Contacts of the helix formed by residues 113 - 129 (chain A) in PDB entry 2VXX
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 ASN 113 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112A PHE* 1.3 77.8 - - - +
114A CYS* 1.3 59.5 + - - +
115A ARG* 3.0 15.4 - - - +
116A GLN* 2.8 32.4 + - - +
117A MET* 3.0 22.2 + - - +
5B ALA* 5.0 10.7 - - - +
6B LEU 5.4 3.8 + - - +
8B ARG* 3.5 30.6 - - + +
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Residues in contact with CYS 114 (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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54A VAL* 4.1 7.2 - - + -
55A GLU 4.6 12.1 - - - +
58A GLU* 4.6 12.1 - - - -
62A LEU* 3.7 30.7 - - + -
66A PHE* 5.1 0.8 - - + -
113A ASN* 1.3 75.4 - - - +
115A ARG* 1.3 61.6 + - - +
117A MET* 3.5 21.9 - - + +
118A LEU* 3.0 35.7 + - - +
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Residues in contact with ARG 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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113A ASN* 3.0 9.3 - - - +
114A CYS* 1.3 81.6 - - - +
116A GLN* 1.3 56.4 - - - +
118A LEU* 3.4 3.2 - - - +
119A SER* 2.7 39.1 - - - +
168A PHE 4.4 3.6 + - - -
169A LEU* 2.7 58.6 + - + +
170A ALA 4.7 4.8 + - - -
171A ASN* 5.2 5.1 + - - +
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Residues in contact with GLN 116 (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 PHE* 4.1 28.9 - - + -
113A ASN* 2.8 29.6 + - - +
115A ARG* 1.3 69.4 + - - +
117A MET* 1.3 61.1 - - - +
119A SER* 3.2 9.5 + - - -
120A ASN* 2.9 61.0 + - - +
123A GLN* 6.0 0.2 + - - -
4B SER* 3.8 17.5 + - - +
5B ALA* 3.6 31.6 - - + +
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Residues in contact with MET 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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50A HIS* 3.3 51.2 - - + +
53A VAL* 3.7 20.0 - - + +
54A VAL* 3.8 33.0 - - + +
55A GLU 5.1 0.9 - - - +
66A PHE* 4.4 6.3 - - + -
107A GLU* 3.9 8.7 - - - +
112A PHE* 3.4 26.2 - - + +
113A ASN 3.0 11.9 + - - +
114A CYS* 3.5 23.8 - - + +
116A GLN* 1.3 77.3 + - - +
118A LEU* 1.3 63.2 + - - +
120A ASN* 3.3 0.7 + - - +
121A ASP* 3.0 28.3 + - - -
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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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62A LEU* 3.8 27.1 - - + -
65A PHE* 4.1 14.6 - - + -
66A PHE* 3.9 22.9 - - + -
114A CYS* 3.0 22.9 + - + +
115A ARG* 3.8 5.2 - - - +
116A GLN 3.3 0.2 - - - +
117A MET* 1.3 75.7 - - - +
119A SER* 1.3 58.8 + - - +
121A ASP* 3.2 5.7 + - - +
122A LEU 2.9 24.6 + - - -
165A ILE* 3.2 29.6 - - + +
168A PHE* 3.8 29.2 - - + +
169A LEU* 3.8 17.9 - - + -
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Residues in contact with SER 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 ARG* 2.7 25.6 - - - +
116A GLN* 3.2 10.9 + - - -
118A LEU* 1.3 72.9 - - - +
120A ASN* 1.3 68.1 + - - +
122A LEU* 3.3 4.4 + - - +
123A GLN* 3.1 39.8 + - - +
169A LEU* 3.7 22.2 - - - +
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Residues in contact with ASN 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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46A GLN* 3.6 17.3 + - - +
104A PHE* 5.4 1.0 - - - -
105A THR 5.7 3.9 - - - +
107A GLU* 2.8 43.8 + - + +
108A PRO* 5.3 1.6 - - - +
112A PHE* 5.7 0.2 - - - -
116A GLN* 2.9 41.6 + - - +
117A MET 3.6 6.5 - - - +
119A SER* 1.3 76.9 - - - +
121A ASP* 1.3 58.4 + - - +
123A GLN* 3.4 15.0 + - - +
124A ALA* 3.0 28.2 + - - +
4B SER* 5.3 1.4 + - - -
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Residues in contact with ASP 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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43A LEU* 4.2 3.5 - - - +
