Contacts of the helix formed by residues 116 - 129 (chain D) in PDB entry 6B5G
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 ASP 116 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112D LEU 3.0 8.8 + - - +
113D VAL 3.3 4.5 - - - +
115D ARG* 1.3 118.0 + - - +
117D ARG* 1.3 62.2 + - - +
118D ALA 3.3 2.7 - - - -
119D VAL* 3.4 12.5 + - + +
120D LEU* 3.1 26.4 + - + +
221D TYR* 2.9 34.5 + - + +
225D LEU* 3.5 12.9 - - + +
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Residues in contact with ARG 117 (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 3.0 7.8 + - - +
114D GLU* 3.3 40.1 + - - +
115D ARG 3.3 3.0 + - - -
116D ASP* 1.3 77.7 - - - +
118D ALA* 1.3 62.8 + - - +
120D LEU* 3.4 0.9 + - - -
121D ALA* 3.0 26.7 + - - +
136D PHE* 2.9 58.5 + - + -
137D TYR* 3.9 11.9 - - - +
140D LEU* 3.7 25.8 - - + +
141D GLN* 3.7 34.4 - - - +
144D ILE* 3.9 13.3 - - + +
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Residues in contact with ALA 118 (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 PRO* 6.2 1.1 - - + -
28D SER 4.6 13.0 - - - +
30D THR* 3.6 8.5 - - - +
115D ARG 5.0 1.8 + - - +
116D ASP 3.3 0.4 - - - -
117D ARG* 1.3 79.2 - - - +
119D VAL* 1.3 65.3 + - + +
122D THR* 3.0 28.4 + - - -
132D PHE* 3.9 4.2 - - + -
136D PHE* 3.9 19.6 - - + -
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Residues in contact with VAL 119 (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 THR* 3.4 27.1 - - + +
33D LEU* 3.7 13.3 - - + +
116D ASP* 3.4 18.9 + - + +
117D ARG 3.3 0.4 - - - -
118D ALA* 1.3 77.2 - - + +
120D LEU* 1.3 58.7 + - - +
122D THR* 3.3 3.5 + - - -
123D MET* 2.9 50.1 + - + +
221D TYR* 4.3 19.7 - - + +
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Residues in contact with LEU 120 (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* 4.1 39.3 - - + +
116D ASP 3.1 21.2 + - - +
117D ARG 4.0 2.7 - - - +
119D VAL* 1.3 75.8 - - - +
121D ALA* 1.3 57.3 + - - +
123D MET* 3.3 6.6 + - - +
124D GLU* 2.8 33.1 + - - +
140D LEU* 4.0 6.7 - - + -
190D LEU* 3.7 28.5 - - + -
218D SER* 4.0 22.9 - - - +
221D TYR* 3.6 35.9 - - + -
222D MET* 4.5 2.7 - - - -
225D LEU* 4.3 4.9 - - + -
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Residues in contact with ALA 121 (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 ARG 3.0 18.7 + - - +
118D ALA 3.9 0.2 - - - +
120D LEU* 1.3 75.7 - - - +
122D THR* 1.3 58.8 + - - +
124D GLU* 3.4 0.6 + - - -
125D SER* 2.9 30.8 + - - -
132D PHE* 3.8 17.4 - - + -
135D ALA* 3.7 10.1 - - - +
136D PHE* 3.7 36.6 - - + +
140D LEU* 4.0 9.3 - - + +
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Residues in contact with THR 122 (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 PRO* 3.2 9.3 - - + +
30D THR* 2.8 44.6 + - - +
33D LEU* 3.7 17.9 - - + -
118D ALA 3.0 16.0 + - - -
119D VAL 3.5 4.3 - - - -
121D ALA* 1.3 77.0 - - - +
123D MET* 1.3 53.8 + - - +
125D SER* 3.2 3.6 + - - -
126D LEU* 2.7 39.2 + - + +
132D PHE* 3.4 8.2 - - - -
353D PHE* 4.0 20.8 - - + -
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Residues in contact with MET 123 (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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33D LEU* 3.8 21.7 - - + +
34D GLU 5.5 1.6 - - - +
35D ILE* 4.2 15.5 - - + -
119D VAL* 2.9 39.2 + - + +
120D LEU* 3.5 11.0 - - - +
121D ALA 3.3 0.2 - - - -
122D THR* 1.3 76.7 - - - +
124D GLU* 1.3 57.8 + - - +
