Contacts of the helix formed by residues 117 - 127 (chain A) in PDB entry 3VJR
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 HIS 117 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A LEU* 3.8 11.9 - - + -
24A HIS* 3.2 24.6 - + - -
71A MET* 3.7 25.6 - - + -
96A HIS* 4.0 8.7 - - + +
97A ASP* 2.8 46.9 + - - -
114A HIS* 2.9 18.1 + - - +
115A GLY 3.3 2.0 + - - -
116A GLY* 1.3 75.3 - - - +
118A ASN* 1.3 59.6 + - - +
119A GLY* 3.1 20.5 + - - -
120A LEU* 3.1 19.0 + - + +
121A LYS* 2.9 29.1 + - - +
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Residues in contact with ASN 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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14A ASN* 5.7 0.2 + - - -
24A HIS* 2.9 33.5 + - - -
71A MET* 3.2 17.8 - - - +
72A ASN* 3.9 24.1 + - + +
116A GLY 3.2 7.2 + - - +
117A HIS* 1.3 71.5 - - - +
119A GLY* 1.3 64.8 + - - +
121A LYS* 3.6 15.4 - - + +
122A ASP* 3.2 22.7 + - - +
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Residues in contact with GLY 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 4.0 8.3 - - - -
71A MET* 3.4 31.6 - - - -
74A SER* 4.0 1.7 - - - -
117A HIS* 3.1 9.3 + - - -
118A ASN* 1.3 85.4 - - - +
120A LEU* 1.3 61.4 + - - +
122A ASP* 3.4 4.9 + - - +
123A ILE* 3.2 26.3 + - - +
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Residues in contact with LEU 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 4.1 2.7 - - + +
94A VAL* 3.9 16.4 - - + -
96A HIS* 3.6 46.9 - - + +
113A GLY 4.5 0.4 - - - +
114A HIS* 3.7 38.8 - - + +
117A HIS* 3.1 16.8 + - + +
119A GLY* 1.3 71.5 - - - +
121A LYS* 1.3 66.6 + - - +
123A ILE* 3.2 5.0 + - + +
124A ILE* 2.9 29.3 + - + +
133A PHE* 3.9 27.6 - - + -
135A ARG* 4.3 11.2 - - + +
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Residues in contact with LYS 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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114A HIS* 3.6 46.5 - - + +
116A GLY* 4.3 18.4 + - - -
117A HIS 2.9 14.0 + - - +
118A ASN* 3.6 17.8 - - + +
120A LEU* 1.3 77.0 - - - +
122A ASP* 1.3 58.2 + - - +
124A ILE* 3.4 4.6 + - - +
125A SER* 3.0 28.1 + - - -
1B G 5.0 9.2 + - - +
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Residues in contact with ASP 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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72A ASN 2.8 31.3 - - - +
73A LEU* 3.1 11.3 - - - +
74A SER 4.4 0.4 - - - +
75A GLY* 2.9 23.7 + - - +
118A ASN 3.2 11.5 + - - +
119A GLY 3.8 4.3 - - - +
120A LEU 3.3 0.2 - - - -
121A LYS* 1.3 77.2 - - - +
123A ILE* 1.3 60.1 + - - +
125A SER* 3.7 5.7 - - - -
126A LYS* 2.9 60.4 + - - +
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Residues in contact with ILE 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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12A LEU* 3.7 31.0 - - + -
74A SER* 4.0 1.3 - - - -
75A GLY* 3.8 21.1 - - - +
78A VAL* 3.9 26.5 - - + -
94A VAL* 3.9 20.6 - - + -
119A GLY 3.2 17.7 + - - +
120A LEU* 3.2 8.9 + - + +
122A ASP* 1.3 73.4 - - - +
124A ILE* 1.3 65.6 + - - +
126A LYS 3.1 1.2 + - - -
127A LEU* 2.9 47.2 + - + +
133A PHE* 3.8 17.0 - - + -
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Residues in contact with ILE 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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112A GLY 4.3 4.3 - - - +
113A GLY* 5.2 0.4 - - - -
114A HIS* 4.2 32.3 - - + +
120A LEU* 2.9 20.6 + - + +
121A LYS* 3.6 4.7 - - - +
123A ILE* 1.3 77.3 - - - +
125A SER* 1.3 58.9 + - - +
127A LEU 3.6 2.9 + - - -
129A ASN* 2.9 42.4 + - - +
130A ASN 3.0 26.0 + - - +
131A PRO* 3.8 22.7 - - + -
133A PHE* 3.7 19.3 - - + -
135A ARG* 4.3 9.9 - - - +
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Residues in contact with SER 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 LYS 3.0 16.7 + - - -
122A ASP* 3.7 10.3 - - - -
123A ILE 3.2 0.2 - - - -
124A ILE* 1.3 78.3 - - - +
126A LYS* 1.3 63.5 + - - +
128A GLY* 3.2 14.7 + - - -
129A ASN* 3.4 12.9 + - - +
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Residues in contact with LYS 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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73A LEU* 4.0 18.9 - - - +
75A GLY* 3.8 15.3 - - - +
76A LYS* 3.6 30.5 - - + +
79A ALA* 3.5 18.9 - - + +
122A ASP* 2.9 48.3 + - - +
123A ILE 3.7 0.4 - - - +
125A SER* 1.3 79.5 + - - +
127A LEU* 1.3 60.8 + - - +
128A GLY 3.2 5.1 + - - -
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Residues in contact with LEU 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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75A GLY* 6.5 0.4 - - - -
78A VAL* 3.9 19.1 - - + -
79A ALA* 4.2 14.6 - - + +
82A ALA* 4.6 6.7 - - + -
89A PRO* 4.4 20.0 - - + +
92A ILE* 4.1 23.1 - - + -
123A ILE* 2.9 35.8 + - + +
124A ILE 4.1 0.4 - - - +
125A SER 3.3 0.4 - - - -
126A LYS* 1.3 80.3 - - - +
128A GLY* 1.3 58.8 + - - +
129A ASN 3.9 0.4 - - - -
130A ASN* 3.7 25.3 + - + +
133A PHE* 3.9 20.4 - - + -
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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