Contacts of the helix formed by residues 132 - 142 (chain D) in PDB entry 3GV5
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 132 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29D VAL* 2.8 19.3 + - + +
31D VAL* 3.7 29.6 - - + +
117D SER* 4.1 7.6 - - - +
130D VAL* 3.8 13.2 - - + +
131D ASP* 1.3 72.2 - - - +
133D THR* 1.3 65.3 + - - +
134D GLU 3.3 2.0 - - - -
135D MSE 3.1 9.8 + - - +
136D VAL* 2.9 32.8 + - + +
176D GLY* 3.8 32.3 - - - +
179D ILE* 3.9 19.3 - - + -
180D ALA 4.8 1.6 - - - +
183D MSE 3.7 29.6 - - + -
199D VAL* 5.1 0.9 - - + -
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Residues in contact with THR 133 (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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27D SER 3.6 20.0 - - - +
28D ARG* 3.3 13.2 - - + +
29D VAL* 3.0 22.8 + - + +
131D ASP* 2.6 25.1 + - - -
132D LEU* 1.3 74.0 - - - +
134D GLU* 1.3 59.6 + - + +
136D VAL* 3.3 5.5 + - - +
137D GLU* 3.0 51.7 + - - +
172D ARG* 4.2 6.3 - - - +
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Residues in contact with GLU 134 (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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131D ASP* 4.8 3.8 + - - +
132D LEU 3.3 0.4 - - - -
133D THR* 1.3 77.7 - - + +
135D MSE 1.3 58.2 + - + +
137D GLU* 3.4 10.2 + - - +
138D LYS* 3.0 30.2 + - - +
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Residues in contact with MSE 135 (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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116D PHE* 3.8 32.8 - - + +
117D SER* 3.5 27.6 - - - +
132D LEU* 3.1 14.8 + - - +
134D GLU* 1.3 77.8 - - + +
136D VAL* 1.3 56.0 + - - +
138D LYS* 3.4 9.8 - - + +
139D ARG* 2.8 56.3 + - - +
179D ILE* 3.8 41.3 - - + -
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Residues in contact with VAL 136 (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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29D VAL* 4.1 11.7 - - + -
132D LEU* 2.9 26.7 + - + +
133D THR 3.6 5.2 - - - +
135D MSE 1.3 74.4 - - - +
137D GLU* 1.3 60.7 + - - +
139D ARG* 3.1 4.4 + - - +
140D LEU* 2.8 36.7 + - + +
172D ARG* 3.7 40.4 - - + +
175D VAL* 4.2 12.1 - - + +
176D GLY* 3.9 21.3 - - - +
179D ILE* 3.9 16.8 - - + -
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Residues in contact with GLU 137 (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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27D SER 4.8 0.9 - - - +
133D THR* 3.0 39.5 + - - +
134D GLU* 3.8 9.1 - - - +
136D VAL* 1.3 75.0 - - + +
138D LYS* 1.3 58.0 + - - +
140D LEU* 3.3 8.7 + - + +
141D GLN* 2.9 49.9 + - - +
172D ARG* 3.8 24.9 + - - +
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Residues in contact with LYS 138 (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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134D GLU 3.0 15.2 + - - +
135D MSE 3.4 14.4 - - - +
137D GLU* 1.3 76.1 - - - +
139D ARG* 1.3 63.6 + - + +
141D GLN* 3.3 21.2 + - - +
142D GLN* 3.4 13.0 + - - +
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Residues in contact with ARG 139 (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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135D MSE 2.8 42.5 + - - +
136D VAL* 3.1 5.4 + - - +
138D LYS* 1.3 75.1 - - + +
140D LEU* 1.3 66.4 + - - +
142D GLN* 2.6 50.8 + - - +
143D LEU* 3.5 5.2 - - - +
175D VAL* 4.1 15.5 - - + +
178D GLN* 4.3 15.2 - - - +
179D ILE* 3.6 35.0 - - + +
182D GLU* 2.8 40.0 + - - -
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Residues in contact with LEU 140 (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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136D VAL* 2.8 26.6 + - + +
137D GLU* 3.6 9.4 - - + +
139D ARG* 1.3 77.3 - - - +
141D GLN* 1.3 61.8 + - + +
142D GLN 3.0 0.2 - - - -
143D LEU* 3.1 38.1 + - + +
148D LEU* 5.4 0.2 - - + -
168D VAL* 5.7 1.3 - - + -
171D ILE* 3.3 34.5 - - + -
172D ARG* 3.1 39.0 - - + +
175D VAL* 3.8 14.4 - - + -
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Residues in contact with GLN 141 (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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137D GLU* 2.9 32.3 + - - +
138D LYS* 3.8 12.1 - - - +
139D ARG 3.3 0.4 - - - -
140D LEU* 1.3 76.3 - - + +
142D GLN* 1.3 59.5 + - - +
143D LEU 3.4 2.8 + - - +
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Residues in contact with GLN 142 (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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138D LYS 3.4 8.3 + - - +
139D ARG* 2.6 48.3 + - - +
140D LEU 3.0 0.8 - - - -
141D GLN* 1.3 79.9 - - - +
143D LEU* 1.3 74.4 + - - +
144D GLN* 3.5 8.1 + - - +
147D GLU* 3.2 13.6 - - - +
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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