 - - - -
128A CYS* 2.8 23.0 + - - +
131A HIS* 1.3 80.4 - - - +
133A PRO* 1.4 65.0 - - - +
134A GLU 3.2 3.4 - - - -
135A ALA* 3.1 21.1 + - + +
137A ILE* 4.3 4.9 - - - +
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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
------------------------------------------------------------
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