Contacts of the helix formed by residues 121 - 132 (chain D) in PDB entry 3SHD
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 PRO 121 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71D TRP* 3.8 28.3 - - + +
74D PRO* 5.6 5.4 - - + -
120D SER* 1.3 85.5 - - - +
122D LEU* 1.3 59.2 + - - +
123D VAL 2.8 7.8 + - - -
124D ALA* 3.2 13.7 + - - +
125D GLU* 3.5 9.5 + - - +
128D ARG* 5.5 0.3 + - - -
144E PHE* 4.0 21.7 - - + -
145E ASN* 4.1 10.5 - - - +
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Residues in contact with LEU 122 (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 HIS* 3.7 31.3 + - + +
71D TRP* 3.7 43.3 - - + -
79D PHE* 5.6 0.9 - - + -
81D ARG* 3.6 40.5 + - + +
120D SER* 3.0 13.6 + - - +
121D PRO* 1.3 77.4 - - - +
123D VAL* 1.3 51.4 + - - +
125D GLU* 3.4 5.6 + - + +
126D SER* 2.5 39.0 + - - -
158D SO4 5.5 1.1 - - - +
144E PHE* 3.6 27.4 - - + -
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Residues in contact with VAL 123 (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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20D VAL* 6.1 1.3 - - + -
31D TRP* 3.9 12.8 - - + +
32D ASN* 3.3 37.9 - - - +
33D GLN* 3.7 20.0 - - - +
81D ARG* 4.7 0.9 - - - +
112D ILE* 5.1 3.4 - - + -
118D LEU* 4.1 23.1 - - + -
119D ARG* 4.0 0.4 - - + +
120D SER* 3.0 35.2 + - - +
121D PRO 2.8 3.8 + - - -
122D LEU* 1.3 74.1 - - - +
124D ALA* 1.3 52.3 + - - +
126D SER* 3.3 5.2 - - - -
127D ILE* 2.4 38.7 - - + +
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Residues in contact with ALA 124 (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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112D ILE* 5.1 0.2 - - - -
113D LEU* 4.1 15.7 - - + +
118D LEU* 3.9 22.4 - - + +
121D PRO 3.2 6.5 + - - +
123D VAL* 1.3 75.4 - - - +
125D GLU* 1.3 70.1 + - - +
126D SER 3.1 1.6 - - - -
127D ILE* 2.9 18.1 + - - +
128D ARG* 3.0 36.2 + - - +
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Residues in contact with GLU 125 (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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67D ARG* 5.6 0.7 + - - -
69D HIS* 4.0 21.5 + - + +
121D PRO 3.5 3.9 + - - +
122D LEU* 3.4 14.6 + - + +
124D ALA* 1.3 75.4 - - - +
126D SER* 1.3 56.1 + - - +
128D ARG* 2.7 53.0 + - - +
129D CYS* 2.8 26.1 + - - -
144E PHE* 2.9 49.5 - - + -
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Residues in contact with SER 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D VAL* 3.9 4.7 - - - +
33D GLN* 3.3 19.9 + - - -
69D HIS* 5.0 1.9 + - - -
81D ARG* 2.9 22.7 + - - -
83D LEU* 3.8 26.0 - - - +
122D LEU 2.5 18.4 + - - -
123D VAL 3.3 13.0 - - - -
125D GLU* 1.3 78.6 - - - +
127D ILE* 1.3 57.1 + - - -
129D CYS* 3.5 5.4 + - - +
130D TYR* 3.1 26.0 + - - +
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Residues in contact with ILE 127 (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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11D VAL* 5.2 3.1 - - + -
18D PHE* 4.8 20.6 - - + -
33D GLN* 3.2 19.3 - - - +
109D ALA* 4.7 13.5 - - + +
112D ILE* 3.6 32.8 - - + -
113D LEU* 3.9 20.4 - - + -
123D VAL* 2.4 35.7 - - + +
124D ALA* 2.9 8.0 + - - +
126D SER* 1.3 74.4 - - - +
128D ARG* 1.3 59.3 + - - +
130D TYR* 3.5 5.7 + - - +
131D GLN* 2.8 49.4 + - + +
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Residues in contact with ARG 128 (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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113D LEU* 3.9 31.3 + - + +
121D PRO 5.5 0.4 + - - -
124D ALA* 3.0 35.5 + - - +
125D GLU* 2.7 33.4 + - - +
127D ILE* 1.3 75.1 - - - +
129D CYS* 1.3 53.7 + - - +
131D GLN* 3.3 14.1 + - + +
132D SER* 2.7 34.2 + - - -
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Residues in contact with CYS 129 (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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66D ILE* 3.8 20.4 - - + -
67D ARG* 4.3 12.8 - - - -
69D HIS* 3.7 32.1 - - - -
83D LEU* 4.5 1.8 - - + -
125D GLU* 2.8 22.8 + - - -
126D SER* 3.5 10.5 - - - +
128D ARG* 1.3 73.9 - - - +
130D TYR* 1.3 64.7 - - - +
132D SER* 2.5 29.3 + - - -
133D GLY 3.7 0.7 + - - -
134D GLN* 4.0 10.8 + - - +
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Residues in contact with TYR 130 (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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11D VAL* 3.7 33.2 - - + -
13D HIS* 3.3 16.3 + + + -
18D PHE* 3.6 27.4 - + - -
66D ILE* 4.3 18.4 - - + +
85D ALA* 4.9 9.2 - - + -
87D GLU* 3.5 17.3 - - - -
126D SER 3.1 8.0 + - - +
127D ILE* 3.6 7.4 - - - +
129D CYS* 1.3 76.6 - - - +
131D GLN* 1.3 75.1 + - + +
132D SER 3.0 1.6 + - - -
133D GLY* 3.0 15.2 + - - -
134D GLN 4.1 3.7 + - - -
113I LEU* 3.8 15.5 - - + +
114I GLN* 5.9 1.8 - - - -
128I ARG* 2.4 34.3 + - - -
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Residues in contact with GLN 131 (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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18D PHE* 5.1 4.5 - - + -
109D ALA* 3.5 26.8 - - - +
113D LEU* 4.1 14.4 - - - +
127D ILE* 2.8 38.4 + - + +
128D ARG* 3.5 12.5 - - + +
130D TYR* 1.3 88.3 - - + +
132D SER* 1.3 62.2 + - - +
133D GLY* 3.1 2.5 + - - -
114I GLN* 5.8 1.8 + - - -
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Residues in contact with SER 132 (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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128D ARG 2.7 16.9 + - - -
129D CYS* 2.5 22.7 + - - -
131D GLN* 1.3 74.1 - - - +
133D GLY* 1.3 57.2 + - - +
134D GLN* 3.4 21.8 + - - +
110F GLU* 5.7 0.9 - - - +
131I GLN 5.2 1.0 - - - +
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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