Contacts of the helix formed by residues 132 - 147 (chain D) in PDB entry 6GL7
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 THR 132 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130D PRO* 4.2 4.3 + - - +
131D VAL* 1.3 81.8 - - + +
133D SER* 1.3 65.1 + - - +
134D ARG 3.1 1.7 + - - -
135D LEU* 3.6 15.2 + - - +
136D SER* 4.4 2.3 + - - -
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Residues in contact with SER 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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97D ARG* 5.7 1.6 - - - -
130D PRO* 2.6 42.3 + - - +
132D THR* 1.3 71.2 + - - +
134D ARG* 1.3 51.0 + - - -
135D LEU 3.1 3.4 - - - -
136D SER* 2.7 20.0 + - - -
137D ASP* 2.6 44.2 + - - -
140D ARG* 4.9 7.0 + - - -
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Residues in contact with ARG 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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126D SER* 5.2 1.0 + - - -
129D GLU* 3.0 41.3 + - + +
130D PRO 3.8 1.1 + - - +
131D VAL* 3.0 49.3 + - - +
133D SER* 1.3 76.9 - - - +
135D LEU* 1.3 61.5 + - - +
137D ASP* 3.3 14.7 + - - +
138D ILE* 3.2 11.1 + - - +
273D ALA* 5.5 3.8 + - - +
274D ASN* 4.2 10.4 + - - +
286D PRO* 6.1 6.0 - - - +
289D ASN* 3.1 26.6 + - - +
292D ALA* 5.0 4.7 - - + -
116E PHE* 5.5 8.7 - - - -
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Residues in contact with LEU 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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132D THR 3.6 10.4 + - - +
133D SER 3.1 0.6 - - - -
134D ARG* 1.3 75.2 - - - +
136D SER* 1.3 60.5 + - - +
138D ILE* 2.8 39.9 + - + +
139D PHE* 3.0 45.4 + - + -
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Residues in contact with SER 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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132D THR 4.8 1.6 + - - -
133D SER* 2.7 27.5 + - - +
135D LEU* 1.3 74.8 - - - +
137D ASP* 1.3 53.7 + - - -
139D PHE* 3.0 18.4 + - - +
140D ARG* 2.8 49.0 + - - +
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Residues in contact with ASP 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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97D ARG* 4.5 14.9 + - - -
133D SER* 2.6 23.1 + - - +
134D ARG* 3.3 17.0 - - - +
135D LEU 3.1 0.2 - - - -
136D SER* 1.3 73.0 - - - +
138D ILE* 1.3 61.7 + - - +
140D ARG* 2.6 40.0 + - - +
141D LEU* 3.3 5.0 + - - +
217D TYR* 5.7 0.5 + - - -
274D ASN* 5.5 1.0 + - - -
289D ASN* 3.8 3.4 - - - +
291D GLN* 3.1 36.6 - - + +
292D ALA* 3.3 34.6 - - - +
295D GLY* 5.7 0.9 - - - -
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Residues in contact with ILE 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 ARG 3.2 8.9 + - - +
135D LEU* 2.8 24.7 + - + +
137D ASP* 1.3 75.5 - - - +
139D PHE* 1.3 72.7 + - + +
141D LEU* 3.0 27.0 + - + +
142D ALA* 3.2 10.0 + - + +
287D ALA* 5.8 8.1 - - + +
289D ASN* 3.4 26.5 - - + +
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Residues in contact with PHE 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 LEU* 3.0 52.3 + - + -
136D SER* 3.0 19.0 + - - +
138D ILE* 1.3 83.3 - - + +
140D ARG* 1.3 63.2 + - + +
142D ALA* 2.9 22.7 + - + +
143D SER* 2.9 16.3 + - - +
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Residues in contact with ARG 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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97D ARG* 5.4 4.1 - - - +
133D SER* 4.3 7.9 + - - -
136D SER* 2.8 30.2 + - - +
137D ASP* 2.6 46.9 + - - +
139D PHE* 1.3 71.6 - - - +
141D LEU* 1.3 57.1 + - - +
143D SER* 3.0 11.4 + - - -
144D ILE* 3.0 29.4 + - - +
213D SER* 3.1 36.9 + - - -
217D TYR* 3.9 18.3 - - + -
291D GLN* 3.9 17.0 - - - +
355D PHE* 4.8 1.5 - - + -
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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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137D ASP 3.6 10.1 - - - +
138D ILE* 3.0 17.3 + - + +
140D ARG* 1.3 77.9 - - - +
142D ALA* 1.3 61.1 + - - +
144D ILE* 3.2 7.4 - - - +
145D PHE* 3.1 22.5 + - - +
288D ASP 5.4 0.7 - - - +
289D ASN* 4.1 8.3 - - - +
290D TYR* 3.8 38.4 - - + +
291D GLN* 3.8 23.1 - - + +
355D PHE* 3.9 25.1 - - + -
359D THR 3.4 25.5 - - - +
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Residues in contact with ALA 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 ILE* 3.2 8.3 + - + +
139D PHE* 2.9 21.0 + - + +
141D LEU* 1.3 75.4 - - - +
143D SER* 1.3 61.0 + - - +
145D PHE* 3.3 20.7 - - - +
146D SER* 3.7 5.7 + - - -
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Residues in contact with SER 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 PHE* 2.9 14.6 + - - +
140D ARG* 3.0 14.4 + - - -
142D ALA* 1.3 76.9 - - - +
144D ILE* 1.3 51.4 + - - +
146D SER* 2.9 9.6 + - - -
147D GLY 2.7 42.1 + - - +
214D GLU* 6.2 4.3 - - - -
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Residues in contact with ILE 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 ARG 3.0 12.4 + - - +
141D LEU* 3.2 15.0 - - - +
143D SER* 1.3 72.1 - - - +
145D PHE* 1.3 72.7 + - - +
146D SER 3.2 1.2 + - - -
147D GLY* 3.5 19.8 + - - +
214D GLU* 5.5 4.0 - - - +
218D ARG* 4.3 26.7 - - + -
355D PHE* 3.7 67.3 - - + +
356D GLY 5.9 0.4 - - - +
358D GLY* 3.9 13.0 - - - -
359D THR 4.4 3.4 - - - -
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Residues in contact with PHE 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 3.1 12.5 + - - +
142D ALA* 3.3 16.8 - - - +
144D ILE* 1.3 80.1 - - - +
146D SER* 1.3 64.6 + - - +
358D GLY* 2.9 34.6 - - - +
359D THR* 4.8 9.2 - - + -
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Residues in contact with SER 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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142D ALA 3.7 4.6 + - - -
143D SER* 2.9 8.4 + - - -
144D ILE 3.8 1.3 - - - -
145D PHE* 1.3 87.1 - - - +
147D GLY* 1.3 56.9 + - - +
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Residues in contact with GLY 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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143D SER* 2.7 32.4 + - - +
144D ILE* 3.5 20.0 + - - -
146D SER* 1.3 77.1 + - - +
214D GLU* 5.6 8.8 - - - +
218D ARG* 5.5 12.6 - - - -
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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