Contacts of the helix formed by residues 108 - 120 (chain A) in PDB entry 3SPD
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 108 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A TYR* 3.5 47.1 - - + -
60A LEU* 4.0 20.0 - - + -
74A LEU* 3.9 25.6 - - + -
103A TYR* 2.9 44.3 + - + +
104A VAL* 4.8 0.9 - - + +
107A ASP* 1.3 83.6 - - + +
109A SER* 1.3 58.6 + - - +
110A GLY 3.4 1.3 - - - -
111A LEU* 3.2 13.2 + - + +
112A ILE* 2.9 44.3 + - + +
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Residues in contact with SER 109 (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 VAL 3.5 21.5 + - - -
105A GLN* 3.7 14.1 + - - -
106A GLY* 2.7 22.6 + - - -
107A ASP 3.4 0.2 - - - -
108A LEU* 1.3 77.5 - - - +
110A GLY* 1.3 68.0 + - - +
112A ILE* 3.3 4.8 + - - +
113A PHE* 3.0 42.3 + - - -
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Residues in contact with GLY 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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106A GLY 4.4 0.8 + - - -
107A ASP 5.0 1.2 + - - -
108A LEU 3.4 0.2 - - - -
109A SER* 1.3 81.3 + - - +
111A LEU* 1.3 63.3 + - - +
113A PHE* 3.3 9.2 + - - +
114A ASP* 3.0 23.1 + - - +
117A ARG* 5.4 0.9 + - - -
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Residues in contact with LEU 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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52A ILE* 3.3 46.4 - - + +
53A TYR* 3.9 18.8 - - + -
60A LEU* 4.0 15.5 - - + -
107A ASP 5.2 2.6 + - - +
108A LEU* 3.2 18.6 + - + +
110A GLY* 1.3 75.8 - - - +
112A ILE* 1.3 57.6 + - - +
114A ASP* 3.2 8.1 + - + +
115A GLU* 3.0 27.2 + - + +
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Residues in contact with ILE 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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60A LEU* 4.2 10.5 - - + -
70A MET* 3.7 23.5 - - + +
72A LEU* 4.1 16.4 - - + -
104A VAL* 4.1 24.9 - - + +
108A LEU* 2.9 36.9 + - + +
109A SER* 3.8 4.5 - - - +
110A GLY 3.3 0.2 - - - -
111A LEU* 1.3 76.4 - - - +
113A PHE* 1.3 58.1 + - + +
115A GLU* 3.3 7.9 + - - +
116A ALA* 2.9 26.7 + - - +
133A ILE* 4.3 14.4 - - + -
150A ILE* 4.2 28.9 - - + -
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Residues in contact with PHE 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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109A SER* 3.0 38.0 + - - +
110A GLY* 3.8 7.9 - - - +
112A ILE* 1.3 77.6 - - + +
114A ASP* 1.3 57.9 + - - +
116A ALA* 3.4 3.2 + - - +
117A ARG* 2.9 42.1 + - - +
126A ASN* 3.5 61.7 - - + +
129A LEU* 3.8 20.0 - - + +
130A ALA* 3.9 23.6 - - + -
133A ILE* 4.4 11.7 - - + -
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Residues in contact with ASP 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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110A GLY 3.0 13.5 + - - +
111A LEU* 3.7 11.5 - - + +
112A ILE 3.2 0.2 - - - -
113A PHE* 1.3 73.4 - - - +
115A GLU* 1.3 67.5 + - - +
117A ARG* 3.3 13.3 + - - +
118A ASN* 2.9 48.4 + - - +
122A GLN* 5.0 4.0 + - - +
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Residues in contact with GLU 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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52A ILE* 4.4 8.6 - - + +
62A ARG* 2.9 47.4 + - - -
70A MET* 3.5 24.6 - - + +
71A HIS 5.5 0.3 + - - -
72A LEU* 3.8 23.5 - - + +
111A LEU* 3.0 14.4 + - + +
112A ILE 3.5 8.7 - - - +
114A ASP* 1.3 77.2 - - - +
116A ALA* 1.3 56.2 + - - +
118A ASN* 3.3 8.7 + - - +
119A CYS* 2.9 49.1 + - - -
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Residues in contact with ALA 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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70A MET* 3.6 21.7 - - - -
112A ILE 2.9 16.2 + - - +
113A PHE* 3.7 5.6 - - - +
115A GLU* 1.3 76.4 - - - +
117A ARG* 1.3 56.2 + - - +
119A CYS 3.2 0.6 + - - +
120A LEU* 2.8 36.8 + - - +
129A LEU* 3.8 26.7 - - + -
133A ILE* 4.5 8.1 - - + -
152A THR* 4.5 10.1 - - + -
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Residues in contact with ARG 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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110A GLY 5.4 0.8 + - - -
113A PHE* 2.9 31.5 + - - +
114A ASP* 3.3 13.6 + - - +
116A ALA* 1.3 75.4 - - - +
118A ASN* 1.3 62.7 + - - +
120A LEU 3.6 0.2 - - - -
121A SER* 3.1 42.9 + - - +
122A GLN* 3.4 43.3 + - - +
124A LEU 2.9 28.5 + - - +
125A THR* 3.8 2.8 - - - +
126A ASN* 2.9 38.5 + - - +
129A LEU* 3.7 9.0 - - + +
704A SO4 4.7 1.4 + - - -
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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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114A ASP* 2.9 42.9 + - - +
115A GLU* 3.6 9.1 - - - +
117A ARG* 1.3 77.8 - - - +
119A CYS* 1.3 63.2 + - - +
120A LEU 3.4 2.1 + - - +
122A GLN* 4.5 9.5 + - - -
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Residues in contact with CYS 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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69A LYS* 3.4 45.7 + - - +
70A MET* 4.0 10.5 - - + -
115A GLU* 2.9 44.3 + - - +
118A ASN* 1.3 79.7 - - - +
120A LEU* 1.3 76.6 + - + +
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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
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69A LYS* 3.6 22.2 + - + +
70A MET* 4.3 0.4 - - + +
116A ALA 2.8 17.6 + - - +
117A ARG 3.6 2.5 - - - -
118A ASN 4.8 1.4 - - - +
119A CYS* 1.3 91.7 - - + +
121A SER* 1.3 64.6 + - - +
124A LEU* 3.7 11.0 - - + -
129A LEU* 4.2 5.6 - - + -
132A TYR* 3.8 35.2 - - + -
152A THR* 3.8 24.2 - - + +
154A ASP* 4.6 0.2 - - - +
222A TYR* 3.5 28.4 + - + +
225A TRP* 4.0 13.7 - - + -
226A LEU* 5.5 0.9 - - - +
704A SO4 4.5 3.5 + - - -
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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