Contacts of the helix formed by residues 136 - 145 (chain D) in PDB entry 6G2T
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 GLN 136 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10D ASP* 4.2 6.5 + - - -
11D ASN 4.4 3.0 + - - -
12D GLY* 4.3 16.0 - - - -
105D THR* 3.1 40.2 + - + +
106D GLU 2.8 16.3 + - - +
107D ALA* 3.7 29.2 - - - +
108D PRO* 4.4 2.6 - - + +
135D ILE* 1.3 74.1 - - - +
137D ALA* 1.3 62.5 + - - +
138D VAL 3.4 0.2 + - - -
139D LEU* 3.4 2.9 + - - +
140D SER* 3.3 17.2 + - - -
153D ASP* 3.2 22.2 - - - +
158D VAL 5.5 0.2 - - - +
160D HIS* 4.2 10.0 + - - -
338D VAL* 3.7 20.5 - - + +
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Residues in contact with ALA 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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108D PRO* 4.9 3.9 - - + +
135D ILE* 3.3 4.0 - - + +
136D GLN* 1.3 78.7 - - - +
138D VAL* 1.3 60.1 + - - +
140D SER* 2.7 23.5 + - - -
141D LEU* 3.4 4.9 + - - +
151D VAL* 3.8 26.5 - - + +
153D ASP* 3.7 11.7 + - + +
160D HIS 5.9 0.2 - - - +
162D VAL* 3.4 43.7 - - + +
164D ILE* 5.8 0.7 - - + -
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Residues in contact with VAL 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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42B VAL* 3.8 24.5 - - + +
43B MET* 3.6 15.3 - - - -
134D ALA* 6.3 0.2 - - + -
135D ILE* 3.3 27.4 + - + +
136D GLN 3.3 0.8 - - - -
137D ALA* 1.3 74.7 - - + +
139D LEU* 1.3 71.1 + - + +
141D LEU* 3.1 18.2 + - - +
142D TYR* 3.1 41.1 - - + -
162D VAL* 5.3 2.0 - - + -
164D ILE* 4.2 22.4 - - + -
345D LEU* 6.2 1.1 - - + -
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Residues in contact with LEU 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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8D VAL* 5.4 2.2 - - + -
103D LEU* 4.5 10.8 - - + -
105D THR* 4.2 17.7 - - - +
134D ALA* 3.4 26.7 - - + -
135D ILE 2.9 27.8 - - - +
136D GLN 3.4 6.0 + - - +
137D ALA 3.4 0.6 - - - -
138D VAL* 1.3 77.5 - - + +
140D SER* 1.3 65.8 + - - +
142D TYR* 3.1 12.4 + - + -
143D ALA 3.2 1.9 + - - -
337D SER 4.1 1.6 - - - -
338D VAL* 3.3 20.9 - - + +
341D GLY* 3.0 26.2 + - - +
342D GLY* 3.4 33.2 - - - +
345D LEU* 4.4 9.9 - - + -
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Residues in contact with SER 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 GLN 3.3 9.2 + - - -
137D ALA* 2.7 21.2 + - - -
139D LEU* 1.3 77.3 - - - +
141D LEU* 1.3 61.9 + - - +
143D ALA* 3.2 5.7 + - - +
144D SER* 3.2 23.5 + - - -
151D VAL* 3.2 19.6 - - - +
297D VAL* 5.0 4.4 - - - +
299D SER* 3.8 26.5 - - - -
337D SER* 3.9 18.7 - - - -
338D VAL* 4.1 8.8 - - - +
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Residues in contact with LEU 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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43B MET* 4.1 22.0 - - + -
137D ALA 3.4 7.8 + - - +
138D VAL* 3.1 10.5 + - - +
140D SER* 1.3 83.8 + - - +
142D TYR* 1.3 57.1 + - - +
144D SER* 3.2 9.9 - - - -
145D GLY 3.0 22.2 + - - -
146D ARG* 3.0 46.7 + - + +
147D THR 4.4 2.9 - - - -
148D THR 4.5 11.9 - - - +
149D GLY* 5.1 1.6 - - - +
151D VAL* 4.5 16.6 - - + -
164D ILE* 3.6 37.0 - - + -
297D VAL* 4.9 10.1 - - + -
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Residues in contact with TYR 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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43B MET* 3.4 23.2 - - + +
44B VAL* 2.7 47.5 + - + +
138D VAL* 3.1 47.7 + - + -
139D LEU* 3.1 12.8 + - + +
141D LEU* 1.3 76.7 - - - +
143D ALA* 1.3 66.1 + - - +
145D GLY* 3.1 14.7 + - - +
146D ARG 5.4 0.9 - - - -
341D GLY* 3.8 4.5 - - - -
344D ILE* 3.6 45.1 - - + +
345D LEU* 4.2 22.9 - - + -
348D LEU* 5.0 9.6 - - + -
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Residues in contact with ALA 143 (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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139D LEU 3.2 2.6 + - - -
140D SER 3.2 7.9 + - - +
142D TYR* 1.3 79.9 - - - +
144D SER* 1.3 62.5 + - - +
145D GLY* 4.5 0.3 - - - -
337D SER* 3.3 41.1 - - - +
340D ILE* 3.6 28.6 - - + +
341D GLY* 4.1 1.0 - - - +
344D ILE* 5.4 0.2 - - - -
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Residues in contact with SER 144 (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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140D SER 3.2 10.6 + - - -
141D LEU* 3.2 13.7 - - - -
143D ALA* 1.3 81.4 - - - +
145D GLY* 1.3 59.2 + - - +
146D ARG* 3.3 28.3 + - - +
297D VAL* 3.7 22.2 - - - +
329D ILE* 5.7 5.8 - - - +
331D PRO* 5.1 11.4 - - - +
337D SER* 5.6 1.4 + - - -
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Residues in contact with GLY 145 (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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141D LEU 3.0 5.6 + - - -
142D TYR* 3.1 14.8 + - - -
143D ALA 3.2 0.6 - - - -
144D SER* 1.3 77.9 - - - +
146D ARG* 1.3 62.0 + - - +
147D THR* 4.2 3.8 + - - +
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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