Contacts of the helix formed by residues 131 - 150 (chain D) in PDB entry 3LOC
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 GLY 131 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D ASP 2.7 17.9 + - - -
129D LEU 3.3 0.4 - - - -
130D THR* 1.3 78.2 + - - +
132D ASP* 1.3 69.4 + - - -
133D LEU 3.1 3.2 + - - -
134D LYS* 3.2 2.6 + - - +
135D ALA* 3.1 21.8 + - - +
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Residues in contact with ASP 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D ARG* 4.6 18.1 + - - +
77D LEU* 6.4 0.2 - - - -
127D ASP 5.1 0.5 - - - +
128D GLU* 3.4 30.3 + - - +
131D GLY* 1.3 75.3 - - - +
133D LEU* 1.3 65.3 + - - +
135D ALA* 3.4 6.6 + - - +
136D LEU* 3.2 21.3 + - - +
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Residues in contact with LEU 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178C GLN* 3.4 39.5 - - + +
182C VAL* 4.8 7.4 - - + -
73D LEU* 4.6 8.3 - - + -
77D LEU* 3.9 40.2 - - + -
128D GLU 3.1 13.4 + - - +
129D LEU* 3.4 26.7 - - + +
132D ASP* 1.3 76.2 - - - +
134D LYS* 1.3 65.2 + - - +
136D LEU* 2.9 15.7 + - + +
137D ILE* 3.0 31.2 + - + +
166D TRP* 4.3 4.7 - - + -
212D URA 4.2 9.0 - - + -
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Residues in contact with LYS 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181C ALA 3.5 24.2 - - - +
182C VAL* 4.1 25.5 + - - -
183C THR 6.0 0.2 - - - -
184C GLY* 5.8 2.2 - - - +
129D LEU 3.0 10.9 + - - +
130D THR* 3.3 26.7 - - - +
131D GLY 3.2 0.4 + - - -
133D LEU* 1.3 78.9 - - - +
135D ALA* 1.3 64.0 + - - +
137D ILE* 3.1 2.8 + - - +
138D ASP* 2.9 57.5 + - - +
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Residues in contact with ALA 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131D GLY 3.1 10.3 + - - +
132D ASP* 3.8 10.1 - - - +
133D LEU 3.1 0.2 - - - -
134D LYS* 1.3 80.1 - - - +
136D LEU* 1.3 62.6 + - - +
138D ASP* 3.6 8.5 + - - +
139D GLU* 3.2 24.0 + - - +
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Residues in contact with LEU 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D LEU* 3.8 36.3 - - + -
80D LEU* 5.3 3.1 - - + -
81D LYS* 3.7 40.2 - - + +
132D ASP 3.2 11.3 + - - +
133D LEU* 2.9 9.5 + - + +
135D ALA* 1.3 80.2 - - - +
137D ILE* 1.3 62.1 + - + +
139D GLU* 3.5 13.1 + - - +
140D LYS* 3.1 50.8 + - + +
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Residues in contact with ILE 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182C VAL* 4.5 24.2 - - + -
77D LEU* 4.6 3.6 - - + -
80D LEU* 3.7 22.7 - - + -
133D LEU* 3.0 32.1 + - + +
134D LYS* 3.9 4.9 - - - +
136D LEU* 1.3 75.5 - - + +
138D ASP* 1.3 58.5 + - - +
140D LYS* 3.6 2.9 - - - +
141D SER* 2.7 49.6 + - - +
159D GLN* 4.9 7.0 - - + +
162D ILE* 4.0 17.0 - - + -
163D PHE* 5.5 1.3 - - + -
166D TRP* 3.6 33.7 - - + -
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Residues in contact with ASP 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182C VAL* 4.3 9.2 - - - +
134D LYS* 2.9 52.9 + - - +
135D ALA* 3.6 8.1 - - - +
137D ILE* 1.3 75.2 - - - +
139D GLU* 1.3 65.7 + - - +
141D SER* 3.2 6.4 + - - -
142D ALA* 2.9 25.0 + - - +
159D GLN* 4.7 7.4 + - - -
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Residues in contact with GLU 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D ARG* 5.6 0.3 + - - -
135D ALA 3.2 10.4 + - - +
136D LEU* 3.6 16.9 - - - +
138D ASP* 1.3 78.7 - - - +
140D LYS* 1.3 86.2 + - + +
142D ALA* 3.3 8.4 - - - +
143D LEU* 3.0 25.7 + - + +
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Residues in contact with LYS 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D LEU* 3.6 50.9 - - + +
81D LYS* 3.7 10.8 - - - +
83D PHE* 3.2 26.5 + - + -
84D ARG* 3.6 15.2 - - - +
136D LEU* 3.1 31.0 + - + +
137D ILE* 4.2 2.7 - - - +
139D GLU* 1.3 98.0 + - - +
141D SER* 1.3 61.2 + - - +
143D LEU* 3.4 23.4 + - + +
144D ILE* 2.9 37.3 + - + +
162D ILE* 5.2 2.0 - - + -
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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
