Contacts of the helix formed by residues 106 - 116 (chain A) in PDB entry 1P4V
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 GLY 106 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A ALA 3.0 12.3 + - - -
81A CYS* 3.2 23.9 + - - +
82A MET* 4.5 2.0 - - - -
83A GLU 5.9 0.7 - - - -
105A VAL* 1.3 75.2 - - - +
107A ASP* 1.3 65.7 + - - -
109A ALA* 2.9 14.1 + - - +
110A LEU* 3.2 10.7 + - - +
405C VAL* 5.4 1.8 - - - -
406C GLY* 6.0 4.5 - - - -
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Residues in contact with ASP 107 (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 ARG* 5.6 2.1 + - - -
83A GLU* 5.1 6.8 - - - +
105A VAL 3.6 0.2 + - - -
106A GLY* 1.3 69.9 - - - -
108A GLY* 1.3 57.5 + - - +
110A LEU* 3.1 13.2 + - - +
111A GLU* 2.8 29.6 + - - +
362C ARG* 4.3 14.0 + - - +
407C ASP* 4.2 19.7 - - - +
478C HIS* 3.6 18.3 - - + +
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Residues in contact with GLY 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A LEU* 4.3 3.2 - - - +
105A VAL 3.4 5.9 + - - -
106A GLY 3.2 1.2 - - - -
107A ASP* 1.3 78.0 - - - +
109A ALA* 1.3 60.9 + - - +
111A GLU* 3.5 4.2 + - - +
112A PHE* 3.0 24.4 + - - +
477C MET* 5.8 0.3 - - - +
478C HIS* 3.3 48.3 + - - +
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Residues in contact with ALA 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A VAL* 4.4 6.7 - - + -
82A MET* 3.7 26.9 - - + +
91A VAL* 4.3 2.4 - - - +
104A LEU* 3.7 35.4 - - + +
105A VAL* 3.4 9.6 + - - -
106A GLY 2.9 10.3 + - - +
108A GLY* 1.3 76.9 - - - +
110A LEU* 1.3 57.8 + - - +
112A PHE* 3.3 2.8 + - - +
113A ALA* 2.9 28.4 + - - +
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Residues in contact with LEU 110 (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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82A MET* 4.0 8.2 - - + +
83A GLU* 3.4 24.9 - - + +
84A HIS* 3.9 28.7 - - + -
85A ILE* 3.6 23.6 - - + -
106A GLY 3.2 6.9 + - - +
107A ASP* 3.1 15.1 + - - +
109A ALA* 1.3 76.6 - - - +
111A GLU* 1.3 60.7 + - - +
113A ALA* 3.1 3.8 + - - +
114A LEU* 2.9 53.9 + - + +
120A LYS* 5.0 8.1 - - + +
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Residues in contact with GLU 111 (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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107A ASP 2.8 19.8 + - - +
108A GLY* 3.8 5.5 - - - +
110A LEU* 1.3 72.7 - - - +
112A PHE* 1.3 64.8 + - - +
114A LEU* 3.4 11.9 + - - +
115A SER* 3.0 21.9 + - - -
360C ASP* 3.8 18.8 - - - +
478C HIS* 4.1 16.4 - - + +
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Residues in contact with PHE 112 (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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91A VAL* 3.9 9.6 - - + -
94A ALA* 3.6 23.1 - - + -
95A VAL* 3.5 30.1 - - + -
98A LYS* 4.1 4.5 - - + -
99A THR* 3.6 25.1 - - + -
104A LEU* 3.7 21.8 - - + -
108A GLY 3.0 18.8 + - - +
109A ALA* 3.6 2.7 - - - +
111A GLU* 1.3 76.0 - - - +
113A ALA* 1.3 67.6 + - - +
115A SER* 2.5 29.5 + - - -
116A GLN* 3.0 38.6 + - + +
477C MET* 3.6 21.8 - - + -
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Residues in contact with ALA 113 (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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82A MET* 4.2 0.4 - - - -
85A ILE* 3.9 20.9 - - + -
91A VAL* 3.8 31.6 - - + -
109A ALA 2.9 14.0 + - - +
110A LEU 3.4 8.1 - - - +
112A PHE* 1.3 78.6 - - - +
114A LEU* 1.3 61.5 + - - +
116A GLN* 3.0 11.2 + - - -
118A PHE* 3.1 32.4 + - + -
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Residues in contact with LEU 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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85A ILE* 4.3 2.7 - - + -
110A LEU* 2.9 44.6 + - + +
111A GLU* 3.7 8.7 - - - +
113A ALA* 1.3 75.8 - - - +
115A SER* 1.3 57.8 + - - +
116A GLN 3.0 0.2 - - - -
117A GLY* 3.0 18.7 + - - -
118A PHE 3.5 20.3 - - - +
120A LYS* 4.1 32.3 - - + +
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Residues in contact with SER 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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111A GLU* 3.0 14.4 + - - -
112A PHE* 2.5 35.7 + - - -
114A LEU* 1.3 76.5 - - - +
116A GLN* 1.3 69.3 + - - +
117A GLY 3.3 1.2 + - - -
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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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94A ALA* 4.2 5.9 - - + +
98A LYS* 3.6 28.6 - - - +
112A PHE* 3.0 49.6 + - + +
113A ALA 3.0 9.9 + - - +
115A SER* 1.3 90.5 + - - +
117A GLY* 1.3 59.2 + - - +
118A PHE* 3.4 20.8 + - + -
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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