Contacts of the helix formed by residues 114 - 129 (chain A) in PDB entry 3QVN
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 SER 114 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A ILE* 3.8 11.7 + - - +
109A VAL* 4.6 7.4 - - - -
112A TYR* 3.0 4.2 + - - +
113A GLY* 1.3 80.2 - - - +
115A VAL* 1.3 65.1 + - - +
116A SER* 3.8 12.1 - - - -
117A ASN* 3.2 28.6 + - - +
118A LEU 3.3 8.5 + - - -
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Residues in contact with VAL 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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97A HIS* 3.8 34.3 - - + +
98A PRO* 3.5 38.8 - - + +
105A GLY* 5.6 2.0 - - - +
108A ILE* 3.7 21.7 - - + +
109A VAL* 5.4 4.0 - - + +
114A SER* 1.3 72.5 - - - +
116A SER* 1.3 62.6 + - - +
118A LEU* 3.2 3.4 + - + +
119A ILE* 3.1 24.4 + - + +
197A TRP* 3.9 22.2 - - + -
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Residues in contact with SER 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A HIS* 5.3 7.8 - - - -
114A SER* 3.1 12.2 - - - -
115A VAL* 1.3 78.4 - - - +
117A ASN* 1.3 57.8 + - - +
119A ILE* 3.1 20.2 + - - +
120A ASP* 2.6 27.1 + - - +
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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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112A TYR* 3.1 31.8 + - - +
114A SER* 3.2 13.0 + - - +
116A SER* 1.3 77.0 - - - +
118A LEU* 1.3 65.0 + - - +
120A ASP* 3.2 14.3 + - - +
121A ILE* 3.1 36.1 + - - +
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Residues in contact with LEU 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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108A ILE* 3.8 39.5 - - + -
112A TYR* 3.6 41.4 - - + +
114A SER 3.3 8.6 + - - +
115A VAL* 3.2 10.0 + - - +
117A ASN* 1.3 79.0 - - - +
119A ILE* 1.3 57.1 + - + +
121A ILE* 3.6 4.0 + - + +
122A THR* 2.9 32.2 + - - +
137A ILE* 3.9 31.6 - - + -
147A LEU* 5.4 0.4 - - + -
149A VAL* 3.7 20.6 - - + -
192A TRP* 5.8 0.4 - - + -
197A TRP* 4.6 8.7 - - + -
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Residues in contact with ILE 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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97A HIS* 4.4 13.7 - - + +
115A VAL* 3.1 29.8 + - + +
116A SER* 3.4 11.0 - - - +
117A ASN 3.1 0.8 - - - -
118A LEU* 1.3 77.2 - - + +
120A ASP* 1.3 61.1 + - - +
122A THR* 3.3 0.7 + - - -
123A ASN* 2.8 39.9 + - - +
192A TRP* 3.3 66.6 - - + +
197A TRP* 4.6 4.0 - - + +
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Residues in contact with ASP 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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116A SER* 2.6 31.8 + - - +
117A ASN* 3.2 15.9 + - - +
119A ILE* 1.3 78.5 - - - +
121A ILE* 1.3 56.8 + - + +
123A ASN* 3.9 8.2 + - - +
124A SER* 3.0 28.1 + - - -
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Residues in contact with ILE 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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112A TYR* 3.5 35.7 - - + -
117A ASN* 3.1 29.0 + - - +
118A LEU* 3.6 7.0 - - - +
120A ASP* 1.3 74.0 - - + +
122A THR* 1.3 66.7 + - - +
124A SER* 3.0 8.0 + - - -
125A LYS* 3.0 35.1 + - + +
149A VAL* 4.2 22.2 - - + -
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Residues in contact with THR 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 LEU 2.9 17.0 + - - -
119A ILE 3.8 0.2 - - - -
121A ILE* 1.3 78.0 - - - +
123A ASN* 1.3 57.9 + - - +
125A LYS* 3.4 2.4 + - - +
126A LEU* 2.9 39.0 + - + +
135A ALA* 4.4 14.1 - - + -
136A PHE 5.8 0.2 - - - -
137A ILE* 4.1 16.7 - - + +
149A VAL* 3.6 29.1 - - + +
169A ILE* 4.2 5.4 - - + -
192A TRP* 3.6 30.2 - - + -
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Residues in contact with ASN 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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119A ILE* 2.8 37.5 + - - +
120A ASP* 3.9 7.8 + - - +
122A THR* 1.3 74.9 - - - +
124A SER* 1.3 59.9 + - - +
126A LEU* 3.4 9.2 + - - +
127A ALA* 2.9 29.5 + - - +
188A PHE* 3.3 23.5 - - + +
189A LYS* 4.2 19.4 - - + +
192A TRP* 2.8 28.4 + - - +
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Residues in contact with SER 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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120A ASP 3.0 14.6 + - - -
121A ILE* 3.0 11.9 + - - -
123A ASN* 1.3 72.5 - - - +
125A LYS* 1.3 65.6 + - - +
127A ALA* 3.5 6.3 + - - +
128A GLY* 3.0 19.1 + - - -
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Residues in contact with LYS 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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121A ILE* 3.0 28.8 + - - +
122A THR 3.5 7.2 - - - +
124A SER* 1.3 77.9 - - - +
126A LEU* 1.3 57.8 + - - +
128A GLY* 2.9 17.4 + - - +
129A ILE* 3.1 14.9 + - - +
135A ALA* 5.1 2.2 - - + -
149A VAL* 3.6 37.5 + - + +
151A THR* 3.8 22.9 + - - +
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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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122A THR* 2.9 24.0 + - + +
123A ASN* 3.7 13.9 - - - +
124A SER 3.4 0.2 - - - -
125A LYS* 1.3 75.8 - - - +
127A ALA* 1.3 61.3 + - - +
128A GLY 3.2 0.7 + - - -
129A ILE* 3.3 24.5 + - + +
135A ALA* 3.4 22.2 - - + -
151A THR* 4.9 0.2 + - - -
169A ILE* 3.6 43.3 - - + +
171A ALA* 3.8 27.3 - - + +
184A LYS* 5.2 1.6 + - - +
188A PHE* 3.6 41.2 - - + -
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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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123A ASN 2.9 18.3 + - - +
124A SER* 3.8 7.0 - - - +
126A LEU* 1.3 75.9 - - - +
128A GLY* 1.3 60.6 + - - +
129A ILE 3.7 1.0 + - - +
184A LYS* 4.0 19.5 + - - +
185A LEU* 3.8 28.5 - - + -
188A PHE* 3.7 9.8 - - + -
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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 SER 3.0 10.8 + - - -
125A LYS* 2.9 10.8 + - - -
127A ALA* 1.3 78.4 - - - +
129A ILE* 1.3 63.0 + - - +
130A GLN* 3.1 15.8 + - - +
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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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125A LYS 3.1 14.0 + - - +
126A LEU* 3.3 18.9 + - + +
127A ALA 4.2 0.3 - - - +
128A GLY* 1.3 75.6 - - - +
130A GLN* 1.3 64.6 + - - +
131A GLY 3.6 21.8 + - - +
132A SER 4.2 3.6 - - - +
133A GLY* 4.1 14.6 - - - +
134A TRP 3.4 30.5 - - - +
151A THR* 3.5 23.6 - - + +
152A THR 4.9 0.4 - - - +
153A ALA* 5.9 1.1 - - + -
171A ALA* 3.6 27.8 - - + -
184A LYS* 4.1 18.5 + - - -
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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