Contacts of the helix formed by residues 140 - 157 (chain D) in PDB entry 6GR2
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 SER 140 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36D GLY* 4.2 2.1 - - - -
37D ARG* 2.9 28.7 + - - +
133D VAL* 4.2 0.4 - - - -
138D GLY* 3.3 6.3 - - - +
139D LEU* 1.3 93.0 + - - +
141D SER* 1.3 65.9 + - - +
142D SER* 3.2 7.2 - - - +
143D ALA* 4.0 6.6 - - - +
144D SER* 3.2 20.1 + - - -
186D ASP* 3.8 33.8 - - - +
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Residues in contact with SER 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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61D THR* 4.5 1.4 + - - -
131D SER* 5.1 1.6 - - - -
133D VAL* 3.6 27.0 - - - +
134D PRO 4.1 4.4 + - - -
135D LEU* 3.6 40.7 - - - +
136D GLY 3.9 5.6 + - - +
139D LEU 3.5 1.8 - - - -
140D SER* 1.3 73.2 - - - +
142D SER* 1.3 61.8 + - - +
144D SER* 3.3 5.5 + - - -
145D LEU* 2.8 31.2 + - - +
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Residues in contact with SER 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109D TYR* 3.6 36.5 - - - -
140D SER* 4.5 7.1 - - - -
141D SER* 1.3 80.8 + - - +
143D ALA* 1.3 66.7 + - - +
145D LEU* 3.1 9.0 + - - +
146D GLU* 2.8 34.3 + - - +
174D GLU* 3.5 18.2 + - - -
186D ASP* 5.5 1.6 + - - +
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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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140D SER* 3.6 8.4 + - - +
141D SER 3.4 0.2 - - - -
142D SER* 1.3 82.3 + - - +
144D SER* 1.3 58.4 + - - +
146D GLU* 3.6 12.1 - - - -
147D VAL* 2.8 37.9 + - - +
186D ASP* 3.6 45.1 - - + +
187D GLN* 3.9 13.9 - - - +
190D SER* 4.5 1.6 - - - -
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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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34D ALA* 2.6 28.3 + - - +
35D PRO 3.5 21.6 + - - -
36D GLY 4.0 2.1 + - - -
61D THR* 2.7 23.6 + - - -
133D VAL* 4.1 3.0 - - - +
140D SER 3.2 13.2 + - - -
141D SER* 3.4 11.0 - - - -
143D ALA* 1.3 77.6 - - - +
145D LEU* 1.3 55.9 + - - +
148D ALA* 2.9 32.7 + - - +
190D SER* 4.0 5.5 + - - -
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Residues in contact with LEU 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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61D THR* 4.0 10.0 + - + +
63D LEU* 5.5 0.9 - - + -
106D TRP* 4.1 22.7 - - + +
109D TYR* 4.0 28.3 - - + -
110D VAL* 4.8 10.3 - - + -
129D VAL* 3.8 36.3 - - + -
141D SER 2.8 16.8 + - - +
142D SER* 3.4 10.5 - - - +
144D SER* 1.3 74.6 - - - +
146D GLU* 1.3 57.2 + - - +
148D ALA* 3.5 1.4 + - + +
149D THR* 2.9 42.9 + - - +
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Residues in contact with GLU 146 (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 TYR* 3.1 36.1 - - + +
113D VAL* 3.9 23.3 - - + +
142D SER 2.8 23.0 + - - +
143D ALA* 3.6 6.0 - - - +
145D LEU* 1.3 72.5 - - - +
147D VAL* 1.3 57.9 + - - +
149D THR* 3.2 5.0 + - - -
150D TYR* 2.8 28.4 + - - +
170D CYS* 3.2 24.9 - - + +
173D ALA* 5.3 0.4 - - + -
174D GLU* 2.6 31.1 + - - +
187D GLN* 3.2 26.2 + - - +
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Residues in contact with VAL 147 (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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34D ALA* 4.0 7.9 - - + -
143D ALA 2.8 24.5 + - - +
146D GLU* 1.3 68.8 - - - +
148D ALA* 1.3 57.7 + - - +
150D TYR* 3.6 1.5 - - - +
151D THR* 2.7 42.2 + - - +
170D CYS* 4.0 19.1 - - + -
187D GLN* 3.9 20.9 - - + +
190D SER* 3.7 34.1 - - - +
191D LEU* 3.5 33.2 - - + -
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Residues in contact with ALA 148 (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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32D VAL* 3.2 25.3 - - + +
34D ALA* 3.4 14.9 - - + +
61D THR* 3.8 23.6 - - + +
63D LEU* 4.4 9.9 - - + -
144D SER 2.9 19.9 + - - +
145D LEU* 3.7 4.0 - - + +
147D VAL* 1.3 77.2 - - - +
149D THR* 1.3 57.3 + - - +
151D THR* 3.3 1.1 + - - -
152D PHE* 2.9 25.8 + - - +
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Residues in contact with THR 149 (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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63D LEU* 4.0 19.7 - - + +