----------------------------------------------------------
137D ILE* 2.7 33.5 + - - +
138D ASP* 3.6 5.6 - - - -
140D LYS* 1.3 71.1 - - - +
142D ALA* 1.3 56.1 + - - +
144D ILE* 3.0 3.0 + - - -
145D ALA* 2.6 38.4 + - - +
158D PRO* 3.7 23.1 - - - +
159D GLN* 3.7 27.1 + - - +
162D ILE* 4.2 2.5 - - - +
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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
----------------------------------------------------------
138D ASP 2.9 12.6 + - - +
139D GLU* 3.3 13.0 - - - +
141D SER* 1.3 76.0 - - - +
143D LEU* 1.3 62.1 + - - +
145D ALA* 3.4 7.8 + - - +
146D GLY* 3.1 19.2 + - - -
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Residues in contact with LEU 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D PHE* 4.1 21.3 - - + +
84D ARG* 3.8 11.7 - - - +
85D GLU* 3.6 31.4 - - + +
139D GLU* 3.0 14.5 + - + +
140D LYS* 3.5 27.1 - - + +
141D SER 3.1 0.2 - - - -
142D ALA* 1.3 78.0 - - - +
144D ILE* 1.3 62.9 + - + +
146D GLY* 3.4 9.1 + - - -
147D TRP* 3.3 50.5 + - + +
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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
----------------------------------------------------------
80D LEU* 5.0 2.5 - - + -
83D PHE* 4.6 22.4 - - + -
93D ILE* 5.5 2.5 - - + -
140D LYS* 2.9 26.7 + - + +
141D SER 3.8 2.5 - - - +
143D LEU* 1.3 74.8 - - + +
145D ALA* 1.3 61.6 + - - +
147D TRP* 2.9 42.0 + - + +
148D VAL* 3.2 6.4 + - + +
153D LEU* 3.9 22.2 - - + -
156D ILE* 5.1 3.8 - - + -
158D PRO* 3.8 20.2 - - + -
161D LEU* 4.3 18.4 - - + -
162D ILE* 4.1 28.9 - - + -
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Residues in contact with ALA 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 SER 2.6 22.5 + - - +
142D ALA* 3.6 8.7 - - - +
144D ILE* 1.3 72.4 - - - +
146D GLY* 1.3 57.4 + - - +
148D VAL* 2.7 33.1 - - + +
149D LYS* 2.8 13.8 + - - +
158D PRO* 3.8 13.0 - - + +
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Residues in contact with GLY 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 3.1 12.9 + - - -
143D LEU 3.4 5.4 + - - -
144D ILE 3.1 0.6 - - - -
145D ALA* 1.3 73.0 - - - +
147D TRP* 1.3 65.8 + - - +
149D LYS* 3.2 7.3 + - - +
150D SER* 2.9 27.4 + - - -
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Residues in contact with TRP 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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83D PHE* 5.0 11.0 - + - -
84D ARG 3.4 6.7 - - - -
85D GLU* 2.7 42.0 - - + -
86D ASP* 4.7 0.2 - - - -
87D PHE* 3.4 27.4 - - + -
89D PRO* 3.5 34.5 + - + +
92D ALA* 6.1 0.4 - - + -
93D ILE* 5.3 2.5 - - + +
143D LEU* 3.3 28.9 + - + +
144D ILE* 2.9 33.2 + - + +
146D GLY* 1.3 74.9 - - - +
148D VAL* 1.3 58.8 + - - +
150D SER* 3.6 7.0 + - - -
151D GLY 3.3 2.4 + - - -
152D LYS* 2.8 39.6 + - + +
153D LEU* 3.2 35.5 + - + -
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Residues in contact with VAL 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144D ILE* 3.2 4.1 + - + +
145D ALA* 2.7 36.8 - - + +
147D TRP* 1.3 77.0 - - - +
149D LYS* 1.3 65.6 + - + +
150D SER 3.1 1.3 - - - -
151D GLY* 2.9 14.9 + - - -
153D LEU* 3.6 13.7 - - + +
154D ALA 3.0 28.3 - - - +
155D PRO* 3.6 16.4 - - + -
156D ILE* 3.9 16.4 - - + +
158D PRO* 5.7 1.1 - - + -
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Residues in contact with LYS 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145D ALA 2.8 20.0 + - - +
146D GLY* 3.7 8.1 - - - +
148D VAL* 1.3 73.3 - - + +
150D SER* 1.3 58.2 + - - +
151D GLY 3.4 2.8 + - - -
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Residues in contact with SER 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146D GLY 2.9 16.9 + - - -
147D TRP* 3.6 8.7 + - - -
148D VAL 3.1 0.2 - - - -
149D LYS* 1.3 75.0 - - - +
151D GLY* 1.3 60.6 + - - +
152D LYS* 3.3 20.0 + - - +
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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
------------------------------------------------------------
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