Contacts of the helix formed by residues 108 - 120 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53D TYR* 3.5 48.2 - - + -
60D LEU* 4.0 20.4 - - + -
74D LEU* 3.8 31.0 - - + -
103D TYR* 2.9 39.3 + - + +
104D VAL* 4.8 0.7 - - + +
107D ASP* 1.3 82.8 - - + +
109D SER* 1.3 58.9 + - - +
110D GLY 3.5 1.8 - - - -
111D LEU* 3.2 12.8 + - + +
112D ILE* 2.9 44.0 + - + +
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Residues in contact with SER 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D VAL 3.4 21.9 + - - -
105D GLN* 3.8 12.8 + - - -
106D GLY 2.7 20.5 + - - -
107D ASP 3.5 0.2 - - - -
108D LEU* 1.3 76.7 - - - +
110D GLY* 1.3 69.5 + - - +
112D ILE* 3.3 5.1 + - - +
113D PHE* 3.0 44.0 + - - -
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Residues in contact with GLY 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D GLY 4.5 0.6 + - - -
107D ASP 5.1 1.2 + - - -
108D LEU 3.5 0.4 - - - -
109D SER* 1.3 82.1 + - - +
111D LEU* 1.3 61.7 + - - +
113D PHE* 3.3 9.9 + - - +
114D ASP* 3.0 24.1 + - - +
117D ARG* 5.4 0.7 + - - -
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Residues in contact with LEU 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D ILE* 3.4 46.4 - - + +
53D TYR* 3.9 19.1 - - + -
60D LEU* 4.0 16.2 - - + -
107D ASP 5.2 1.9 + - - +
108D LEU* 3.2 18.4 + - + +
110D GLY* 1.3 77.2 - - - +
112D ILE* 1.3 57.1 + - - +
114D ASP* 3.3 8.4 + - + +
115D GLU* 3.0 27.6 + - + +
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Residues in contact with ILE 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D LEU* 4.2 10.5 - - + -
70D MET* 3.7 23.4 - - + +
72D LEU* 4.1 16.8 - - + -
104D VAL* 4.1 29.8 - - + +
108D LEU* 2.9 34.5 + - + +
109D SER* 3.8 4.7 - - - +
111D LEU* 1.3 75.0 - - - +
113D PHE* 1.3 58.7 - - + +
115D GLU* 3.3 7.3 + - - +
116D ALA* 2.9 27.4 + - - +
133D ILE* 4.2 14.4 - - + -
150D ILE* 4.2 25.1 - - + -
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Residues in contact with PHE 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D SER* 3.0 38.6 + - - +
110D GLY* 3.8 7.6 - - - +
112D ILE* 1.3 76.6 - - + +
114D ASP* 1.3 57.9 + - - +
116D ALA* 3.3 4.4 + - - +
117D ARG* 2.9 41.7 + - - +
126D ASN* 3.5 61.0 - - + +
129D LEU* 3.8 18.7 - - + +
130D ALA* 3.9 23.8 - - + -
133D ILE* 4.4 11.7 - - + -
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Residues in contact with ASP 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D GLY 3.0 14.1 + - - +
111D LEU* 3.3 12.6 + - + +
113D PHE* 1.3 72.5 - - - +
115D GLU* 1.3 67.2 + - - +
117D ARG* 3.2 14.2 + - - +
118D ASN* 2.9 48.0 + - - +
122D GLN* 5.0 4.0 + - - +
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Residues in contact with GLU 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D ILE* 4.5 7.5 - - + +
62D ARG* 2.9 48.9 + - - -
70D MET* 3.5 24.6 - - + +
71D HIS 5.5 0.3 + - - -
72D LEU* 3.8 23.0 - - + +
111D LEU* 3.0 14.2 + - + +
112D ILE 3.5 8.7 - - - +
114D ASP* 1.3 77.8 - - - +
116D ALA* 1.3 56.8 + - - +
118D ASN* 3.3 8.3 + - - +
119D CYS* 2.9 50.7 + - - -
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Residues in contact with ALA 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D MET* 3.6 21.5 - - + -
112D ILE 2.9 16.9 + - - +
113D PHE* 3.7 6.1 - - - +
114D ASP 3.2 0.4 - - - -
115D GLU* 1.3 76.9 - - - +
117D ARG* 1.3 56.5 + - - +
119D CYS 3.2 0.2 + - - -
120D LEU* 2.8 41.4 + - - +
129D LEU* 3.8 26.0 - - + -
133D ILE* 4.6 5.8 - - + -
152D THR* 4.5 7.4 - - + -
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Residues in contact with ARG 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D GLY 5.4 0.8 + - - -
113D PHE* 2.9 30.9 + - - +
114D ASP* 3.8 12.5 + - - +
116D ALA* 1.3 76.6 - - - +
118D ASN* 1.3 64.8 + - - +
121D SER* 3.1 41.6 + - - +
122D GLN* 3.4 43.4 + - - +
124D LEU 2.9 28.5 + - - +
125D THR* 3.8 2.4 - - - +
126D ASN* 2.9 39.2 + - - +
129D LEU* 3.7 9.2 - - + +
704D SO4 4.8 1.0 + - - -
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Residues in contact with ASN 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D ASP* 2.9 42.4 + - - +
115D GLU* 3.7 9.3 - - - +
117D ARG* 1.3 79.8 - - - +
119D CYS* 1.3 63.4 + - - +
120D LEU 4.8 1.4 - - - +
122D GLN* 4.4 10.3 + - - -
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Residues in contact with CYS 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D LYS* 3.4 47.1 + - - +
70D MET* 3.9 10.3 - - + -
115D GLU* 2.9 44.9 + - - +
118D ASN* 1.3 80.3 - - - +
120D LEU* 1.3 74.9 + - + +
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Residues in contact with LEU 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D LYS* 3.7 18.2 - - + -
70D MET* 4.3 0.7 - - + +
116D ALA 2.8 18.1 + - - +
117D ARG 3.7 1.6 - - - -
118D ASN 4.8 1.1 - - - +
119D CYS* 1.3 91.9 - - + +
121D SER* 1.3 64.8 + - - +
124D LEU* 3.7 11.4 - - + -
129D LEU* 4.4 4.3 - - + -
132D TYR* 3.8 35.2 - - + -
152D THR* 3.6 25.6 - - + +
154D ASP* 4.5 0.2 - - - +
222D TYR* 3.6 33.7 + - + +
225D TRP* 3.9 10.1 - - + -
226D LEU* 5.5 0.7 - - - +
704D SO4 4.4 3.3 + - - -
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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