110D VAL* 3.8 33.1 - - + +
113D VAL* 3.9 22.7 - - + -
114D ILE* 4.8 1.6 - - + -
125D PHE* 5.7 2.7 - - + -
145D LEU* 2.9 21.1 + - - +
146D GLU* 3.2 10.5 + - - -
148D ALA* 1.3 76.1 - - - +
150D TYR* 1.3 63.8 + - - +
152D PHE* 3.0 5.1 + - + +
153D LEU* 2.8 34.8 + - + +
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Residues in contact with TYR 150 (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 VAL* 3.9 11.0 - - + -
117D TYR* 3.4 27.3 - + - -
118D PRO* 3.4 19.8 - - + +
146D GLU 2.8 19.8 + - - +
147D VAL* 3.2 6.5 + - + +
149D THR* 1.3 73.0 - - - +
151D THR* 1.3 64.2 + - - +
153D LEU* 3.2 6.1 + - - +
154D GLN* 3.0 31.5 + - + +
159D ASP* 2.6 25.4 + - - -
165D ALA* 5.1 1.2 - - - +
166D ARG* 3.3 36.9 + - + +
169D VAL* 3.5 38.8 - - + +
170D CYS* 3.8 15.9 - - - -
191D LEU* 5.6 3.1 - - + -
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Residues in contact with THR 151 (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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32D VAL* 3.4 24.7 - - + -
33D SER 4.7 7.8 + - - +
147D VAL* 2.7 35.5 + - - +
148D ALA* 3.7 4.7 - - - -
150D TYR* 1.3 72.4 - - - +
152D PHE* 1.3 60.5 + - - +
154D GLN* 3.3 22.5 + - - +
155D GLN* 2.9 34.1 + - - +
191D LEU* 4.9 4.7 - - - +
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Residues in contact with PHE 152 (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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30D LEU* 4.0 21.8 - - + -
32D VAL* 3.9 8.2 - - + +
63D LEU* 3.2 42.4 - - + -
65D GLY* 3.6 35.9 - - - -
66D SER 4.0 2.9 - - - -
125D PHE* 3.4 36.1 - + + -
148D ALA 2.9 13.4 + - - +
149D THR* 3.3 9.2 - - + +
151D THR* 1.3 74.3 - - - +
153D LEU* 1.3 65.8 + - + +
155D GLN* 2.8 31.7 + - + +
156D LEU* 3.3 31.9 + - + +
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Residues in contact with LEU 153 (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 VAL* 4.0 12.3 - - + +
114D ILE* 3.9 20.6 - - + -
117D TYR* 3.5 48.5 + - + -
122D LEU* 3.8 17.9 - - + +
125D PHE* 3.8 35.4 - - + -
149D THR* 2.8 22.3 + - + +
150D TYR 3.8 1.3 - - - +
152D PHE* 1.3 75.4 - - + +
154D GLN* 1.3 57.1 + - - +
156D LEU* 3.1 15.2 + - + +
157D CYS* 2.8 30.7 + - - +
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Residues in contact with GLN 154 (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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117D TYR* 3.1 18.6 + - - +
150D TYR* 3.0 37.6 + - + +
151D THR* 3.4 27.1 + - - +
152D PHE 3.1 0.4 - - - -
153D LEU* 1.3 78.1 - - - +
155D GLN* 1.3 67.9 + - - +
157D CYS 3.8 1.1 - - - -
158D PRO* 3.1 29.4 - - + +
159D ASP* 3.5 11.0 + - - +
166D ARG* 3.3 38.1 + - - +
191D LEU* 5.5 1.9 - - - +
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Residues in contact with GLN 155 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30D LEU* 3.8 40.2 - - + +
31D ALA 5.1 3.8 - - - +
32D VAL* 4.3 10.9 - - + +
151D THR* 2.9 30.1 + - - +
152D PHE* 2.8 20.4 + - + +
154D GLN* 1.3 87.9 - - - +
156D LEU* 1.3 61.2 + - - +
158D PRO* 4.6 3.5 - - - +
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Residues in contact with LEU 156 (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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30D LEU* 3.8 22.4 - - + -
67D PRO* 4.1 29.4 - - + -
121D PRO 4.8 0.7 - - - +
122D LEU* 4.1 3.6 - - + -
123D PRO* 3.8 29.0 - - + +
125D PHE* 3.4 34.3 - - + -
152D PHE* 3.7 26.0 - - + +
153D LEU* 3.1 20.3 + - + +
155D GLN* 1.3 77.0 - - - +
157D CYS* 1.3 62.1 + - - +
158D PRO* 4.3 2.1 - - - +
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Residues in contact with CYS 157 (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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117D TYR* 2.8 26.1 + - + -
119D ALA* 3.6 22.8 - - - +
120D ALA* 3.6 31.0 - - - -
121D PRO* 3.7 15.3 - - - +
122D LEU* 3.9 15.9 - - + -
153D LEU 2.8 7.9 + - - -
154D GLN 3.4 2.5 - - - -
155D GLN 3.3 0.6 - - - -
156D LEU* 1.3 77.9 - - - +
158D PRO* 1.3 74.0 - - - +
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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