126D LEU* 3.8 3.9 - - + +
127D ASN* 2.8 36.4 + - - +
217D LEU* 3.8 42.8 - - + +
218D SER* 3.9 11.7 - - - +
221D TYR* 4.0 23.6 - - + -
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Residues in contact with GLU 124 (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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120D LEU 2.8 23.9 + - - +
121D ALA 3.7 4.3 - - - +
123D MET* 1.3 72.7 - - - +
125D SER* 1.3 55.6 + - - +
127D ASN* 4.9 3.3 - - - +
128D GLY* 2.7 34.3 + - - +
129D GLY 3.6 0.5 + - - -
130D LYS* 4.1 15.4 + - + +
135D ALA* 4.1 13.9 - - + -
139D ASP* 4.6 6.5 - - + +
140D LEU* 4.6 6.1 - - + -
188D PHE 4.3 0.3 - - - -
189D PRO* 3.1 29.5 - - - +
190D LEU* 2.9 37.3 + - + +
191D LEU 4.6 0.2 + - - -
215D THR* 5.5 0.2 - - - -
218D SER* 2.8 29.9 + - - +
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Residues in contact with SER 125 (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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59D ASN* 5.0 0.3 - - - +
121D ALA 2.9 17.9 + - - -
122D THR 3.6 3.6 - - - -
124D GLU* 1.3 74.5 - - - +
126D LEU* 1.3 61.3 + - - +
129D GLY* 2.9 27.7 + - - -
130D LYS* 3.1 28.0 + - - +
132D PHE* 3.9 15.4 + - - -
135D ALA* 4.6 1.1 - - - +
352D PRO* 3.2 15.3 - - - +
353D PHE* 3.1 24.1 - - - -
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Residues in contact with LEU 126 (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 ASN 5.7 1.1 - - - +
33D LEU* 4.3 30.7 - - + +
35D ILE* 4.4 10.1 - - + -
59D ASN* 3.3 42.5 - - + +
60D PRO* 3.4 5.7 - - - +
66D VAL* 3.6 38.6 - - + -
122D THR* 2.7 21.2 + - + +
123D MET* 3.8 3.8 - - + +
125D SER* 1.3 74.7 + - - +
127D ASN* 1.3 61.8 + - + +
217D LEU* 5.6 1.1 - - + -
353D PHE* 4.3 16.8 - - + -
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Residues in contact with ASN 127 (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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57D VAL* 3.5 18.4 - - - +
58D TYR 3.6 9.6 + - - +
60D PRO* 3.3 14.6 - - - +
66D VAL* 5.9 1.3 - - + -
123D MET 2.8 21.8 + - - +
124D GLU* 4.9 3.8 - - - +
126D LEU* 1.3 76.8 - - + +
128D GLY* 1.3 56.2 + - - +
129D GLY 3.5 0.2 - - - -
189D PRO* 6.4 0.2 - - + -
214D GLN 2.9 21.7 + - - +
215D THR* 3.2 29.3 - - + +
216D PRO* 3.8 0.7 - - - +
217D LEU* 3.4 33.0 + - + +
218D SER 5.0 0.6 + - - +
363D ILE* 4.0 4.2 - - - +
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Residues in contact with GLY 128 (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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60D PRO* 3.8 5.3 - - - +
124D GLU* 2.7 20.2 + - - +
127D ASN* 1.3 75.5 - - - +
129D GLY* 1.3 60.1 + - - +
130D LYS* 3.2 13.8 + - - +
186D TRP 5.3 1.7 - - - +
189D PRO* 5.3 6.5 - - - +
215D THR* 4.2 7.6 - - - -
316D GLN* 5.0 1.2 + - - -
318D GLN* 4.9 7.1 + - - -
361D PRO 4.7 5.5 - - - +
363D ILE* 4.0 18.0 - - - +
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Residues in contact with GLY 129 (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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59D ASN* 5.6 0.4 - - - -
60D PRO* 3.5 18.6 - - - +
125D SER 2.9 14.8 + - - -
128D GLY* 1.3 78.0 - - - +
130D LYS* 1.3 64.2 + - - +
131D PRO* 3.5 2.1 - - - +
316D GLN* 4.1 4.8 + - - -
352D PRO* 3.6 8.2 - - - +
360D GLY* 3.6 8.8 - - - -
361D PRO* 3.4 29.5 - - - +
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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