46A GLN* 2.9 27.3 + - - +
47A TYR* 3.3 39.7 - - + +
50A HIS* 2.7 28.3 + - - -
66A PHE* 3.4 11.1 - - + -
117A MET 3.0 14.4 + - - +
118A LEU* 3.5 8.5 - - - +
120A ASN* 1.3 72.4 - - - +
122A LEU* 1.3 65.2 + - - +
124A ALA* 3.3 3.9 + - - +
125A GLU* 3.0 27.7 + - - +
165A ILE* 3.9 7.6 - - + -
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Residues in contact with LEU 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 14.1 + - - +
119A SER* 3.7 9.2 - - - +
121A ASP* 1.3 74.6 - - - +
123A GLN* 1.3 53.1 + - + +
125A GLU* 3.0 5.5 + - - +
126A GLN* 2.8 56.4 + - - +
162A ALA* 3.3 36.8 - - + +
165A ILE* 3.8 12.4 - - + +
166A GLY* 4.6 6.1 - - - -
169A LEU* 4.2 19.3 - - + -
18C VAL* 3.8 30.7 - - + -
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Residues in contact with GLN 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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104A PHE* 4.9 2.5 - - + -
119A SER* 3.1 32.0 + - - +
120A ASN* 3.7 13.4 + - - +
122A LEU* 1.3 75.5 - - + +
124A ALA* 1.3 62.5 + - - +
126A GLN* 3.3 20.0 + - - +
127A ALA* 3.0 25.1 + - - +
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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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43A LEU* 3.7 23.1 - - + -
46A GLN* 4.2 1.3 - - - +
104A PHE* 3.6 39.3 - - + +
120A ASN 3.0 18.0 + - - +
121A ASP 3.5 5.2 - - - +
123A GLN* 1.3 76.2 - - - +
125A GLU* 1.3 62.2 + - - +
127A ALA* 3.5 2.3 + - - +
128A ILE* 3.1 31.3 + - - +
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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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43A LEU* 3.4 14.1 - - + +
47A TYR* 2.6 31.8 + - - +
121A ASP 3.0 20.4 + - - +
122A LEU 3.5 6.3 - - - +
124A ALA* 1.3 75.9 - - - +
126A GLN* 1.3 52.4 + - - +
128A ILE* 3.3 5.5 + - - +
129A ILE* 2.8 39.7 + - - +
158A THR* 3.2 13.7 - - - +
161A ARG* 2.8 46.2 + - - +
162A ALA* 4.0 19.7 - - + -
165A ILE* 3.9 9.6 - - + -
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Residues in contact with GLN 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 LEU* 2.8 34.0 + - + +
123A GLN* 3.3 31.4 + - - +
125A GLU* 1.3 74.3 - - + +
127A ALA* 1.3 64.2 + - - +
129A ILE* 3.3 13.2 + - + +
130A GLY* 3.1 18.9 + - - -
18C VAL* 2.9 37.0 - - - +
20C LEU* 4.1 33.4 - - + +
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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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103A CYS* 3.8 28.3 - - + +
104A PHE* 3.9 11.2 - - + -
123A GLN 3.0 16.9 + - - +
124A ALA 3.7 4.9 - - - +
126A GLN* 1.3 75.2 - - - +
128A ILE* 1.3 62.4 + - - +
130A GLY* 3.3 3.7 + - - -
131A VAL* 3.3 25.6 + - - +
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Residues in contact with ILE 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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36A LEU* 3.9 10.5 - - + -
39A SER* 3.9 25.8 - - - +
40A PHE* 3.5 37.5 - - + -
43A LEU* 3.8 27.1 - - + -
103A CYS* 3.7 19.3 - - - -
104A PHE* 4.2 5.4 - - + -
124A ALA 3.1 19.5 + - - +
125A GLU* 3.7 5.6 - - - +
127A ALA* 1.3 74.3 - - - +
129A ILE* 1.3 60.1 + - - +
131A VAL* 3.1 6.1 + - - +
132A LEU* 2.9 37.1 + - + +
158A THR* 4.3 3.8 - - + -
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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 GLU 2.8 25.7 + - - +
126A GLN* 3.5 10.8 - - - +
128A ILE* 1.3 73.0 - - - +
130A GLY* 1.3 63.0 + - - +
132A LEU* 3.5 2.7 + - - +
133A ARG* 3.2 61.7 + - - +
155A LEU* 3.8 10.9 - - + +
158A THR* 3.8 14.6 - - + +
159A GLU* 3.8 35.4 - - + +
162A ALA* 3.9 18.6 - - + -
19C ILE* 3.9 16.2 - - + +
20C LEU* 5.7 2.0 - - + -
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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